diff --git a/DESCRIPTION b/DESCRIPTION index 6ea44640..01e80961 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,5 +20,5 @@ Imports: dplyr Suggests: testthat -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Encoding: UTF-8 diff --git a/docs/404.html b/docs/404.html index 32320e8d..adefa480 100644 --- a/docs/404.html +++ b/docs/404.html @@ -18,7 +18,7 @@ - +
@@ -50,7 +50,7 @@
- +
@@ -78,16 +78,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 797fa41f..77319957 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -3,7 +3,7 @@ - +
@@ -29,7 +29,7 @@
- +
@@ -242,15 +242,15 @@

NA

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/authors.html b/docs/authors.html index 43ac0a38..feb204c7 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -3,7 +3,7 @@ - +
@@ -29,7 +29,7 @@
- +
@@ -38,29 +38,29 @@

Authors and Citation

- +

Citation

- +

Developers D (2024). dsBaseClient: DataSHIELD Client Functions. -R package version 6.3.1.9000. +R package version 6.3.1. 

@Manual{,
   title = {dsBaseClient: DataSHIELD Client Functions},
   author = {DataSHIELD Developers},
   year = {2024},
-  note = {R package version 6.3.1.9000},
+  note = {R package version 6.3.1},
 }
@@ -74,15 +74,15 @@

Citation

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/index.html b/docs/index.html index 97ceda79..8271c328 100644 --- a/docs/index.html +++ b/docs/index.html @@ -19,7 +19,7 @@ - +
@@ -51,7 +51,7 @@
- +
@@ -183,16 +183,16 @@

Developers

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index d55156ae..b87df44a 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,6 +1,5 @@ pandoc: 2.9.2.1 -pkgdown: 2.0.9 +pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-06-10T09:16Z - +last_built: 2024-09-28T15:53Z diff --git a/docs/reference/checkClass.html b/docs/reference/checkClass.html index 4e067b6b..8a4483b3 100644 --- a/docs/reference/checkClass.html +++ b/docs/reference/checkClass.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Checks that an object has the same class in all studies

- +
@@ -49,20 +49,20 @@

Checks that an object has the same class in all studies

Arguments

-
datasources
+ + +
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

-
obj
+
obj

a string character, the name of the object to check for.

Value

- - -

a message or the class of the object if the object has the same class in all studies.

+

a message or the class of the object if the object has the same class in all studies.

Details

@@ -82,15 +82,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/colPercent.html b/docs/reference/colPercent.html index c2c8ca1a..4f2acdc8 100644 --- a/docs/reference/colPercent.html +++ b/docs/reference/colPercent.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Produces column percentages

- +
@@ -49,15 +49,15 @@

Produces column percentages

Arguments

-
dataframe
+ + +
dataframe

a data frame

Value

- - -

a data frame

+

a data frame

Details

@@ -80,15 +80,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.Boole.html b/docs/reference/ds.Boole.html index e52b4304..2445ed80 100644 --- a/docs/reference/ds.Boole.html +++ b/docs/reference/ds.Boole.html @@ -1,12 +1,12 @@ -Converts a server-side R object into Boolean indicators — ds.Boole • dsBaseClientConverts a server-side R object into Boolean indicators — ds.Boole • dsBaseClient - +
@@ -32,20 +32,20 @@
- +

Converts a server-side R object into Boolean indicators

- +
-

It compares R objects using the standard set of +

It compares R objects using the standard set of Boolean operators (==, !=, >, >=, <, <=) to create a -vector with Boolean indicators that can be of class logical (TRUE/FALSE) +vector with Boolean indicators that can be of class logical (TRUE/FALSE) or numeric (1/0).

@@ -63,50 +63,50 @@

Converts a server-side R object into Boolean indicators

Arguments

-
V1
+ + +
V1

A character string specifying the name of the vector to which the Boolean operator is to be applied.

-
V2
+
V2

A character string specifying the name of the vector to compare with V1.

-
Boolean.operator
+
Boolean.operator

A character string specifying one of six possible Boolean operators: '==', '!=', '>', '>=', '<' and '<='.

-
numeric.output
+
numeric.output

logical. If TRUE the output variable should be of class numeric (1/0). -If FALSE the output variable should be of class logical (TRUE/FALSE). +If FALSE the output variable should be of class logical (TRUE/FALSE). Default TRUE.

-
na.assign
+
na.assign

A character string taking values 'NA','1' or '0'. Default 'NA'. For more information see details.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output object that is stored on the data servers. Default boole.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.Boole returns the object specified by the newobj argument +

ds.Boole returns the object specified by the newobj argument which is written to the server-side. Also, two validity messages are returned -to the client-side indicating the name of the newobj which -has been created in each data source and if +to the client-side indicating the name of the newobj which +has been created in each data source and if it is in a valid form.

@@ -116,10 +116,10 @@

Details

binary/Boolean vectors together. In this way, observations taking the value 1 in every vector will then take the value 1 in the final vector (after multiplication) while all others will take the value 0. Instead the combination using OR operator -can be obtained by the sum of two or more vectors and applying +can be obtained by the sum of two or more vectors and applying ds.Boole using the operator >= 1.

-

In na.assign if 'NA' is specified, the missing values -remain as NAs in the output vector. If '1' or '0' is specified the +

In na.assign if 'NA' is specified, the missing values +remain as NAs in the output vector. If '1' or '0' is specified the missing values are converted to 1 or 0 respectively or TRUE or FALSE depending on the argument numeric.output.

@@ -134,7 +134,7 @@

Author

Examples


-if (FALSE) {
+if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -188,7 +188,7 @@ 
Examples

   
   # Clear the Datashield R sessions and logout           
   datashield.logout(connections)
-}
+} # }
@@ -204,15 +204,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.abs.html b/docs/reference/ds.abs.html index fbe89743..65f8640c 100644 --- a/docs/reference/ds.abs.html +++ b/docs/reference/ds.abs.html @@ -1,10 +1,10 @@ -Computes the absolute values of a variable — ds.abs • dsBaseClientComputes the absolute values of a variable — ds.abs • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Computes the absolute values of a variable

- +
-

Computes the absolute values for a specified numeric or integer vector. +

Computes the absolute values for a specified numeric or integer vector. This function is similar to R function abs.

@@ -51,34 +51,34 @@

Computes the absolute values of a variable

Arguments

-
x
+ + +
x

a character string providing the name of a numeric or an integer vector.

-
newobj
+
newobj

a character string that provides the name for the output variable that is stored on the data servers. Default name is set to abs.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.abs assigns a vector for each study that includes the absolute values of +

ds.abs assigns a vector for each study that includes the absolute values of the input numeric or integer vector specified in the argument x. The created vectors are stored in the servers.

Details

-

The function calls the server-side function absDS that computes the -absolute values of the elements of a numeric or integer vector and assigns a new vector -with those absolute values on the server-side. The name of the new generated vector is +

The function calls the server-side function absDS that computes the +absolute values of the elements of a numeric or integer vector and assigns a new vector +with those absolute values on the server-side. The name of the new generated vector is specified by the user through the argument newobj, otherwise is named by default to abs.newobj.

@@ -89,7 +89,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   # Connecting to the Opal servers
 
@@ -138,7 +138,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections) 
 
-}
+} # }
@@ -154,15 +154,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asCharacter.html b/docs/reference/ds.asCharacter.html index 747bca31..df1c7cb9 100644 --- a/docs/reference/ds.asCharacter.html +++ b/docs/reference/ds.asCharacter.html @@ -1,10 +1,10 @@ -Converts a server-side R object into a character class — ds.asCharacter • dsBaseClientConverts a server-side R object into a character class — ds.asCharacter • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Converts a server-side R object into a character class

- +
-

Converts the input object into a character class. +

Converts the input object into a character class. This function is based on the native R function as.character.

@@ -51,29 +51,29 @@

Converts a server-side R object into a character class

Arguments

-
x.name
+ + +
x.name

a character string providing the name of the input object to be coerced to class character.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default ascharacter.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.asCharacter returns the object converted into a class character +

ds.asCharacter returns the object converted into a class character that is written to the server-side. Also, two validity messages are returned to the client-side -indicating the name of the newobj which has been created in each data source and if +indicating the name of the newobj which has been created in each data source and if it is in a valid form.

@@ -87,7 +87,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -121,7 +121,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -136,15 +136,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asDataMatrix.html b/docs/reference/ds.asDataMatrix.html index f6437b88..b8ceb870 100644 --- a/docs/reference/ds.asDataMatrix.html +++ b/docs/reference/ds.asDataMatrix.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Converts a server-side R object into a matrix

- +
@@ -51,31 +51,31 @@

Converts a server-side R object into a matrix

Arguments

-
x.name
-

a character string providing the name of the input object to be coerced to + + +

x.name
+

a character string providing the name of the input object to be coerced to a matrix.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default asdatamatrix.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.asDataMatrix returns the object converted into a matrix -that is written to the server-side. Also, two validity messages are returned +

ds.asDataMatrix returns the object converted into a matrix +that is written to the server-side. Also, two validity messages are returned to the client-side -indicating the name of the newobj which -has been created in each data source and if +indicating the name of the newobj which +has been created in each data source and if it is in a valid form.

@@ -90,7 +90,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -124,7 +124,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -139,15 +139,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asFactor.html b/docs/reference/ds.asFactor.html index bbcad704..a75085f9 100644 --- a/docs/reference/ds.asFactor.html +++ b/docs/reference/ds.asFactor.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Converts a server-side numeric vector into a factor

- +
@@ -56,48 +56,48 @@

Converts a server-side numeric vector into a factor

Arguments

-
input.var.name
-

a character string which provides + + +

input.var.name
+

a character string which provides the name of the variable to be converted to a factor.

-
newobj.name
-

a character string that provides the name for the output variable +

newobj.name
+

a character string that provides the name for the output variable that is stored on the data servers. Default asfactor.newobj.

-
forced.factor.levels
-

the levels that the user wants to split the input variable. +

forced.factor.levels
+

the levels that the user wants to split the input variable. If NULL (default) a vector with all unique levels from all studies are created.

-
fixed.dummy.vars
-

boolean. If TRUE the input variable is converted to a factor -but presented as a matrix of dummy variables. +

fixed.dummy.vars
+

boolean. If TRUE the input variable is converted to a factor +but presented as a matrix of dummy variables. If FALSE (default) the input variable is converted to a factor and assigned as a vector.

-
baseline.level
-

an integer indicating the baseline level -to be used in the creation of the matrix with dummy variables. +

baseline.level
+

an integer indicating the baseline level +to be used in the creation of the matrix with dummy variables. If the fixed.dummy.vars is set to FALSE then any value of the baseline level is not taken into account.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.asFactor returns the unique levels of the converted -variable in ascending order and a validity -message with the name of the created object on the client-side and +

ds.asFactor returns the unique levels of the converted +variable in ascending order and a validity +message with the name of the created object on the client-side and the output matrix or vector in the server-side.

@@ -140,30 +140,30 @@

Details

variable to a factor. Because you do not need to share unique factor levels between sources, there is then no disclosure issue.

To understand how the matrix of the dummy variable is created let's assume that we have the vector -(1, 2, 1, 3, 4, 4, 1, 3, 4, 5) of ten integer numbers. +(1, 2, 1, 3, 4, 4, 1, 3, 4, 5) of ten integer numbers. If we set the argument fixed.dummy.vars = TRUE, -baseline.level = 1 and forced.factor.levels = c(1,2,3,4,5). +baseline.level = 1 and forced.factor.levels = c(1,2,3,4,5). The input vector is converted to the following matrix of dummy variables:

DV2DV3DV4DV50
00010
00000
00100
00100
01000
00010
00010

For the same example if the baseline.level = 3 then the matrix is:

-

DV1DV2DV4DV5
1000
0100
1000
0000
0010
0010
1000
0000
0010
0001

In the first instance the first row of the matrix has zeros in all entries indicating -that the first data point belongs to level 1 (as the baseline level is equal to 1). +

DV1DV2DV4DV5
1000
0100
1000
0000
0010
0010
1000
0000
0010
0001

In the first instance the first row of the matrix has zeros in all entries indicating +that the first data point belongs to level 1 (as the baseline level is equal to 1). The second row has 1 at the first (DV2) column and zeros elsewhere, -indicating that the second data point belongs to level 2. -In the second instance (second matrix) where the baseline level is equal to 3, +indicating that the second data point belongs to level 2. +In the second instance (second matrix) where the baseline level is equal to 3, the first row of the matrix has 1 at the -first (DV1) column and zeros elsewhere, +first (DV1) column and zeros elsewhere, indicating again that the first data point belongs to level 1. -Also as we can see the fourth row of the second matrix has all its elements equal +Also as we can see the fourth row of the second matrix has all its elements equal to zero indicating that the fourth data point belongs to level 3 (as the baseline level, in that case, is 3).

-

If the baseline.level is set to be equal to a value +

If the baseline.level is set to be equal to a value that is not one of the levels of the factor then a matrix of dummy variables is created having as many columns as the number of levels. -In that case in each row there is a unique entry equal to 1 at a +In that case in each row there is a unique entry equal to 1 at a certain column indicating the level of each data point. So, for the above example where the vector has five levels if we set the baseline.level equal to a value that does not -belong to those five levels (baseline.level=8) +belong to those five levels (baseline.level=8) the matrix of dummy variables is:

DV1DV2DV3DV4DV5
10000
01000
10000
00100
00010
00010
10000
00100
00010
00001

Server functions called: asFactorDS1 and asFactorDS2

@@ -174,7 +174,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -218,7 +218,7 @@ 
Examples

 
    # Clear the Datashield R sessions and logout  
    datashield.logout(connections) 
-}
+} # }
@@ -233,15 +233,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asFactorSimple.html b/docs/reference/ds.asFactorSimple.html index 4cf3a637..2b19b9b3 100644 --- a/docs/reference/ds.asFactorSimple.html +++ b/docs/reference/ds.asFactorSimple.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Converts a numeric vector into a factor

- +
@@ -55,33 +55,33 @@

Converts a numeric vector into a factor

Arguments

-
input.var.name
-

a character string which provides + + +

input.var.name
+

a character string which provides the name of the variable to be converted to a factor.

-
newobj.name
-

a character string that provides the name for the output variable +

newobj.name
+

a character string that provides the name for the output variable that is stored on the data servers. Default asfactor.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

an output vector of class factor to the serverside. In addition, returns a validity +

an output vector of class factor to the serverside. In addition, returns a validity message with the name of the created object on the client-side and if creation fails an error message which can be viewed using datashield.errors().

Details

-

The function converts the input variable into a factor. Unlike +

The function converts the input variable into a factor. Unlike ds.asFactor and its serverside functions, ds.asFactorSimple does no more than coerce the class of a variable to make it a factor on the serverside in each data source. It does not check for or enforce consistency of factor levels across sources or allow you to @@ -107,15 +107,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asInteger.html b/docs/reference/ds.asInteger.html index 1c10bc60..76cc6f13 100644 --- a/docs/reference/ds.asInteger.html +++ b/docs/reference/ds.asInteger.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Converts a server-side R object into an integer class

- +
@@ -51,40 +51,40 @@

Converts a server-side R object into an integer class

Arguments

-
x.name
-

a character string providing the name of the input object to be coerced to + + +

x.name
+

a character string providing the name of the input object to be coerced to an integer.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default asinteger.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.asInteger returns the R object converted into an integer +

ds.asInteger returns the R object converted into an integer that is written to the server-side. Also, two validity messages are returned to the -client-side indicating the name of the newobj which -has been created in each data source and if +client-side indicating the name of the newobj which +has been created in each data source and if it is in a valid form.

Details

-

This function is based on the native R function as.integer. - The only difference is that the DataSHIELD -function first converts the values of the input object into characters and then convert -those to integers. This addition, +

This function is based on the native R function as.integer. + The only difference is that the DataSHIELD +function first converts the values of the input object into characters and then convert +those to integers. This addition, it is important for the case where the input object is of class -factor having integers as levels. +factor having integers as levels. In that case, the native R as.integer function returns the underlying level codes and not the values as integers. For example as.integer in R @@ -102,7 +102,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -137,7 +137,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -152,15 +152,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asList.html b/docs/reference/ds.asList.html index 5e72b020..d7fe3876 100644 --- a/docs/reference/ds.asList.html +++ b/docs/reference/ds.asList.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Converts a server-side R object into a list

- +
@@ -51,29 +51,29 @@

Converts a server-side R object into a list

Arguments

-
x.name
-

a character string providing the name of the input object to be coerced to + + +

x.name
+

a character string providing the name of the input object to be coerced to a list.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default aslist.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.asList returns the R object converted into a list +

ds.asList returns the R object converted into a list which is written to the server-side. Also, two validity messages are returned to the -client-side indicating the name of the newobj which has been created in each data +client-side indicating the name of the newobj which has been created in each data source and if it is in a valid form.

@@ -87,7 +87,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -122,7 +122,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -137,15 +137,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asLogical.html b/docs/reference/ds.asLogical.html index 52f3f28e..e07cc3c3 100644 --- a/docs/reference/ds.asLogical.html +++ b/docs/reference/ds.asLogical.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Converts a server-side R object into a logical class

- +
@@ -51,30 +51,30 @@

Converts a server-side R object into a logical class

Arguments

-
x.name
-

a character string providing the name of the + + +

x.name
+

a character string providing the name of the input object to be coerced to a logical.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default aslogical.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.asLogical returns the R object converted into a logical +

ds.asLogical returns the R object converted into a logical that is written to the server-side. Also, two validity messages are returned -to the client-side indicating the name of the newobj which -has been created in each data source and if +to the client-side indicating the name of the newobj which +has been created in each data source and if it is in a valid form.

@@ -88,7 +88,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -123,7 +123,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -138,15 +138,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asMatrix.html b/docs/reference/ds.asMatrix.html index 17624831..d3e7a9b3 100644 --- a/docs/reference/ds.asMatrix.html +++ b/docs/reference/ds.asMatrix.html @@ -1,10 +1,10 @@ -Converts a server-side R object into a matrix — ds.asMatrix • dsBaseClientConverts a server-side R object into a matrix — ds.asMatrix • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Converts a server-side R object into a matrix

- +
-

Coerces an R object into a matrix. +

Coerces an R object into a matrix. This converts all columns into character class.

@@ -51,34 +51,34 @@

Converts a server-side R object into a matrix

Arguments

-
x.name
-

a character string providing the name of the input object to be coerced to + + +

x.name
+

a character string providing the name of the input object to be coerced to a matrix.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default asmatrix.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.asMatrix returns the object converted into a matrix +

ds.asMatrix returns the object converted into a matrix that is written to the server-side. Also, two validity messages are returned -to the client-side indicating the name of the newobj which +to the client-side indicating the name of the newobj which has been created in each data source and if it is in a valid form.

Details

-

This function is based on the native R function as.matrix. +

This function is based on the native R function as.matrix. If this function is applied to a data frame, all columns are converted into a character class. If you wish to convert a data frame to a matrix but maintain all data columns in their original class you should use the function ds.asDataMatrix.

@@ -91,7 +91,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -125,7 +125,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-} 
+} # }
@@ -140,15 +140,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.asNumeric.html b/docs/reference/ds.asNumeric.html index 2f93a38b..1bcda160 100644 --- a/docs/reference/ds.asNumeric.html +++ b/docs/reference/ds.asNumeric.html @@ -1,10 +1,10 @@ -Converts a server-side R object into a numeric class — ds.asNumeric • dsBaseClientConverts a server-side R object into a numeric class — ds.asNumeric • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Converts a server-side R object into a numeric class

- +
-

Coerces an R object into a numeric class. +

Coerces an R object into a numeric class. This function is based on the native R function as.numeric.

@@ -51,46 +51,46 @@

Converts a server-side R object into a numeric class

Arguments

-
x.name
-

a character string providing the name of the input object to be coerced to + + +

x.name
+

a character string providing the name of the input object to be coerced to a numeric.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default asnumeric.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.asNumeric returns the R object converted into a numeric class -that is written to the server-side. Also, two validity messages are returned -to the client-side indicating the name of the newobj which -has been created in each data source and if +

ds.asNumeric returns the R object converted into a numeric class +that is written to the server-side. Also, two validity messages are returned +to the client-side indicating the name of the newobj which +has been created in each data source and if it is in a valid form.

Details

This function is based on the native R function as.numeric. -However, it behaves differently with some specific classes of variables. For example, if the input +However, it behaves differently with some specific classes of variables. For example, if the input object is of class factor, it first converts its values into characters and then convert those to numerics. This behavior is important for the case where the input object is of class factor having -numbers as levels. In that case, the native R -as.numeric function returns the underlying level codes and not the values as numbers. +numbers as levels. In that case, the native R +as.numeric function returns the underlying level codes and not the values as numbers. For example as.numeric in R converts the factor vector:
0 1 1 2 1 0 1 0 2 2 2 1
Levels: 0 1 2
to the following numeric vector: 1 2 2 3 2 1 2 1 3 3 3 2
-In contrast DataSHIELD converts an input factor with numeric +In contrast DataSHIELD converts an input factor with numeric levels to its original numeric values.

Server function called: asNumericDS

@@ -101,7 +101,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -136,7 +136,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -151,15 +151,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.assign.html b/docs/reference/ds.assign.html index bf16610a..8057c1a4 100644 --- a/docs/reference/ds.assign.html +++ b/docs/reference/ds.assign.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Assigns an R object to a name in the server-side

- +
@@ -49,33 +49,33 @@

Assigns an R object to a name in the server-side

Arguments

-
toAssign
+ + +
toAssign

a character string providing the object to assign.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default assign.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.assign returns the R object assigned to a name +

ds.assign returns the R object assigned to a name that is written to the server-side.

Details

The new object is stored on the server-side.

-

ds.assign causes a remote assignment by using DSI::datashield.assign. -The toAssign argument is checked at the server and +

ds.assign causes a remote assignment by using DSI::datashield.assign. +The toAssign argument is checked at the server and assigned the variable called newobj on the server-side.

@@ -85,7 +85,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -119,7 +119,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -135,15 +135,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.auc.html b/docs/reference/ds.auc.html index f21f6356..28540596 100644 --- a/docs/reference/ds.auc.html +++ b/docs/reference/ds.auc.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Calculates the Area under the curve (AUC)

- +
@@ -51,26 +51,26 @@

Calculates the Area under the curve (AUC)

Arguments

-
pred
+ + +
pred

the name of the vector of the predicted values

-
y
-

the name of the outcome variable. Note that this variable should include +

y
+

the name of the outcome variable. Note that this variable should include the complete cases that are used in the regression model.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

returns the AUC and its standard error

+

returns the AUC and its standard error

Details

@@ -93,15 +93,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.boxPlot.html b/docs/reference/ds.boxPlot.html index a42485e9..323aab95 100644 --- a/docs/reference/ds.boxPlot.html +++ b/docs/reference/ds.boxPlot.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Draw boxplot

- +
@@ -60,50 +60,50 @@

Draw boxplot

Arguments

-
x
+ + +
x

character Name of the data frame (or numeric vector) on the server side that holds the information to be plotted

-
variables
+
variables

character vector Name of the column(s) of the data frame to include on the boxplot

-
group
+
group

character (default NULL) Name of the first grouping variable.

-
group2
+
group2

character (default NULL) Name of the second grouping variable.

-
xlabel
+
xlabel

caracter (default "x axis") Label to put on the x axis of the plot

-
ylabel
+
ylabel

caracter (default "y axis") Label to put on the y axis of the plot

-
type
+
type

character Return a pooled plot ("pooled") or a split plot (one for each study server "split")

-
datasources
+
datasources

a list of DSConnection-class (default NULL) objects obtained after login

Value

- - -

ggplot object

+

ggplot object

Examples

- +
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.boxPlotGG.html b/docs/reference/ds.boxPlotGG.html index 9041b68f..4736517a 100644 --- a/docs/reference/ds.boxPlotGG.html +++ b/docs/reference/ds.boxPlotGG.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Renders boxplot

- +
@@ -59,8 +59,10 @@

Renders boxplot

Arguments

-
x
-

character Name on the server side of the data frame to form a boxplot. Structure on the server + + +

x
+

character Name on the server side of the data frame to form a boxplot. Structure on the server of this object must be:

Column 'x': Names on the X axis of the boxplot, aka variables to plot
Column 'value': Values for that variable (raw data of columns rbinded)
@@ -68,36 +70,34 @@

Arguments

Column 'group2': (Optional) Values of the second grouping variable

-
group
+
group

character (default NULL) Name of the first grouping variable.

-
group2
+
group2

character (default NULL) Name of the second grouping variable.

-
xlabel
+
xlabel

caracter (default "x axis") Label to put on the x axis of the plot

-
ylabel
+
ylabel

caracter (default "y axis") Label to put on the y axis of the plot

-
type
+
type

character Return a pooled plot ("pooled") or a split plot (one for each study server "split")

-
datasources
+
datasources

a list of DSConnection-class (default NULL) objects obtained after login

Value

- - -

ggplot object

+

ggplot object

@@ -112,15 +112,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.boxPlotGG_data_Treatment.html b/docs/reference/ds.boxPlotGG_data_Treatment.html index d8b87648..51205d21 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Take a data frame on the server side an arrange it to pass it to the boxplot function

- +
@@ -55,47 +55,36 @@

Take a data frame on the server side an arrange it to pass it to the boxplot

Arguments

-
table
+ + +
table

character Name of the table on the server side that holds the information to be plotted later

-
variables
+
variables

character vector Name of the column(s) of the data frame to include on the boxplot

-
group
+
group

character (default NULL) Name of the first grouping variable.

-
group2
+
group2

character (default NULL) Name of the second grouping variable.

-
datasources
+
datasources

a list of DSConnection-class (default NULL) objects obtained after login

Value

- - -

Does not return nothing, it creates the table "boxPlotRawData" on the server arranged to be passed to the +

Does not return nothing, it creates the table "boxPlotRawData" on the server arranged to be passed to the ggplot boxplot function. Structure of the created table:

- - - -

Column 'x': Names on the X axis of the boxplot, aka variables to plot

- - -

Column 'value': Values for that variable (raw data of columns rbinded)

- - -

Column 'group': (Optional) Values of the grouping variable

- - -

Column 'group2': (Optional) Values of the second grouping variable

- - +

Column 'x': Names on the X axis of the boxplot, aka variables to plot
+ Column 'value': Values for that variable (raw data of columns rbinded)
+ Column 'group': (Optional) Values of the grouping variable
+ Column 'group2': (Optional) Values of the second grouping variable

@@ -110,15 +99,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html index 612a1953..476f6b4e 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Take a vector on the server side an arrange it to pass it to the boxplot function

- +
@@ -49,29 +49,22 @@

Take a vector on the server side an arrange it to pass it to the boxplot fun

Arguments

-
vector
+ + +
vector

character Name of the table on the server side that holds the information to be plotted later

-
datasources
+
datasources

a list of DSConnection-class (default NULL) objects obtained after login

Value

- - -

Does not return nothing, it creates the table "boxPlotRawDataNumeric" on the server arranged to be passed to the +

Does not return nothing, it creates the table "boxPlotRawDataNumeric" on the server arranged to be passed to the ggplot boxplot function. Structure of the created table:

- - - -

Column 'x': Names on the X axis of the boxplot, aka name of the vector (vector argument)

- - -

Column 'value': Values for that variable

- - +

Column 'x': Names on the X axis of the boxplot, aka name of the vector (vector argument)
+ Column 'value': Values for that variable

@@ -86,15 +79,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.boxPlotGG_numeric.html b/docs/reference/ds.boxPlotGG_numeric.html index 9cabfffa..4b9845e7 100644 --- a/docs/reference/ds.boxPlotGG_numeric.html +++ b/docs/reference/ds.boxPlotGG_numeric.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Draw boxplot with information from a numeric vector

- +
@@ -55,32 +55,32 @@

Draw boxplot with information from a numeric vector

Arguments

-
x
+ + +
x

character Name of the numeric vector on the server side that holds the information to be plotted

-
xlabel
+
xlabel

caracter (default "x axis") Label to put on the x axis of the plot

-
ylabel
+
ylabel

caracter (default "y axis") Label to put on the y axis of the plot

-
type
+
type

character Return a pooled plot ("pooled") or a split plot (one for each study server "split")

-
datasources
+
datasources

a list of DSConnection-class (default NULL) objects obtained after login

Value

- - -

ggplot object

+

ggplot object

@@ -95,15 +95,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.boxPlotGG_table.html b/docs/reference/ds.boxPlotGG_table.html index 7d6c7c9b..ad10740a 100644 --- a/docs/reference/ds.boxPlotGG_table.html +++ b/docs/reference/ds.boxPlotGG_table.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Draw boxplot with information from a data frame

- +
@@ -58,44 +58,44 @@

Draw boxplot with information from a data frame

Arguments

-
x
+ + +
x

character Name of the table on the server side that holds the information to be plotted

-
variables
+
variables

character vector Name of the column(s) of the data frame to include on the boxplot

-
group
+
group

character (default NULL) Name of the first grouping variable.

-
group2
+
group2

character (default NULL) Name of the second grouping variable.

-
xlabel
+
xlabel

caracter (default "x axis") Label to put on the x axis of the plot

-
ylabel
+
ylabel

caracter (default "y axis") Label to put on the y axis of the plot

-
type
+
type

character Return a pooled plot ("pooled") or a split plot (one for each study server "split")

-
datasources
+
datasources

a list of DSConnection-class (default NULL) objects obtained after login

Value

- - -

ggplot object

+

ggplot object

@@ -110,15 +110,15 @@

Value

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.bp_standards.html b/docs/reference/ds.bp_standards.html index 00e39367..82247836 100644 --- a/docs/reference/ds.bp_standards.html +++ b/docs/reference/ds.bp_standards.html @@ -1,12 +1,12 @@ Calculates Blood pressure z-scores — ds.bp_standards • dsBaseClient - +
@@ -32,19 +32,19 @@
- +

Calculates Blood pressure z-scores

- +

The function calculates blood pressure z-scores in two steps: -Step 1. Calculates z-score of height according to CDC growth chart (Not the +Step 1. Calculates z-score of height according to CDC growth chart (Not the WHO growth chart!). Step 2. Calculates z-score of BP according to the fourth report on BP management, USA

@@ -63,47 +63,47 @@

Calculates Blood pressure z-scores

Arguments

-
sex
+ + +
sex

the name of the sex variable. The variable should be coded as 1 for males -and 2 for females. If it is coded differently (e.g. 0/1), then you can use the -ds.recodeValues function to recode the categories to 1/2 before the use of +and 2 for females. If it is coded differently (e.g. 0/1), then you can use the +ds.recodeValues function to recode the categories to 1/2 before the use of ds.bp_standards

-
age
+
age

the name of the age variable in years.

-
height
+
height

the name of the height variable in cm.

-
bp
+
bp

the name of the blood pressure variable.

-
systolic
-

logical. If TRUE (default) the function assumes conversion of -systolic blood pressure. If FALSE the function assumes conversion of diastolic +

systolic
+

logical. If TRUE (default) the function assumes conversion of +systolic blood pressure. If FALSE the function assumes conversion of diastolic blood pressure.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default name is set to bp.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

assigns a new object on the server-side. The assigned object is a list +

assigns a new object on the server-side. The assigned object is a list with two elements: the 'Zbp' which is the zscores of the blood pressure and 'perc' which is the percentiles of the BP zscores.

@@ -130,15 +130,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.c.html b/docs/reference/ds.c.html index 10e2bb19..7a04d7dd 100644 --- a/docs/reference/ds.c.html +++ b/docs/reference/ds.c.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Combines values into a vector or list in the server-side

- +
@@ -49,33 +49,33 @@

Combines values into a vector or list in the server-side

Arguments

-
x
+ + +
x

a vector of character string providing the names of the objects to be combined.

-
newobj
-

a character string that provides the name for the output object +

newobj
+

a character string that provides the name for the output object that is stored on the data servers. Default c.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.c returns the vector of concatenating R +

ds.c returns the vector of concatenating R objects which are written to the server-side.

Details

-

To avoid combining the character names and not the -vectors on the client-side, the names are coerced into a list -and the server-side function loops through that list to +

To avoid combining the character names and not the +vectors on the client-side, the names are coerced into a list +and the server-side function loops through that list to concatenate the list's elements into a vector.

Server function called: cDS

@@ -86,7 +86,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -121,7 +121,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}    
+} # }
@@ -136,15 +136,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.cbind.html b/docs/reference/ds.cbind.html index 342d98bb..7b771803 100644 --- a/docs/reference/ds.cbind.html +++ b/docs/reference/ds.cbind.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Combines R objects by columns in the server-side

- +
@@ -58,11 +58,13 @@

Combines R objects by columns in the server-side

Arguments

-
x
+ + +
x

a character vector with the name of the objects to be combined.

-
DataSHIELD.checks
+
DataSHIELD.checks

logical. if TRUE does four checks:
1. the input object(s) is(are) defined in all the studies.
2. the input object(s) is(are) of the same legal class in all the studies.
@@ -71,45 +73,41 @@

Arguments

Default FALSE.

-
force.colnames
-

can be NULL (recommended) or a vector of characters that specifies -column names of the output object. If it is not NULL the user should take some caution. +

force.colnames
+

can be NULL (recommended) or a vector of characters that specifies +column names of the output object. If it is not NULL the user should take some caution. For more information see Details.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Defaults cbind.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

-
notify.of.progress
+
notify.of.progress

specifies if console output should be produced to indicate progress. Default FALSE.

Value

- - -

ds.cbind returns a data frame combining the columns of the R -objects specified in the function which is written to the server-side. -It also returns to the client-side two messages with the name of newobj

- - -

that has been created in each data source and DataSHIELD.checks result.

+

ds.cbind returns a data frame combining the columns of the R +objects specified in the function which is written to the server-side. +It also returns to the client-side two messages with the name of newobj +that has been created in each data source and DataSHIELD.checks result.

Details

A sequence of vector, matrix or data-frame arguments is combined column by column to produce a data-frame that is written to the server-side.

This function is similar to the native R function cbind.

-

In DataSHIELD.checks the checks are relatively slow. +

In DataSHIELD.checks the checks are relatively slow. Default DataSHIELD.checks value is FALSE.

If force.colnames is NULL (which is recommended), the column names are inferred from the names or column names of the first object specified in the x argument. @@ -129,7 +127,7 @@

Author

Examples


-if (FALSE) {
+if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki 
   
   # Connecting to the Opal servers
@@ -196,7 +194,7 @@ 
Examples

                    
   # Clear the Datashield R sessions and logout  
   datashield.logout(connections) 
-  }
+  } # }
@@ -212,15 +210,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.changeRefGroup.html b/docs/reference/ds.changeRefGroup.html index c8abb723..10fb7b25 100644 --- a/docs/reference/ds.changeRefGroup.html +++ b/docs/reference/ds.changeRefGroup.html @@ -1,11 +1,11 @@ -Changes the reference level of a factor in the server-side — ds.changeRefGroup • dsBaseClientChanges the reference level of a factor in the server-side — ds.changeRefGroup • dsBaseClient - +
@@ -31,18 +31,18 @@
- +

Changes the reference level of a factor in the server-side

- +
-

Change the reference level of a factor, by putting +

Change the reference level of a factor, by putting the reference group first.

This function is similar to R function relevel.

@@ -59,44 +59,44 @@

Changes the reference level of a factor in the server-side

Arguments

-
x
+ + +
x

a character string providing the name of the input vector of type factor.

-
ref
+
ref

the reference level.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the server-side. Default changerefgroup.newobj.

-
reorderByRef
+
reorderByRef

logical, if TRUE the new vector should be ordered by the reference group (i.e. putting the reference group first). The default is to not re-order (see the reasons in the details).

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.changeRefGroup returns a new vector with the specified level as a reference +

ds.changeRefGroup returns a new vector with the specified level as a reference which is written to the server-side.

Details

This function allows the user to re-order the vector, putting the reference -group first. It should be mentioned that by default the reference is -the first level in the vector of levels. +group first. It should be mentioned that by default the reference is +the first level in the vector of levels. If the user chooses the re-order a warning is issued as this can introduce a mismatch of values if the vector is put back into a table that is not reordered in the same way. Such mismatch @@ -118,7 +118,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -188,7 +188,7 @@ 
Examples

            
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -203,15 +203,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.class.html b/docs/reference/ds.class.html index 88b425cb..4bed09e2 100644 --- a/docs/reference/ds.class.html +++ b/docs/reference/ds.class.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Class of the R object in the server-side

- +
@@ -51,21 +51,21 @@

Class of the R object in the server-side

Arguments

-
x
+ + +
x

a character string providing the name of the input R object.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.class returns the type of the R object.

+

ds.class returns the type of the R object.

Details

@@ -83,7 +83,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -119,7 +119,7 @@ 
Examples

            
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -134,15 +134,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.colnames.html b/docs/reference/ds.colnames.html index db12b7db..6dc70fbb 100644 --- a/docs/reference/ds.colnames.html +++ b/docs/reference/ds.colnames.html @@ -1,10 +1,10 @@ -Produces column names of the R object in the server-side — ds.colnames • dsBaseClientProduces column names of the R object in the server-side — ds.colnames • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Produces column names of the R object in the server-side

- +
-

Retrieves column names of an R object on the server-side. +

Retrieves column names of an R object on the server-side. This function is similar to R function colnames.

@@ -51,21 +51,21 @@

Produces column names of the R object in the server-side

Arguments

-
x
+ + +
x

a character string providing the name of the input data frame or matrix.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.colnames returns the column names of +

ds.colnames returns the column names of the specified server-side data frame or matrix.

@@ -84,7 +84,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -116,7 +116,7 @@ 
Examples

               datasources = connections[1]) #only the first server ("study1") is used
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -131,15 +131,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.completeCases.html b/docs/reference/ds.completeCases.html index 8570affd..2e200009 100644 --- a/docs/reference/ds.completeCases.html +++ b/docs/reference/ds.completeCases.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Identifies complete cases in server-side R objects

- +
@@ -51,37 +51,37 @@

Identifies complete cases in server-side R objects

Arguments

-
x1
+ + +
x1

a character denoting the name of the input object which can be a data frame, matrix or vector.

-
newobj
+
newobj

a character string that provides the name for the complete-cases object -that is stored on the data servers. If the user does not specify a name, then the function -generates a name for the generated object that is the name of the input object with the +that is stored on the data servers. If the user does not specify a name, then the function +generates a name for the generated object that is the name of the input object with the suffix "_complete.cases"

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified, the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.completeCases generates a modified data frame, matrix or vector from which +

ds.completeCases generates a modified data frame, matrix or vector from which all rows containing at least one NA have been deleted. The output object is stored on the server-side. Only two validity messages are returned to the client-side indicating the name of the newobj that has been created in each data source and if it is in a valid form.

Details

-

In the case of a data frame or matrix, ds.completeCases deletes -all rows containing one or more missing values. However ds.completeCases +

In the case of a data frame or matrix, ds.completeCases deletes +all rows containing one or more missing values. However ds.completeCases in vectors only deletes the observation recorded as NA.

Server function called: completeCasesDS

@@ -92,7 +92,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
 
@@ -135,7 +135,7 @@ 
Examples

                    
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-  }
+  } # }
@@ -151,15 +151,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.contourPlot.html b/docs/reference/ds.contourPlot.html index 923d2df2..2858a022 100644 --- a/docs/reference/ds.contourPlot.html +++ b/docs/reference/ds.contourPlot.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates a contour plot

- +
@@ -61,31 +61,33 @@

Generates a contour plot

Arguments

-
x
+ + +
x

a character string providing the name of a numerical vector.

-
y
+
y

a character string providing the name of a numerical vector.

-
type
+
type

a character string that represents the type of graph to display. If type is set to 'combine', a combined contour plot displayed and if type is set to 'split', each contour is plotted separately.

-
show
+
show

a character that represents where the plot should focus. If show is set to 'all', the ranges of the variables are used as plot limits. If show is set to 'zoomed', the plot is zoomed to the region where the actual data are.

-
numints
+
numints

number of intervals for a density grid object.

-
method
+
method

a character that defines which contour will be created. If method is set to 'smallCellsRule' (default), the contour plot of the actual variables is created but grids with low counts are replaced with grids with zero counts. If method is @@ -94,31 +96,29 @@

Arguments

method is set to 'probabilistic', then the contour of 'noisy' variables is generated.

-
k
+
k

the number of the nearest neighbours for which their centroid is calculated. For more information see details.

-
noise
+
noise

the percentage of the initial variance that is used as the variance of the embedded noise if the argument method is set to 'probabilistic'. For more information see details.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.contourPlot returns a contour plot to the client-side.

+

ds.contourPlot returns a contour plot to the client-side.

Details

-

The ds.contourPlot function first generates +

The ds.contourPlot function first generates a density grid and uses it to plot the graph. The cells of the grid density matrix that hold a count of less than the filter set by DataSHIELD (usually 5) are considered invalid and turned into 0 to avoid potential @@ -126,19 +126,19 @@

Details

The ranges returned by each study and used in the process of getting the grid density matrix are not the exact minimum and maximum values but rather close approximates of the real minimum and maximum value. This was done to reduce the risk of potential disclosure.

-

In the k parameter the user can choose any value for k equal to or greater -than the pre-specified threshold used as a disclosure control for this method -and lower than the number of observations minus the value of this threshold. -k default value is 3 (we suggest k to be equal to, or bigger than, 3). +

In the k parameter the user can choose any value for k equal to or greater +than the pre-specified threshold used as a disclosure control for this method +and lower than the number of observations minus the value of this threshold. +k default value is 3 (we suggest k to be equal to, or bigger than, 3). Note that the function fails if the user -uses the default value but the study has set a bigger threshold. -The value of k is used only if the argument method is set to 'deterministic'. +uses the default value but the study has set a bigger threshold. +The value of k is used only if the argument method is set to 'deterministic'. Any value of k is ignored if the argument method is set to 'probabilistic' or 'smallCellsRule'.

In noise any value of noise is ignored if the argument method is set to 'deterministic' or 'smallCellsRule'. The user can choose any value for noise equal to or greater than the pre-specified threshold 'nfilter.noise'. -Default noise value is 0.25. +Default noise value is 0.25. The added noise follows a normal distribution with zero mean and variance equal to a percentage of the initial variance of each input variable.

Server functions called: heatmapPlotDS, rangeDS and densityGridDS

@@ -150,7 +150,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -192,7 +192,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -207,15 +207,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.cor.html b/docs/reference/ds.cor.html index 46a3b46b..f86dd9b9 100644 --- a/docs/reference/ds.cor.html +++ b/docs/reference/ds.cor.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Calculates the correlation of R objects in the server-side

- +
@@ -51,32 +51,32 @@

Calculates the correlation of R objects in the server-side

Arguments

-
x
+ + +
x

a character string providing the name of the input vector, data frame or matrix.

-
y
+
y

a character string providing the name of the input vector, data frame or matrix. Default NULL.

-
type
-

a character string that represents the type of analysis to carry out. +

type
+

a character string that represents the type of analysis to carry out. This must be set to 'split' or 'combine'. Default 'split'. For more information see details.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.cor returns a list containing the number of missing values in each variable, -the number of missing variables casewise, the correlation matrix, +

ds.cor returns a list containing the number of missing values in each variable, +the number of missing variables casewise, the correlation matrix, the number of used complete cases. The function applies two disclosure controls. The first disclosure control checks that the number of variables is not bigger than a percentage of the individual-level records (the allowed percentage is pre-specified by the 'nfilter.glm'). The second disclosure control checks that none of them is dichotomous @@ -88,7 +88,7 @@

Details

number of complete cases and a table outlining the number of missing values to allow the user to decide the 'relevance' of the correlation based on the number of complete cases included in the correlation calculations.

-

If the argument y is not NULL, the dimensions of the object have to be +

If the argument y is not NULL, the dimensions of the object have to be compatible with the argument x.

The function calculates the pairwise correlations based on casewise complete cases which means that it omits all the rows in the input data frame that include at least one cell with a missing value, @@ -97,7 +97,7 @@

Details

variance-correlation matrix of an input data frame and the number of complete cases and missing values are returned for every single study. If type is set to 'combine', the pooled correlation, the total number of complete cases and the total number of missing values aggregated -from all the involved studies, are returned.

+from all the involved studies, are returned.

Server function called: corDS

@@ -107,7 +107,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
 ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -145,7 +145,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -160,15 +160,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.corTest.html b/docs/reference/ds.corTest.html index f243a37e..8190dca4 100644 --- a/docs/reference/ds.corTest.html +++ b/docs/reference/ds.corTest.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Tests for correlation between paired samples in the server-side

- +
@@ -57,50 +57,50 @@

Tests for correlation between paired samples in the server-side

Arguments

-
x
+ + +
x

a character string providing the name of a numerical vector.

-
y
+
y

a character string providing the name of a numerical vector.

-
method
+
method

a character string indicating which correlation coefficient is to be -used for the test. One of "pearson", "kendall", or "spearman", can be abbreviated. +used for the test. One of "pearson", "kendall", or "spearman", can be abbreviated. Default is set to "pearson".

-
exact
+
exact

a logical indicating whether an exact p-value should be computed. Used for Kendall's tau and Spearman's rho. See ‘Details’ of R stats function cor.test for the meaning of NULL (the default).

-
conf.level
+
conf.level

confidence level for the returned confidence interval. Currently only used for the Pearson product moment correlation coefficient if there are at least 4 complete pairs of observations. Default is set to 0.95.

-
type
-

a character string that represents the type of analysis to carry out. -This must be set to 'split' or 'combine'. Default is set to 'split'. If -type is set to "combine" then an approximated pooled correlation is estimated based on +

type
+

a character string that represents the type of analysis to carry out. +This must be set to 'split' or 'combine'. Default is set to 'split'. If +type is set to "combine" then an approximated pooled correlation is estimated based on Fisher's z transformation.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.corTest returns to the client-side the results of the correlation test.

+

ds.corTest returns to the client-side the results of the correlation test.

Details

@@ -115,7 +115,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -150,7 +150,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -166,15 +166,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.cov.html b/docs/reference/ds.cov.html index 566aede3..b97c414b 100644 --- a/docs/reference/ds.cov.html +++ b/docs/reference/ds.cov.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Calculates the covariance of R objects in the server-side

- +
@@ -57,42 +57,42 @@

Calculates the covariance of R objects in the server-side

Arguments

-
x
+ + +
x

a character string providing the name of the input vector, data frame or matrix.

-
y
-

a character string providing the name of the input vector, +

y
+

a character string providing the name of the input vector, data frame or matrix. Default NULL.

-
naAction
+
naAction

a character string giving a method for computing covariances in the presence of missing values. This must be set to 'casewise.complete' or 'pairwise.complete'. Default 'pairwise.complete'. For more information see details.

-
type
-

a character string that represents the type of analysis to carry out. +

type
+

a character string that represents the type of analysis to carry out. This must be set to 'split' or 'combine'. Default 'split'. For more information see details.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.cov returns a list containing the number of missing values in each variable, the number of missing values +

ds.cov returns a list containing the number of missing values in each variable, the number of missing values casewise or pairwise depending on the argument naAction, the covariance matrix, the number of used complete cases and an error message which indicates whether or not the input variables pass the disclosure controls. The first disclosure control checks that the number of variables is not bigger than a percentage of the individual-level records (the allowed percentage is pre-specified by the 'nfilter.glm'). The second disclosure control checks that none of them is dichotomous -with a level having fewer counts than the pre-specified 'nfilter.tab' threshold. If any of the input variables do not pass +with a level having fewer counts than the pre-specified 'nfilter.tab' threshold. If any of the input variables do not pass the disclosure controls then all the output values are replaced with NAs. If all the variables are valid and pass the controls, then the output matrices are returned and also an error message is returned but it is replaced by NA.

@@ -102,20 +102,20 @@

Details

number of complete cases and a table outlining the number of missing values to allow for the user to decide about the 'relevance' of the covariance based on the number of complete cases included in the covariance calculations.

-

If the argument y is not NULL, the dimensions of the object have to be +

If the argument y is not NULL, the dimensions of the object have to be compatible with the argument x.

If naAction is set to 'casewise.complete', then the function omits all the rows in the whole data frame that include at least one cell with a missing value before the calculation of covariances. If naAction is set to 'pairwise.complete' (default), -then the function divides the input data frame to -subset data frames formed by each pair between two variables +then the function divides the input data frame to +subset data frames formed by each pair between two variables (all combinations are considered) and omits the rows with missing values at each pair separately and then calculates the covariances of those pairs.

If type is set to 'split' (default), the covariance of two variables or the -variance-covariance matrix of an input data frame and the number of -complete cases and missing values are returned for every single study. -If type is set to 'combine', the pooled covariance, the total number of complete cases -and the total number of missing values aggregated from all the involved studies, are returned.

+variance-covariance matrix of an input data frame and the number of +complete cases and missing values are returned for every single study. +If type is set to 'combine', the pooled covariance, the total number of complete cases +and the total number of missing values aggregated from all the involved studies, are returned.

Server function called: covDS

@@ -125,7 +125,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
 ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -170,7 +170,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -185,15 +185,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.dataFrame.html b/docs/reference/ds.dataFrame.html index 00264fb5..f32cf6bc 100644 --- a/docs/reference/ds.dataFrame.html +++ b/docs/reference/ds.dataFrame.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates a data frame object in the server-side

- +
@@ -62,39 +62,41 @@

Generates a data frame object in the server-side

Arguments

-
x
+ + +
x

a character string that provides the name of the objects to be combined.

-
row.names
+
row.names

NULL, integer or character string that provides the row names of the output data frame.

-
check.rows
+
check.rows

logical. If TRUE then the rows are checked for consistency of length and names. Default is FALSE.

-
check.names
-

logical. If TRUE the column names +

check.names
+

logical. If TRUE the column names in the data frame are checked to ensure that is unique. Default is TRUE.

-
stringsAsFactors
+
stringsAsFactors

logical. If true the character vectors are converted to factors. Default TRUE.

-
completeCases
-

logical. If TRUE rows with one or more +

completeCases
+

logical. If TRUE rows with one or more missing values will be deleted from the output data frame. Default is FALSE.

-
DataSHIELD.checks
-

logical. Default FALSE. If TRUE undertakes all DataSHIELD checks +

DataSHIELD.checks
+

logical. Default FALSE. If TRUE undertakes all DataSHIELD checks (time-consuming) which are:
1. the input object(s) is(are) defined in all the studies
2. the input object(s) is(are) of the same legal class in all the studies
@@ -103,27 +105,25 @@

Arguments

are the same

-
newobj
+
newobj

a character string that provides the name for the output data frame that is stored on the data servers. Default dataframe.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. -If the datasources argument is not specified +

datasources
+

a list of DSConnection-class objects obtained after login. +If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

-
notify.of.progress
+
notify.of.progress

specifies if console output should be produced to indicate progress. Default is FALSE.

Value

- - -

ds.dataFrame returns the object specified by the newobj argument +

ds.dataFrame returns the object specified by the newobj argument which is written to the serverside. Also, two validity messages are returned to the client-side indicating the name of the newobj that has been created in each data source and if it is in a valid form.

@@ -132,8 +132,8 @@

Value

Details

It creates a data frame by combining pre-existing data frames, matrices or variables.

-

The length of all component variables and the number of rows -of the data frames or matrices must be the same. The output +

The length of all component variables and the number of rows +of the data frames or matrices must be the same. The output data frame will have the same number of rows.

Server functions called: classDS, colnamesDS, dataFrameDS

@@ -145,7 +145,7 @@

Author

Examples


-if (FALSE) {
+if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki 
   # Connecting to the Opal servers
@@ -188,7 +188,7 @@ 
Examples

 
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -203,15 +203,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.dataFrameFill.html b/docs/reference/ds.dataFrameFill.html index 9d6849c5..e6c29795 100644 --- a/docs/reference/ds.dataFrameFill.html +++ b/docs/reference/ds.dataFrameFill.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Creates missing values columns in the server-side

- +
@@ -49,27 +49,27 @@

Creates missing values columns in the server-side

Arguments

-
df.name
+ + +
df.name

a character string representing the name of the input data frame that will be filled with extra columns of missing values.

-
newobj
+
newobj

a character string that provides the name for the output data frame that is stored on the data servers. Default value is "dataframefill.newobj".

-
datasources
-

a list of DSConnection-class objects obtained after login. -If the datasources argument is not specified +

datasources
+

a list of DSConnection-class objects obtained after login. +If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.dataFrameFill returns the object specified by the newobj argument which +

ds.dataFrameFill returns the object specified by the newobj argument which is written to the server-side. Also, two validity messages are returned to the client-side indicating the name of the newobj that has been created in each data source and if it is in a valid form.

@@ -79,8 +79,8 @@

Details

This function checks if the input data frames have the same variables (i.e. the same column names) in all of the used studies. When a study does not have some of the variables, the function generates those variables as vectors of missing values and combines them as columns to -the input data frame. If any of the generated variables are of class factor, the function -assigns to those the corresponding levels of the factors given from the studies where such +the input data frame. If any of the generated variables are of class factor, the function +assigns to those the corresponding levels of the factors given from the studies where such factors exist.

Server function called: dataFrameFillDS

@@ -91,7 +91,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki 
   # Connecting to the Opal servers
@@ -139,7 +139,7 @@ 
Examples

 
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -154,15 +154,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.dataFrameSort.html b/docs/reference/ds.dataFrameSort.html index 3a0a0716..efa19b70 100644 --- a/docs/reference/ds.dataFrameSort.html +++ b/docs/reference/ds.dataFrameSort.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Sorts data frames in the server-side

- +
@@ -56,59 +56,59 @@

Sorts data frames in the server-side

Arguments

-
df.name
+ + +
df.name

a character string providing the name of the data frame to be sorted.

-
sort.key.name
+
sort.key.name

a character string providing the name for the sort key.

-
sort.descending
+
sort.descending

logical, if TRUE the data frame will be sorted. by the sort key in descending order. Default = FALSE (sort order ascending).

-
sort.method
-

a character string that specifies the method to be used -to sort the data frame. This can be set as +

sort.method
+

a character string that specifies the method to be used +to sort the data frame. This can be set as "alphabetic","a" or "numeric", "n".

-
newobj
-

a character string that provides the name for the output data frame -that is stored on the data servers. Default dataframesort.newobj. +

newobj
+

a character string that provides the name for the output data frame +that is stored on the data servers. Default dataframesort.newobj. where df.name is the first argument of ds.dataFrameSort().

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.dataFrameSort returns the sorted data frame is written to the server-side. +

ds.dataFrameSort returns the sorted data frame is written to the server-side. Also, two validity messages are returned to the client-side -indicating the name of the newobj which -has been created in each data source and if +indicating the name of the newobj which +has been created in each data source and if it is in a valid form.

Details

It sorts a specified data.frame on the serverside using a sort key also on the server-side. The -sort key can either sit in the data.frame or outside it. +sort key can either sit in the data.frame or outside it. The sort key can be forced to be interpreted as alphabetic or numeric.

-

When a numeric vector is sorted alphabetically, the order can look confusing. -For example, if we have a numeric vector to sort:
+

When a numeric vector is sorted alphabetically, the order can look confusing. +For example, if we have a numeric vector to sort:
vector.2.sort = c(-192, 76, 841, NA, 1670, 163, 147, 101, -112, -231, -9, 119, 112, NA)

When sorting numbers in an ascending (default) manner, -the largest negative numbers get ordered first +the largest negative numbers get ordered first leading up to the largest positive numbers and finally (by default in R) NAs being positioned at the end of the vector:
numeric.sort = c(-231, -192, -112, -9, 76, 101, 112, 119, 147, 163, 841, 1670, NA, NA)

@@ -123,7 +123,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -160,7 +160,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -175,15 +175,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.dataFrameSubset.html b/docs/reference/ds.dataFrameSubset.html index 19a92fc2..f1559f19 100644 --- a/docs/reference/ds.dataFrameSubset.html +++ b/docs/reference/ds.dataFrameSubset.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Sub-sets data frames in the server-side

- +
@@ -60,78 +60,78 @@

Sub-sets data frames in the server-side

Arguments

-
df.name
+ + +
df.name

a character string providing the name of the data frame to be subseted.

-
V1.name
-

A character string specifying the name of the vector +

V1.name
+

A character string specifying the name of the vector to which the Boolean operator is to be applied to define the subset. For more information see details.

-
V2.name
-

A character string specifying the name of the vector to compare +

V2.name
+

A character string specifying the name of the vector to compare with V1.name.

-
Boolean.operator
+
Boolean.operator

A character string specifying one of six possible Boolean operators: '==', '!=', '>', '>=', '<' and '<='.

-
keep.cols
+
keep.cols

a numeric vector specifying the numbers of the columns to be kept in the final subset.

-
rm.cols
-

a numeric vector specifying the numbers of the columns to be removed from +

rm.cols
+

a numeric vector specifying the numbers of the columns to be removed from the final subset.

-
keep.NAs
-

logical, if TRUE the missing values are included in the subset. +

keep.NAs
+

logical, if TRUE the missing values are included in the subset. If FALSE or NULL all rows with at least one missing values are removed from the subset.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output object that is stored on the data servers. Default dataframesubset.newobj.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the datasources the default set of connections will be used: see datashield.connections_default.

-
notify.of.progress
+
notify.of.progress

specifies if console output should be produced to indicate progress. Default FALSE.

Value

- - -

ds.dataFrameSubset returns +

ds.dataFrameSubset returns the object specified by the newobj argument -which is written to the server-side. +which is written to the server-side. Also, two validity messages are returned to the client-side indicating the name of the newobj which has been created in each data source and if it is in a valid form.

Details

-

Subset a pre-existing data frame using the standard -set of Boolean operators (==, !=, >, >=, <, <=). +

Subset a pre-existing data frame using the standard +set of Boolean operators (==, !=, >, >=, <, <=). The subsetting is made by rows, but it is also possible to select columns to keep or remove. Instead, if you wish to keep all rows in the subset (e.g. if the primary plan is to subset by columns -and not by rows) the V1.name and V2.name parameters can be used +and not by rows) the V1.name and V2.name parameters can be used to specify a vector of the same length -as the data frame to be subsetted in each study in which every element is 1 and +as the data frame to be subsetted in each study in which every element is 1 and there are no missing values. For more information see the example 2 below.

Server functions called: dataFrameSubsetDS1 and dataFrameSubsetDS2

@@ -142,7 +142,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -205,7 +205,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -220,15 +220,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.densityGrid.html b/docs/reference/ds.densityGrid.html index a37c1e31..03906004 100644 --- a/docs/reference/ds.densityGrid.html +++ b/docs/reference/ds.densityGrid.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates a density grid in the client-side

- +
@@ -57,38 +57,38 @@

Generates a density grid in the client-side

Arguments

-
x
+ + +
x

a character string providing the name of the input numerical vector.

-
y
+
y

a character string providing the name of the input numerical vector.

-
numints
-

an integer, the number of intervals for the grid density object. +

numints
+

an integer, the number of intervals for the grid density object. The default value is 20.

-
type
-

a character string that represents the type of graph to display. +

type
+

a character string that represents the type of graph to display. If type is set to -'combine', a pooled grid density matrix is generated, +'combine', a pooled grid density matrix is generated, instead if type is set to 'split' one grid density matrix is generated. Default 'combine'.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.densityGrid returns a grid density matrix.

+

ds.densityGrid returns a grid density matrix.

Details

@@ -96,10 +96,10 @@

Details

and the count is set to 0.

In DataSHIELD the user does not have access to the micro-data so and extreme values such as the maximum and the minimum are potentially non-disclosive so this function does not allow -for the user to set the limits of the density grid and +for the user to set the limits of the density grid and the minimum and maximum values of the x -and y vectors. These elements are set by the server-side function -densityGridDS to 'valid' values +and y vectors. These elements are set by the server-side function +densityGridDS to 'valid' values (i.e. values that do not lead to leakage of micro-data to the user).

Server function called: densityGridDS

@@ -110,7 +110,7 @@

Author

Examples

- +
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.dim.html b/docs/reference/ds.dim.html index 1751c294..3469f8ad 100644 --- a/docs/reference/ds.dim.html +++ b/docs/reference/ds.dim.html @@ -1,10 +1,10 @@ -Retrieves the dimension of a server-side R object — ds.dim • dsBaseClientRetrieves the dimension of a server-side R object — ds.dim • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Retrieves the dimension of a server-side R object

- +
-

Gives the dimensions of an R object on the server-side. +

Gives the dimensions of an R object on the server-side. This function is similar to R function dim.

@@ -51,46 +51,46 @@

Retrieves the dimension of a server-side R object

Arguments

-
x
+ + +
x

a character string providing the name of the input object.

-
type
-

a character string that represents the type of analysis to carry out. +

type
+

a character string that represents the type of analysis to carry out. If type is set to 'combine', 'combined', 'combines' or 'c', - the global dimension is returned. -If type is set to 'split', 'splits' or 's', + the global dimension is returned. +If type is set to 'split', 'splits' or 's', the dimension is returned separately for each study. If type is set to 'both' or 'b', both sets of outputs are produced. Default 'both'.

-
checks
+
checks

logical. If TRUE undertakes all DataSHIELD checks (time-consuming). Default FALSE.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.dim retrieves to the client-side the dimension of the object +

ds.dim retrieves to the client-side the dimension of the object in the form of a vector where the first element indicates the number of rows and the second element indicates the number of columns.

Details

-

The function returns the dimension of the server-side +

The function returns the dimension of the server-side input object (e.g. array, matrix or data frame) -from every single study and the pooled dimension of the object by summing up the individual +from every single study and the pooled dimension of the object by summing up the individual dimensions returned from each study.

-

In checks parameter is suggested that checks should only be undertaken once the +

In checks parameter is suggested that checks should only be undertaken once the function call has failed.

Server function called: dimDS

@@ -109,7 +109,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -155,7 +155,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -171,15 +171,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.dmtC2S.html b/docs/reference/ds.dmtC2S.html index 846a90ce..3b453ecb 100644 --- a/docs/reference/ds.dmtC2S.html +++ b/docs/reference/ds.dmtC2S.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Copy a clientside data.frame, matrix or tibble to the serverside

- +
@@ -51,18 +51,20 @@

Copy a clientside data.frame, matrix or tibble to the serverside

Arguments

-
dfdata
-

is a character string that specifies the name of the DMT + + +

dfdata
+

is a character string that specifies the name of the DMT to be copied from the clientside to the serverside

-
newobj
-

A character string specifying the name of the DMT on the serverside +

newobj
+

A character string specifying the name of the DMT on the serverside to which the output is to be written. If no <newobj> argument is specified or it is NULL the name of the copied DMT defaults to "dmt.copied.C2S".

-
datasources
+
datasources

specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with called opals.a, opals.w2, and connection.xyz, you can choose which of @@ -85,9 +87,7 @@

Arguments

Value

- - -

the object specified by the <newobj> argument (or default name "dmt.copied.C2S") +

the object specified by the <newobj> argument (or default name "dmt.copied.C2S") which is written as a data.frame/matrix/tibble to the serverside.

@@ -96,7 +96,7 @@

Details

function simple (though less flexible), a number of the parameters specifying the DMT to be generated on the serverside are fixed by the characteristics of the DMT to be copied rather than explicitly -specifying them as selected arguments. In consequence, +specifying them as selected arguments. In consequence, they have been removed from the list of arguments and are instead given invariant values in the first few lines of code. These include: from="clientside.dmt", nrows.scalar=NULL, ncols.scalar=NULL, byrow = FALSE. The specific value @@ -124,15 +124,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.elspline.html b/docs/reference/ds.elspline.html index 899dc0ce..102add33 100644 --- a/docs/reference/ds.elspline.html +++ b/docs/reference/ds.elspline.html @@ -6,7 +6,7 @@ - +
@@ -32,13 +32,13 @@
- +

Basis for a piecewise linear spline with meaningful coefficients

- +
@@ -62,39 +62,39 @@

Basis for a piecewise linear spline with meaningful coefficients

Arguments

-
x
+ + +
x

the name of the input numeric variable

-
n
+
n

integer greater than 2, knots are computed such that they cut n equally-spaced intervals along the range of x

-
marginal
+
marginal

logical, how to parametrize the spline, see Details

-
names
+
names

character, vector of names for constructed variables

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default elspline.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

an object of class "lspline" and "matrix", which its name is specified by the +

an object of class "lspline" and "matrix", which its name is specified by the newobj argument (or its default name "elspline.newobj"), is assigned on the serverside.

@@ -123,15 +123,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.exists.html b/docs/reference/ds.exists.html index fbb9b734..08944f12 100644 --- a/docs/reference/ds.exists.html +++ b/docs/reference/ds.exists.html @@ -1,10 +1,10 @@ -Checks if an object is defined on the server-side — ds.exists • dsBaseClientChecks if an object is defined on the server-side — ds.exists • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Checks if an object is defined on the server-side

- +
-

Looks if an R object of the given name is defined on the server-side. +

Looks if an R object of the given name is defined on the server-side. This function is similar to the R function exists.

@@ -51,28 +51,28 @@

Checks if an object is defined on the server-side

Arguments

-
x
+ + +
x

a character string providing the name of the object to look for.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.exists returns a logical object. +

ds.exists returns a logical object. TRUE if the object is on the server-side and FALSE otherwise.

Details

In DataSHIELD it is not possible to see the data on the servers of the collaborating studies. It is only possible to get summaries of objects stored on the -server-side. +server-side. It is however important to know if an object is defined (i.e. exists) on the server-side. This function checks if an object does exist on the server-side.

Server function called: exists

@@ -90,7 +90,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -126,7 +126,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -142,15 +142,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.exp.html b/docs/reference/ds.exp.html index db30f85b..134f9743 100644 --- a/docs/reference/ds.exp.html +++ b/docs/reference/ds.exp.html @@ -1,10 +1,10 @@ -Computes the exponentials in the server-side — ds.exp • dsBaseClientComputes the exponentials in the server-side — ds.exp • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Computes the exponentials in the server-side

- +
-

Computes the exponential values for a specified numeric vector. +

Computes the exponential values for a specified numeric vector. This function is similar to R function exp.

@@ -51,26 +51,26 @@

Computes the exponentials in the server-side

Arguments

-
x
+ + +
x

a character string providing the name of a numerical vector.

-
newobj
+
newobj

a character string that provides the name for the output variable that is stored on the data servers. Default exp.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. -If the datasources argument is not specified +

datasources
+

a list of DSConnection-class objects obtained after login. +If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.exp returns a vector for each study of the exponential values for the numeric vector +

ds.exp returns a vector for each study of the exponential values for the numeric vector specified in the argument x. The created vectors are stored in the server-side.

@@ -84,7 +84,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki 
   # Connecting to the Opal servers
@@ -120,7 +120,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections) 
 
-}
+} # }
@@ -136,15 +136,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.extractQuantiles.html b/docs/reference/ds.extractQuantiles.html index 3ceba174..8056889b 100644 --- a/docs/reference/ds.extractQuantiles.html +++ b/docs/reference/ds.extractQuantiles.html @@ -12,7 +12,7 @@ - +
@@ -38,13 +38,13 @@
- +

Secure ranking of a vector across all sources and use of these ranks to estimate global quantiles across all studies

- +
@@ -73,7 +73,9 @@

Secure ranking of a vector across all sources and use of these ranks to esti

Arguments

-
extract.quantiles
+ + +
extract.quantiles

one of a restricted set of character strings. The value of this argument is set in choosing the value of the argument <quantiles.for.estimation> in ds.ranksSecure. In summary: to mitigate @@ -81,7 +83,7 @@

Arguments

generated: c(0.025,0.05,0.10,0.20,0.25,0.30,0.3333,0.40,0.50,0.60,0.6667, 0.70,0.75,0.80,0.90,0.95,0.975). The allowable formats for the argument are of the general form: "0.025-0.975" where the first number is the lowest -quantile to be estimated and the second number is the equivalent highest +quantile to be estimated and the second number is the equivalent highest quantile to estimate. These two quantiles are then estimated along with all allowable quantiles in between. The allowable argument values are then: "0.025-0.975", "0.05-0.95", "0.10-0.90", "0.20-0.80". Two alternative values @@ -90,8 +92,8 @@

Arguments

"secure.global.ranking.docx". Also see the header file for ds.ranksSecure.

-
extract.summary.output.ranks.df
-

a character string which specifies +

extract.summary.output.ranks.df
+

a character string which specifies the optional name for the summary data.frame written to the serverside on each data source that contains 5 of the key output variables from the ranking procedure pertaining to that particular data source. If no name has been @@ -102,12 +104,12 @@

Arguments

called by ds.ranksSecure and almost the final command of ds.extractQuantiles to print out the name of the data frame containing the summarised ranking information generated by ds.ranksSecure and the order in which the -data frame is laid out. This therefore appears as the last output produced +data frame is laid out. This therefore appears as the last output produced when ds.ranksSecure is run, and when this happens it is clear this relates to the main output of ds.ranksSecure not of ds.extractQuantiles.

-
extract.ranks.sort.by
+
extract.ranks.sort.by

a character string taking two possible values. These are "ID.orig" and "vals.orig". This is set via the argument <ranks.sort.by> in ds.ranksSecure. For more details see the associated @@ -115,7 +117,7 @@

Arguments

file for ds.ranksSecure.

-
extract.rm.residual.objects
+
extract.rm.residual.objects

logical value. Default = TRUE: at the beginning and end of each run of ds.ranksSecure delete all extraneous objects that are otherwise left behind. These are not usually needed, but could be of value @@ -123,7 +125,7 @@

Arguments

the residual objects

-
extract.datasources
+
extract.datasources

specifies the particular opal object(s) to use. This is set via the argument<datasources> in ds.ranksSecure. For more details see the associated document entitled "secure.global.ranking.docx". Also see @@ -132,10 +134,8 @@

Arguments

Value

- - -

the final main output of ds.extractQuantiles is a data frame object -named "final.quantile.df". This contains two vectors. The first named +

the final main output of ds.extractQuantiles is a data frame object +named "final.quantile.df". This contains two vectors. The first named "evaluation.quantiles" lists the full set of quantiles you have requested for evaluation as specified by the argument "quantiles.for.estimation" in ds.ranksSecure and explained in more detail above under the information for @@ -155,7 +155,7 @@

Details

be called from within the clientside function ds.ranksSecure.If you try to call ds.extractQuantiles directly(i.e. not by running ds.ranksSecure) you are almost certainly going to have to set up quite a few vectors and scalars -that are normally set by ds.ranksSecure and this is likely to be difficult. +that are normally set by ds.ranksSecure and this is likely to be difficult. ds.extractQuantiles itself calls two serverside functions extractQuantilesDS1 and extractQuantilesDS2. For more details about the cluster of functions that collectively enable secure global ranking and estimation of global quantiles @@ -180,15 +180,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.forestplot.html b/docs/reference/ds.forestplot.html index 125bfe8e..a651872d 100644 --- a/docs/reference/ds.forestplot.html +++ b/docs/reference/ds.forestplot.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Forestplot for SLMA models

- +
@@ -51,30 +51,32 @@

Forestplot for SLMA models

Arguments

-
mod
-

list List outputed by any of the SLMA models of DataSHIELD (ds.glmerSLMA, + + +

mod
+

list List outputed by any of the SLMA models of DataSHIELD (ds.glmerSLMA, ds.glmSLMA, ds.lmerSLMA)

-
variable
-

character (default NULL) Variable to meta-analyze and visualize, by setting this +

variable
+

character (default NULL) Variable to meta-analyze and visualize, by setting this argument to NULL (default) the first independent variable will be used.

-
method
-

character (Default "ML") Method to estimate the between study variance. +

method
+

character (Default "ML") Method to estimate the between study variance. See details from ?meta::metagen for the different options.

-
layout
-

character (default "JAMA") Layout of the plot. +

layout
+

character (default "JAMA") Layout of the plot. See details from ?meta::metagen for the different options.

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   # Run a logistic regression
   
   builder <- DSI::newDSLoginBuilder()
@@ -104,7 +106,7 @@ 
Examples

                 
   # Plot the results of the model
   ds.forestplot(mod)
-}
+} # }
@@ -120,15 +122,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.gamlss.html b/docs/reference/ds.gamlss.html index f49c2791..4e92d7c7 100644 --- a/docs/reference/ds.gamlss.html +++ b/docs/reference/ds.gamlss.html @@ -1,15 +1,15 @@ -Generalized Additive Models for Location Scale and Shape — ds.gamlss • dsBaseClient - +
@@ -35,23 +35,23 @@
- +

Generalized Additive Models for Location Scale and Shape

- +
-

This function calls the gamlssDS that is a wrapper function from -the gamlss R package. The function returns an object of class "gamlss", which -is a generalized additive model for location, scale and shape (GAMLSS). The -function also saves the residuals as an object on the server-side with a name -specified by the newobj argument. In addition, if the argument centiles is set -to TRUE, the function calls the centiles function from the gamlss package and +

This function calls the gamlssDS that is a wrapper function from +the gamlss R package. The function returns an object of class "gamlss", which +is a generalized additive model for location, scale and shape (GAMLSS). The +function also saves the residuals as an object on the server-side with a name +specified by the newobj argument. In addition, if the argument centiles is set +to TRUE, the function calls the centiles function from the gamlss package and returns the sample percentages below each centile curve.

@@ -79,122 +79,122 @@

Generalized Additive Models for Location Scale and Shape

Arguments

-
formula
-

a formula object, with the response on the left of an ~ operator, + + +

formula
+

a formula object, with the response on the left of an ~ operator, and the terms, separated by + operators, on the right. Nonparametric smoothing -terms are indicated by pb() for penalised beta splines, cs for smoothing splines, -lo for loess smooth terms and random or ra for random terms, +terms are indicated by pb() for penalised beta splines, cs for smoothing splines, +lo for loess smooth terms and random or ra for random terms, e.g. 'y~cs(x,df=5)+x1+x2*x3'.

-
sigma.formula
+
sigma.formula

a formula object for fitting a model to the sigma parameter, as in the formula above, e.g. sigma.formula='~cs(x,df=5)'.

-
nu.formula
-

a formula object for fitting a model to the nu parameter, +

nu.formula
+

a formula object for fitting a model to the nu parameter, e.g. nu.formula='~x'.

-
tau.formula
-

a formula object for fitting a model to the tau parameter, +

tau.formula
+

a formula object for fitting a model to the tau parameter, e.g. tau.formula='~cs(x,df=2)'.

-
family
-

a gamlss.family object, which is used to define the distribution -and the link functions of the various parameters. The distribution families -supported by gamlss() can be found in gamlss.family. Functions such as 'BI()' +

family
+

a gamlss.family object, which is used to define the distribution +and the link functions of the various parameters. The distribution families +supported by gamlss() can be found in gamlss.family. Functions such as 'BI()' (binomial) produce a family object. Also can be given without the parentheses i.e. 'BI'. Family functions can take arguments, as in 'BI(mu.link=probit)'.

-
data
-

a data frame containing the variables occurring in the formula. +

data
+

a data frame containing the variables occurring in the formula. If this is missing, the variables should be on the parent environment.

-
method
+
method

a character indicating the algorithm for GAMLSS. Can be either -'RS', 'CG' or 'mixed'. If method='RS' the function will use the Rigby and -Stasinopoulos algorithm, if method='CG' the function will use the Cole and +'RS', 'CG' or 'mixed'. If method='RS' the function will use the Rigby and +Stasinopoulos algorithm, if method='CG' the function will use the Cole and Green algorithm, and if method='mixed' the function will use the RS algorithm twice before switching to the Cole and Green algorithm for up to 10 extra iterations.

-
mu.fix
+
mu.fix

logical, indicate whether the mu parameter should be kept fixed in the fitting processes.

-
sigma.fix
+
sigma.fix

logical, indicate whether the sigma parameter should be kept fixed in the fitting processes.

-
nu.fix
-

logical, indicate whether the nu parameter should be kept fixed +

nu.fix
+

logical, indicate whether the nu parameter should be kept fixed in the fitting processes.

-
tau.fix
+
tau.fix

logical, indicate whether the tau parameter should be kept fixed in the fitting processes.

-
control
-

this sets the control parameters of the outer iterations algorithm -using the gamlss.control function. This is a vector of 7 numeric values: (i) c.crit -(the convergence criterion for the algorithm), (ii) n.cyc (the number of cycles of -the algorithm), (iii) mu.step (the step length for the parameter mu), (iv) sigma.step +

control
+

this sets the control parameters of the outer iterations algorithm +using the gamlss.control function. This is a vector of 7 numeric values: (i) c.crit +(the convergence criterion for the algorithm), (ii) n.cyc (the number of cycles of +the algorithm), (iii) mu.step (the step length for the parameter mu), (iv) sigma.step (the step length for the parameter sigma), (v) nu.step (the step length for the parameter nu), (vi) tau.step (the step length for the parameter tau), (vii) gd.tol -(global deviance tolerance level). The default values for these 7 parameters are +(global deviance tolerance level). The default values for these 7 parameters are set to c(0.001, 20, 1, 1, 1, 1, Inf).

-
i.control
-

this sets the control parameters of the inner iterations of the -RS algorithm using the glim.control function. This is a vector of 4 numeric values: -(i) cc (the convergence criterion for the algorithm), (ii) cyc (the number of -cycles of the algorithm), (iii) bf.cyc (the number of cycles of the backfitting -algorithm), (iv) bf.tol (the convergence criterion (tolerance level) for the -backfitting algorithm). The default values for these 4 parameters are set to +

i.control
+

this sets the control parameters of the inner iterations of the +RS algorithm using the glim.control function. This is a vector of 4 numeric values: +(i) cc (the convergence criterion for the algorithm), (ii) cyc (the number of +cycles of the algorithm), (iii) bf.cyc (the number of cycles of the backfitting +algorithm), (iv) bf.tol (the convergence criterion (tolerance level) for the +backfitting algorithm). The default values for these 4 parameters are set to c(0.001, 50, 30, 0.001).

-
centiles
-

logical, indicating whether the function centiles() will be used to +

centiles
+

logical, indicating whether the function centiles() will be used to tabulate the sample percentages below each centile curve. Default is set to FALSE.

-
xvar
-

the unique explanatory variable used in the centiles() function. This +

xvar
+

the unique explanatory variable used in the centiles() function. This variable is used only if the centiles argument is set to TRUE. A restriction in the centiles function is that it applies to models with one explanatory variable only.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default gamlss_res.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

a gamlss object with all components as in the native R gamlss function. -Individual-level information like the components y (the response response) and -residuals (the normalised quantile residuals of the model) are not disclosed to +

a gamlss object with all components as in the native R gamlss function. +Individual-level information like the components y (the response response) and +residuals (the normalised quantile residuals of the model) are not disclosed to the client-side.

@@ -219,15 +219,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.getWGSR.html b/docs/reference/ds.getWGSR.html index c2d4ae59..9f647c02 100644 --- a/docs/reference/ds.getWGSR.html +++ b/docs/reference/ds.getWGSR.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Computes the WHO Growth Reference z-scores of anthropometric data

- +
@@ -60,14 +60,16 @@

Computes the WHO Growth Reference z-scores of anthropometric data

Arguments

-
sex
+ + +
sex

the name of the binary variable that indicates the sex of the subject. This must be coded as 1 = male and 2 = female. If in your project the variable sex has different -levels, you should recode the levels to 1 for males and 2 for females using the +levels, you should recode the levels to 1 for males and 2 for females using the ds.recodeValues DataSHIELD function before the use of the ds.getWGSR.

-
firstPart
+
firstPart

Name of variable specifying:
Weight (kg) for BMI/A, W/A, W/H, or W/L
Head circumference (cm) for HC/A
@@ -80,7 +82,7 @@

Arguments

height, length, head circumference, and MUAC in cm; skinfolds in mm).

-
secondPart
+
secondPart

Name of variable specifying:
Age (days) for H/A, HC/A, L/A, MUAC/A, SSF/A, or TSF/A
Height (cm) for BMI/A, or W/H
@@ -89,7 +91,7 @@

Arguments

height and length in cm).

-
index
+
index

The index to be calculated and added to data. One of:
bfa BMI for age
hca Head circumference for age
@@ -104,14 +106,14 @@

Arguments

Give a quoted index name as in (e.g.) "wfh".

-
standing
+
standing

Variable specifying how stature was measured. If NA (default) then age (for "hfa" or "lfa") or height rules (for "wfh" or "wfl") will be applied. This must be coded as -1 = Standing; 2 = Supine; 3 = Unknown. Missing values will be recoded to 3 = Unknown. +1 = Standing; 2 = Supine; 3 = Unknown. Missing values will be recoded to 3 = Unknown. Give a single value (e.g."1"). If no value is specified then height and age rules will be applied.

-
thirdPart
+
thirdPart

Name of variable specifying age (in days) for BMI/A. Give a quoted variable name as in (e.g.) "age". Be careful with units (age in days). If age is given in different units you should convert it in age in days using the ds.make DataSHIELD function before the use @@ -119,32 +121,30 @@

Arguments

by the formula $age_days=age_months*(365.25/12)$.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Defaults getWGSR.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.getWGSR assigns a vector for each study that includes the z-scores for the +

ds.getWGSR assigns a vector for each study that includes the z-scores for the specified index. The created vectors are stored in the servers.

Details

-

The function calls the server-side function getWGSRDS that computes the WHO +

The function calls the server-side function getWGSRDS that computes the WHO Growth Reference z-scores of anthropometric data for weight, height or length, MUAC (middle upper arm circumference), head circumference, sub-scapular skinfold and triceps skinfold. Note that the function might fail or return NAs when the variables are outside the ranges given in the WGS (WHO Child Growth Standards) reference (i.e. 45 to 120 cm for height and -0 to 60 months for age). It is up to the user to check the ranges and the units of their +0 to 60 months for age). It is up to the user to check the ranges and the units of their data.

@@ -154,7 +154,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   # Connecting to the Opal servers
 
@@ -192,7 +192,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections) 
 
-}
+} # }
@@ -208,15 +208,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.glm.html b/docs/reference/ds.glm.html index f2cd48af..3ece7fc8 100644 --- a/docs/reference/ds.glm.html +++ b/docs/reference/ds.glm.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Fits Generalized Linear Model

- +
@@ -64,122 +64,97 @@

Fits Generalized Linear Model

Arguments

-
formula
+ + +
formula

an object of class formula describing -the model to be fitted. For more information see +the model to be fitted. For more information see Details.

-
data
+
data

a character string specifying the name of an (optional) data frame that contains all of the variables in the GLM formula.

-
family
+
family

identifies the error distribution function to use in -the model. -This can be set as "gaussian", "binomial" and "poisson". +the model. +This can be set as "gaussian", "binomial" and "poisson". For more information see Details.

-
offset
+
offset

a character string specifying the name of a variable to be used as an offset. ds.glm does not allow an offset vector to be written directly into the GLM formula. For more information see Details.

-
weights
+
weights

a character string specifying the name of a variable containing -prior regression weights for the fitting process. +prior regression weights for the fitting process. ds.glm does not allow a weights vector to be written directly into the GLM formula.

-
checks
-

logical. If TRUE ds.glm checks the structural integrity +

checks
+

logical. If TRUE ds.glm checks the structural integrity of the model. Default FALSE. For more information see Details.

-
maxit
+
maxit

a numeric scalar denoting the maximum number of iterations that are permitted before ds.glm declares that the model has failed to converge.

-
CI
+
CI

a numeric value specifying the confidence interval. Default 0.95.

-
viewIter
-

logical. If TRUE the results of the intermediate iterations are +

viewIter
+

logical. If TRUE the results of the intermediate iterations are printed. If FALSE only final results are shown. Default FALSE.

-
viewVarCov
+
viewVarCov

logical. If TRUE the variance-covariance matrix of parameter estimates is returned. Default FALSE.

-
viewCor
+
viewCor

logical. If TRUE the correlation matrix of parameter estimates is returned. Default FALSE.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

Many of the elements of the output list returned by ds.glm are +

Many of the elements of the output list returned by ds.glm are equivalent to those returned by the glm() function in native R. However, potentially disclosive elements -such as individual-level residuals and linear predictor values are blocked. +such as individual-level residuals and linear predictor values are blocked. In this case, only non-disclosive elements are returned from each study separately.

- -

The list of elements returned by ds.glm is mentioned below:

- -

Nvalid: total number of valid observational units across all studies.

- -

Nmissing: total number of observational units across all studies with at least one data item missing.

- - -

Ntotal: total of observational units across all studies, the +

Ntotal: total of observational units across all studies, the sum of valid and missing units.

- -

disclosure.risk: risk of disclosure, - the value 1 indicates that one of the disclosure traps + the value 1 indicates that one of the disclosure traps has been triggered in that study.

- -

errorMessage: explanation for any errors or disclosure risks identified.

- - -

nsubs: total number of observational units used by ds.glm function.

-

-

nb usually is the same as nvalid.

- - +

nsubs: total number of observational units used by ds.glm function. + nb usually is the same as nvalid.

iter: total number of iterations before convergence achieved.

- -

family: error family and link function.

- -

formula: model formula, see description of formula as an input parameter (above).

- - -

coefficients: a matrix with 5 columns:

-

-
First
+

coefficients: a matrix with 5 columns:

First

: the names of all of the regression parameters (coefficients) in the model

second
@@ -194,28 +169,22 @@

Value

fifth

: the p-value treating that as a standardised normal deviate

- -

dev: residual deviance.

- +

dev: residual deviance.

df: residual degrees of freedom. nb residual degrees of freedom + number of parameters in model = nsubs.

- - -

output.information: reminder to the user that there +

output.information: reminder to the user that there is more information at the top of the output.

- -

Also, the estimated coefficients and standard errors expanded with estimated confidence intervals - with % coverage specified by ci argument are returned. + with % coverage specified by ci argument are returned. For the poisson model, - the output is generated on the scale of the linear predictor (log rates and log rate ratios) + the output is generated on the scale of the linear predictor (log rates and log rate ratios) and the natural scale after exponentiation (rates and rate ratios).

Details

Fits a GLM on data from a single source or multiple sources on the server-side. -In the latter case, the data are co-analysed (when using ds.glm) +In the latter case, the data are co-analysed (when using ds.glm) by using an approach that is mathematically equivalent to placing all individual-level data from all sources in one central warehouse and analysing those data using the conventional glm() function in R. In this situation marked heterogeneity between sources should be corrected @@ -228,35 +197,35 @@

Details

function is also allowed by ds.glm.

Many GLMs can be fitted very simply using a formula such as:

$$y~a+b+c+d$$

-

which simply means fit a GLM with y as the outcome variable and -a, b, c and d as covariates. +

which simply means fit a GLM with y as the outcome variable and +a, b, c and d as covariates. By default all such models also include an intercept (regression constant) term.

Instead, if you need to fit a more complex model, for example:

$$EVENT~1+TID+SEXF*AGE.60$$

-

In the above model the outcome variable is EVENT -and the covariates -TID (factor variable with level values between 1 and 6 denoting the period time), +

In the above model the outcome variable is EVENT +and the covariates +TID (factor variable with level values between 1 and 6 denoting the period time), SEXF (factor variable denoting sex) -and AGE.60 (quantitative variable representing age-60 in years). +and AGE.60 (quantitative variable representing age-60 in years). The term 1 forces -the model to include an intercept term, in contrast if you use the term 0 the +the model to include an intercept term, in contrast if you use the term 0 the intercept term is removed. The * symbol between SEXF and AGE.60 means fit all possible main effects and interactions for and between those two covariates. - This takes the value 0 in all males 0 * AGE.60 + This takes the value 0 in all males 0 * AGE.60 and in females 1 * AGE.60. - This model is in example 1 of the section Examples. In this case the logarithm of - the survival time is added as an offset (log(survtime)).

+ This model is in example 1 of the section Examples. In this case the logarithm of + the survival time is added as an offset (log(survtime)).

In the family argument can be specified three types of models to fit:

"gaussian"

: conventional linear model with normally distributed errors

- +
"binomial"

: conventional unconditional logistic regression model

"poisson"
-

: Poisson regression model which is the most used in survival analysis. +

: Poisson regression model which is the most used in survival analysis. The model used Piecewise Exponential Regression (PER) which typically closely approximates Cox regression in its main estimates and standard errors.

@@ -266,12 +235,12 @@

Details

logistic link function and the poisson family with a log link function.

The data argument avoids you having to specify the name of the -data frame in front of each covariate in the formula. +data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you avoid having to write: \(DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d\)

-

The checks argument verifies that the variables in the model are all defined (exist) +

The checks argument verifies that the variables in the model are all defined (exist) on the server-side at every study -and that they have the correct characteristics required to fit the model. +and that they have the correct characteristics required to fit the model. It is suggested to make checks argument TRUE if an unexplained problem in the model fit is encountered because the running process takes several minutes.

In maxit Logistic regression and Poisson regression @@ -279,7 +248,7 @@

Details

regression constant is far away from its actual value that the GLM is trying to estimate. In consequence we often set maxit=30 but depending on the nature of the models you wish to fit, you may wish -to be alerted much more quickly than this if there is a delay in convergence, +to be alerted much more quickly than this if there is a delay in convergence, or you may wish to all more iterations.

Privacy protected iterative fitting of a GLM is explained here:

@@ -340,7 +309,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -446,7 +415,7 @@ 
Examples

 
 # Clear the Datashield R sessions and logout
 datashield.logout(connections) 
-}
+} # }
@@ -462,15 +431,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.glmPredict.html b/docs/reference/ds.glmPredict.html index 7bf7903f..228bed88 100644 --- a/docs/reference/ds.glmPredict.html +++ b/docs/reference/ds.glmPredict.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Applies predict.glm() to a serverside glm object

- +
@@ -61,13 +61,15 @@

Applies predict.glm() to a serverside glm object

Arguments

-
glmname
+ + +
glmname

is a character string identifying the glm object on serverside to which predict.glm is to be applied. Equivalent to <object> argument in native R's predict.glm which is described as: a fitted object of class inheriting from 'glm'.

-
newdataname
+
newdataname

is a character string identifying an (optional) dataframe on the serverside in which to look for new covariate values with which to predict. If omitted, @@ -76,7 +78,7 @@

Arguments

predict.glm function in native R.

-
output.type
+
output.type

a character string taking the values 'response', 'link' or 'terms'. The value 'response' generates predictions on the scale of the original outcome, e.g. as proportions in a logistic regression. These @@ -95,7 +97,7 @@

Arguments

native R's predict.glm function.

-
se.fit
+
se.fit

logical if standard errors for the fitted predictions are required. Defaults to FALSE when the output contains only a vector (or vectors) of predicted values. If TRUE, the output also contains corresponding vectors for the standard @@ -105,7 +107,7 @@

Arguments

argument is equivalent to the <type> argument in native R's predict.glm function.

-
dispersion
+
dispersion

numeric value specifying the dispersion of the GLM fit to be assumed in computing the standard errors. If omitted, that returned by summary applied to the glm object is used. e.g. if <dispersion> is unspecified @@ -116,14 +118,14 @@

Arguments

is precisely equivalent to the corresponding argument in predict.glm in native R.

-
terms
+
terms

a character vector specifying a subset of terms to return in the prediction. Only applies if output.type='terms'. ds.glmPredict's <terms> argument is precisely equivalent to the corresponding argument in predict.glm in native R.

-
na.action
+
na.action

character string determining what should be done with missing values in the data.frame identified by <newdataname>. Default is na.pass which predicts from the specified new data.frame with all NAs left in place. na.omit @@ -131,14 +133,14 @@

Arguments

NAs anywhere in the data.frame. For further details see help in native R.

-
newobj
+
newobj

a character string specifying the name of the serverside object to which the output object from the call to ds.glmPredict is to be written in each study. If no <newobj> argument is specified, the output object on the serverside defaults to the name "predict_glm".

-
datasources
+
datasources

specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with called opals.a, opals.w2, and connection.xyz, you can choose which of @@ -161,9 +163,7 @@

Arguments

Value

- - -

ds.glmPredict calls the serverside assign function glmPredictDS.as +

ds.glmPredict calls the serverside assign function glmPredictDS.as which writes a new object to the serverside containing output precisely equivalent to predict.glm in native R. The name for this serverside object is given by the newobj argument or if that argument is missing or null it is called "predict_glm". @@ -174,10 +174,8 @@

Value

in 'fit'. The non-disclosive summary statistics for the vector(s) include: length, the total number of valid (non-missing) values, the number of missing values, the mean and standard deviation of the valid -values and the 5

- - -

the output always includes: the name of the serverside glm object being predicted from, +values and the 5 +the output always includes: the name of the serverside glm object being predicted from, the name - if one was specified - of the dataframe being used as the basis for predictions, the output.type specified ('link', 'response' or 'terms'), the value of the dispersion parameter if one had been specified and the residual scale parameter (which is @@ -204,7 +202,7 @@

Details

can then be applied to the newobj to interpret the output. For example, it could be used as the basis for regression diagnostic plots. Second, the call to the aggregate function creates a non-disclosive summary of all the -information held in the newobj created by the assign function +information held in the newobj created by the assign function and returns this summary to the clientside. For example, the full list of predicted/fitted values generated by the model could be disclosive. So although the newobj holds the full vector of fitted values, only the @@ -233,15 +231,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.glmSLMA.html b/docs/reference/ds.glmSLMA.html index 286040d6..83204ac5 100644 --- a/docs/reference/ds.glmSLMA.html +++ b/docs/reference/ds.glmSLMA.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)

- +
@@ -63,76 +63,76 @@

Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analy

Arguments

-
formula
+ + +
formula

an object of class formula describing -the model to be fitted. For more information see +the model to be fitted. For more information see Details.

-
family
+
family

identifies the error distribution function to use in the model.

-
offset
+
offset

a character string specifying the name of a variable to be used as an offset.ds.glmSLMA does not allow an offset vector to be written directly into the GLM formula.

-
weights
+
weights

a character string specifying the name of a variable containing prior regression weights for the fitting process. ds.glmSLMA does not allow a weights vector to be written directly into the GLM formula.

-
combine.with.metafor
+
combine.with.metafor

logical. If TRUE the estimates and standard errors for each regression coefficient are pooled across studies using random-effects meta-analysis under maximum likelihood (ML), restricted maximum likelihood (REML) or fixed-effects meta-analysis (FE). Default TRUE.

-
newobj
+
newobj

a character string specifying the name of the object to which the glm object representing the model fit on the serverside in each study is to be written. If no <newobj> argument is specified, the output object defaults to "new.glm.obj".

-
dataName
+
dataName

a character string specifying the name of an (optional) data frame that contains all of the variables in the GLM formula.

-
checks
-

logical. If TRUE ds.glmSLMA checks the structural integrity +

checks
+

logical. If TRUE ds.glmSLMA checks the structural integrity of the model. Default FALSE. For more information see Details.

-
maxit
+
maxit

a numeric scalar denoting the maximum number of iterations that -are permitted before ds.glmSLMA declares that the model has failed to converge. +are permitted before ds.glmSLMA declares that the model has failed to converge. For more information see Details.

-
notify.of.progress
+
notify.of.progress

specifies if console output should be produced to indicate progress. Default FALSE.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

The serverside aggregate functions glmSLMADS1 and glmSLMADS2 return +

The serverside aggregate functions glmSLMADS1 and glmSLMADS2 return output to the clientside, while the assign function glmSLMADS.assign simply writes the glm object to the serverside created by the model fit on a given server as a permanent object on that same server. @@ -145,128 +145,68 @@

Value

ds.glmSLMA include: a mixture of non-disclosive elements of the glm object reported separately by study included in a list object called output.summary; and a series of other list objects that represent inferences aggregated across studies.

- -

the study specific items include:

- - -

coefficients: a matrix with 5 columns:

-

-
First
+

coefficients: a matrix with 5 columns:

First

: the names of all of the regression parameters (coefficients) in the model

- +
second

: the estimated values

- +
third

: corresponding standard errors of the estimated values

- +
fourth

: the ratio of estimate/standard error

- +
fifth

: the p-value treating that as a standardised normal deviate

- +

family: indicates the error distribution and link function used in the GLM.

- -

formula: model formula, see description of formula as an input parameter (above).

- -

df.resid: the residual degrees of freedom around the model.

- -

deviance.resid: the residual deviance around the model.

- -

df.null: the degrees of freedom around the null model (with just an intercept).

- -

dev.null: the deviance around the null model (with just an intercept).

- -

CorrMatrix: the correlation matrix of parameter estimates.

- -

VarCovMatrix: the variance-covariance matrix of parameter estimates.

- -

weights: the name of the vector (if any) holding regression weights.

- -

offset: the name of the vector (if any) holding an offset (enters glm with a coefficient of 1.00).

- -

cov.scaled: equivalent to VarCovMatrix.

- -

cov.unscaled: equivalent to VarCovMatrix but assuming dispersion (scale) parameter is 1.

- -

Nmissing: the number of missing observations in the given study.

- -

Nvalid: the number of valid (non-missing) observations in the given study.

- - -

Ntotal: the total number of observations in the given study +

Ntotal: the total number of observations in the given study (Nvalid + Nmissing).

- -

data: equivalent to input parameter dataName (above).

- -

dispersion: the estimated dispersion parameter: deviance.resid/df.resid for a gaussian family multiple regression model, 1.00 for logistic and poisson regression.

- -

call: summary of key elements of the call to fit the model.

- - -

na.action: chosen method of dealing with missing values. This is +

na.action: chosen method of dealing with missing values. This is usually, na.action = na.omit - see help in native R.

- -

iter: the number of iterations required to achieve convergence of the glm model in each separate study.

- - -

Once the study-specific output has been returned, ds.glmSLMA

- - -

returns a series of lists relating to the aggregated inferences across studies. +

Once the study-specific output has been returned, ds.glmSLMA +returns a series of lists relating to the aggregated inferences across studies. These include the following:

- -

num.valid.studies: the number of studies with valid output included in the combined analysis

- -

betamatrix.all: matrix with a row for each regression coefficient and a column for each study reporting the estimated regression coefficients by study.

- -

sematrix.all: matrix with a row for each regression coefficient and a column for each study reporting the standard errors of the estimated regression coefficients by study.

- -

betamatrix.valid: matrix with a row for each regression coefficient and a column for each study reporting the estimated regression coefficients by study but only for studies with valid output (eg not violating disclosure traps)

- -

sematrix.all: matrix with a row for each regression coefficient and a column for each study reporting the standard errors of the estimated regression coefficients by study but only for studies with valid output (eg not violating disclosure traps)

- -

SLMA.pooled.estimates.matrix: a matrix with a row for each regression coefficient and six columns. The first two columns contain the pooled estimate of each regression coefficients and its standard error with @@ -277,8 +217,6 @@

Value

argument combine.with.metafor is set to TRUE. Otherwise, users can take the betamatrix.valid and sematrix.valid matrices and enter them into their meta-analysis package of choice.

- -

is.object.created and validity.check are standard items returned by an assign function when the designated newobj appears to have been successfuly created on the serverside at each study. This output is @@ -287,9 +225,9 @@

Value

Details

-

ds.glmSLMA specifies the structure of a Generalized Linear Model +

ds.glmSLMA specifies the structure of a Generalized Linear Model to be fitted separately on each study or data source. Calls serverside functions -glmSLMADS1 (aggregate),glmSLMADS2 (aggregate) and glmSLMADS.assign (assign). +glmSLMADS1 (aggregate),glmSLMADS2 (aggregate) and glmSLMADS.assign (assign). From a mathematical perspective, the SLMA approach (using ds.glmSLMA) differs fundamentally from the alternative approach using ds.glm. ds.glm fits the model iteratively across all studies together. At each @@ -344,31 +282,31 @@

Details

function is also allowed by ds.glmSLMA.

Many glms can be fitted very simply using a formula such as:

$$y~a+b+c+d$$

-

which simply means fit a glm with y as the outcome variable and -a, b, c and d as covariates. +

which simply means fit a glm with y as the outcome variable and +a, b, c and d as covariates. By default all such models also include an intercept (regression constant) term.

Instead, if you need to fit a more complex model, for example:

$$EVENT~1+TID+SEXF*AGE.60$$

-

In the above model the outcome variable is EVENT -and the covariates -TID (factor variable with level values between 1 and 6 denoting the period time), +

In the above model the outcome variable is EVENT +and the covariates +TID (factor variable with level values between 1 and 6 denoting the period time), SEXF (factor variable denoting sex) -and AGE.60 (quantitative variable representing age-60 in years). +and AGE.60 (quantitative variable representing age-60 in years). The term 1 forces -the model to include an intercept term, in contrast if you use the term 0 the +the model to include an intercept term, in contrast if you use the term 0 the intercept term is removed. The * symbol between SEXF and AGE.60 means fit all possible main effects and interactions for and between those two covariates. - This takes the value 0 in all males 0 * AGE.60 - and in females 1 * AGE.60. - This model is in example 1 of the section Examples. In this case the logarithm of + This takes the value 0 in all males 0 * AGE.60 + and in females 1 * AGE.60. + This model is in example 1 of the section Examples. In this case the logarithm of the survival time is added as an offset (log(survtime)).

In the family argument a range of model types can be fitted. This range has recently been extended to include a number of model types that are non-standard but are used relatively widely.

The standard models include:

"gaussian"

: conventional linear model with normally distributed errors

- +
"binomial"

: conventional unconditional logistic regression model

@@ -391,7 +329,7 @@

Details

which is estimated during the model fit and if it takes the value K it means that the expected variance is K x the expected mean, which implies that all standard errors will be sqrt(K) times larger than in a standard Poisson model - fitted to the same data. This allows for the extra uncertainty which is associated + fitted to the same data. This allows for the extra uncertainty which is associated with 'overdispersion' that occurs very commonly with Poisson distributed data, and typically arises when the count/rate data being modelled occur in blocks which exhibit heterogeneity of underlying risk which is not being fully @@ -415,20 +353,20 @@

Details

identity link, the poisson family the log link, the binomial/Bernoulli family the logit link and the the gamma family the reciprocal link.

The dataName argument avoids you having to specify the name of the -data frame in front of each covariate in the formula. +data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you avoid having to write: \(DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d\)

-

The checks argument verifies that the variables in the model are all defined (exist) +

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study -and that they have the correct characteristics required to fit the model. +and that they have the correct characteristics required to fit the model. It is suggested to make checks argument TRUE only if an unexplained - problem in the model fit is encountered because the running process takes several minutes.

+ problem in the model fit is encountered because the running process takes several minutes.

In maxit Logistic regression and Poisson regression models can require many iterations, particularly if the starting value of the regression constant is far away from its actual value that the GLM is trying to estimate. In consequence we often set maxit=30 but depending on the nature of the models you wish to fit, you may wish -to be alerted much more quickly than this if there is a delay in convergence, +to be alerted much more quickly than this if there is a delay in convergence, or you may wish to allow more iterations.

Server functions called: glmSLMADS1, glmSLMADS2, glmSLMADS.assign

@@ -440,7 +378,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -543,7 +481,7 @@ 
Examples

 
 # Clear the Datashield R sessions and logout
 datashield.logout(connections) 
-}
+} # }
@@ -559,15 +497,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.glmSummary.html b/docs/reference/ds.glmSummary.html index 11005770..327060d8 100644 --- a/docs/reference/ds.glmSummary.html +++ b/docs/reference/ds.glmSummary.html @@ -1,12 +1,12 @@ -Summarize a glm object on the serverside — ds.glmSummary • dsBaseClientSummarize a glm object on the serverside — ds.glmSummary • dsBaseClient - +
@@ -32,19 +32,19 @@

- +

Summarize a glm object on the serverside

- +
-

Summarize a glm object on the serverside to create a -summary_glm object. Also identify and return components of +

Summarize a glm object on the serverside to create a +summary_glm object. Also identify and return components of both the glm object and the summary_glm object that can safely be sent to the clientside without a risk of disclosure

@@ -55,19 +55,21 @@

Summarize a glm object on the serverside

Arguments

-
x.name
+ + +
x.name

a character string providing the name of a glm object on the serverside that has previously been created e.g. using ds.glmSLMA

-
newobj
+
newobj

a character string specifying the name of the object to which the summary_glm object representing the output of summary(glm object) in each study is to be written. If no <newobj> argument is specified, the output object on the serverside defaults to "summary_glm.newobj".

-
datasources
+
datasources

specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with called opals.a, opals.w2, and connection.xyz, you can choose which of @@ -90,9 +92,7 @@

Arguments

Value

- - -

ds.glmSummary writes a new object to the serverside with name given by +

ds.glmSummary writes a new object to the serverside with name given by the newobj argument or if that argument is missing or null it is called "summary_glm.newobj". In addition, ds.glmSummary returns an object containing two lists to the clientside the two lists are named "glm.obj" and "glm.summary.obj" which contain all of the @@ -100,7 +100,7 @@

Value

but with all potentially disclosive components set to NA or masked in another way see "details" above. The elements that are returned with a non-NA value in the glm.obj list object are: "coefficients", "rank", "family", "deviance", "aic", -"null.deviance", "iter", "df.residual", "df.null", "converged", "boundary", +"null.deviance", "iter", "df.residual", "df.null", "converged", "boundary", "call", "formula", "terms", "data", "control", "method", "contrasts", "xlevels". The elements that are returned with a non-NA value in the glm.summary.obj list object are: "call", "terms", "family", "deviance", @@ -123,7 +123,7 @@

Details

disclosive. They are all therefore set to NA and so convey no information when returned to the clientside: 1.residuals, 2.fitted.values, 3.effects, 4.R, 5.qr, 6.linear.predictors, -7.weights, 8.prior.weights, 9.y, 10.model, 11. na.action, 12.x, 13. offset. +7.weights, 8.prior.weights, 9.y, 10.model, 11. na.action, 12.x, 13. offset. In addition the list element "data" which identifies a data.frame that was identified as containing all of the variables required for the model is also disclosive because it doesn't list @@ -158,15 +158,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.glmerSLMA.html b/docs/reference/ds.glmerSLMA.html index b278fbcc..a65c5f30 100644 --- a/docs/reference/ds.glmerSLMA.html +++ b/docs/reference/ds.glmerSLMA.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Fits Generalized Linear Mixed-Effect Models via Study-Level Meta-Analysis

- +
@@ -69,224 +69,190 @@

Fits Generalized Linear Mixed-Effect Models via Study-Level Meta-Analysis

Arguments

-
formula
-

an object of class formula describing the model to be fitted. + + +

formula
+

an object of class formula describing the model to be fitted. For more information see Details.

-
offset
+
offset

a character string specifying the name of a variable to be used as an offset.

-
weights
+
weights

a character string specifying the name of a variable containing prior regression weights for the fitting process.

-
combine.with.metafor
+
combine.with.metafor

logical. If TRUE the estimates and standard errors for each regression coefficient are pooled across studies using random-effects meta-analysis under maximum likelihood (ML), restricted maximum likelihood (REML) or fixed-effects meta-analysis (FE). Default TRUE.

-
dataName
+
dataName

a character string specifying the name of a data frame that contains all of the variables in the GLME formula. For more information see Details.

-
checks
-

logical. If TRUE ds.glmerSLMA checks the structural integrity +

checks
+

logical. If TRUE ds.glmerSLMA checks the structural integrity of the model. Default FALSE. For more information see Details.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

-
family
+
family

a character string specifying the distribution of the observed value of the outcome variable around the predictions generated by the linear predictor. -This can be set as "binomial" or "poisson". +This can be set as "binomial" or "poisson". For more information see Details.

-
control_type
+
control_type

an optional character string vector specifying the nature of a parameter (or parameters) to be modified in the convergence control options which can be viewed or -modified via the glmerControl function of the package lme4. +modified via the glmerControl function of the package lme4. For more information see Details.

-
control_value
+
control_value

numeric representing the new value which you want to allocate the -control parameter corresponding to the control-type. +control parameter corresponding to the control-type. For more information see Details.

-
nAGQ
-

an integer value indicating the number of points per axis for evaluating the adaptive +

nAGQ
+

an integer value indicating the number of points per axis for evaluating the adaptive Gauss-Hermite approximation to the log-likelihood. Defaults 1, corresponding to the Laplace approximation. For more information see R glmer function help.

-
verbose
+
verbose

an integer value. If \(verbose > 0\) the output is generated during the optimization of -the parameter estimates. If \(verbose > 1\) the output is generated during the individual penalized -iteratively reweighted least squares (PIRLS) steps. Default verbose +the parameter estimates. If \(verbose > 1\) the output is generated during the individual penalized +iteratively reweighted least squares (PIRLS) steps. Default verbose value is 0 which means no additional output.

-
start_theta
+
start_theta

a numeric vector of length equal to the number of random effects. Specify to retain more control over the optimisation. See glmer() for more details.

-
start_fixef
-

a numeric vector of length equal to the number of fixed effects (NB including the intercept). +

start_fixef
+

a numeric vector of length equal to the number of fixed effects (NB including the intercept). Specify to retain more control over the optimisation. See glmer() for more details.

-
notify.of.progress
+
notify.of.progress

specifies if console output should be produced to indicate progress. Default FALSE.

-
assign
+
assign

a logical, indicates whether the function will call a second server-side function (an assign) in order to save the regression outcomes (i.e. a glmerMod object) on each server. Default FALSE.

-
newobj
+
newobj

a character string specifying the name of the object to which the glmerMod object -representing the model fit on the serverside in each study is to be written. This argument is +representing the model fit on the serverside in each study is to be written. This argument is used only when the argument assign is set to TRUE. If no <newobj> argument is specified, the output object defaults to "new.glmer.obj".

Value

- - -

Many of the elements of the output list returned by ds.glmerSLMA are +

Many of the elements of the output list returned by ds.glmerSLMA are equivalent to those returned by the glmer() function in native R. However, potentially disclosive elements -such as individual-level residuals and linear predictor values are blocked. +such as individual-level residuals and linear predictor values are blocked. In this case, only non-disclosive elements are returned from each study separately.

- -

The list of elements returned by ds.glmerSLMA is mentioned below:

- - -

coefficients: a matrix with 5 columns:

-

-
First
+

coefficients: a matrix with 5 columns:

First

: the names of all of the regression parameters (coefficients) in the model

- +
second

: the estimated values

- +
third

: corresponding standard errors of the estimated values

- +
fourth

: the ratio of estimate/standard error

- +
fifth

: the p-value treating that as a standardised normal deviate

- - -

CorrMatrix: the correlation matrix of parameter estimates.

+

CorrMatrix: the correlation matrix of parameter estimates.

VarCovMatrix: the variance-covariance matrix of parameter estimates.

- -

weights: the vector (if any) holding regression weights.

- -

offset: the vector (if any) holding an offset.

- -

cov.scaled: equivalent to VarCovMatrix.

- -

Nmissing: the number of missing observations in the given study.

- -

Nvalid: the number of valid (non-missing) observations in the given study.

- - -

Ntotal: the total number of observations +

Ntotal: the total number of observations in the given study (Nvalid + Nmissing).

- -

data: equivalent to input parameter dataName (above).

- -

call: summary of key elements of the call to fit the model.

- -

Once the study-specific output has been returned, the function returns the number of elements relating to the pooling of estimates across studies via study-level meta-analysis. These are as follows:

- -

input.beta.matrix.for.SLMA: a matrix containing the vector of coefficient estimates from each study.

- -

input.se.matrix.for.SLMA: a matrix containing the vector of standard error estimates for coefficients from each study.

- -

SLMA.pooled.estimates: a matrix containing pooled estimates for each regression coefficient across all studies with pooling under SLMA via random-effects meta-analysis under maximum likelihood (ML), restricted maximum likelihood (REML) or via fixed-effects meta-analysis (FE).

- -

convergence.error.message: reports for each study whether the model converged. If it did not some information about the reason for this is reported.

Details

-

ds.glmerSLMA fits a generalized linear mixed-effects model (GLME) +

ds.glmerSLMA fits a generalized linear mixed-effects model (GLME) - e.g. a logistic or Poisson regression model including both fixed and random effects - - on data from single or multiple sources.

-

This function is similar to glmer function from lme4 package in native R.

-

When there are multiple data sources, the GLME is fitted to convergence + on data from single or multiple sources.

+

This function is similar to glmer function from lme4 package in native R.

+

When there are multiple data sources, the GLME is fitted to convergence in each data source independently. The estimates and standard errors returned to the client-side which enable cross-study pooling using Study-Level Meta-Analysis (SLMA). - The SLMA used by default metafor package - but as the SLMA occurs on the client-side (a standard R environment), the user can choose - any approach to meta-analysis. Additional information about fitting GLMEs - using glmer function can be obtained using R help for glmer and the lme4 package.

+ The SLMA used by default metafor package + but as the SLMA occurs on the client-side (a standard R environment), the user can choose + any approach to meta-analysis. Additional information about fitting GLMEs + using glmer function can be obtained using R help for glmer and the lme4 package.

In formula most shortcut notation allowed by glmer() function is -also allowed by ds.glmerSLMA. +also allowed by ds.glmerSLMA. Many GLMEs can be fitted very simply using a formula like: -$$y~a+b+(1|c)$$ -which simply means fit an GLME with y as the outcome variable (e.g. +$$y~a+b+(1|c)$$ +which simply means fit an GLME with y as the outcome variable (e.g. a binary case-control using a logistic regression model or a count or a survival time using a Poisson regression model), a and b as fixed effects, and c as a random effect or grouping factor.

-

It is also possible to fit models with random slopes by specifying a model such as -$$y~a+b+(1+b|c)$$ +

It is also possible to fit models with random slopes by specifying a model such as +$$y~a+b+(1+b|c)$$ where the effect of b can vary randomly between groups defined by c. Implicit nesting can be specified with formulas such as: \(y~a+b+(1|c/d)\) or \(y~a+b+(1|c)+(1|c:d)\).

The dataName argument avoids you having to specify the name of the -data frame in front of each covariate in the formula. -For example, if the data frame is called DataFrame you avoid having to write: +data frame in front of each covariate in the formula. +For example, if the data frame is called DataFrame you avoid having to write: \(DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)\).

-

The checks argument verifies that the variables in the model are all defined (exist) +

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study -and that they have the correct characteristics required to fit the model. +and that they have the correct characteristics required to fit the model. It is suggested to make checks argument TRUE if an unexplained problem in the model fit is encountered because the running process takes several minutes.

@@ -298,10 +264,10 @@

Details

Note if you are fitting a gaussian model (a standard linear mixed -model) you should use ds.lmerSLMA and not ds.glmerSLMA. +model) you should use ds.lmerSLMA and not ds.glmerSLMA. For more information you can see R help for lmer and glmer.

In control_type at present only one such parameter can be modified, -namely the tolerance of the convergence criterion to the gradient of the log-likelihood +namely the tolerance of the convergence criterion to the gradient of the log-likelihood at the maximum likelihood achieved. We have enabled this because our practical experience suggests that in situations where the model looks to have converged with sensible parameter values but formal convergence is not being declared if we allow the model to be more @@ -328,7 +294,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -399,7 +365,7 @@ 
Examples

   
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-  }
+  } # }
   
 
 
@@ -417,15 +383,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.
- - + + diff --git a/docs/reference/ds.heatmapPlot.html b/docs/reference/ds.heatmapPlot.html index cf31a8ea..dd26dbd3 100644 --- a/docs/reference/ds.heatmapPlot.html +++ b/docs/reference/ds.heatmapPlot.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Generates a Heat Map plot

- +
@@ -59,70 +59,70 @@

Generates a Heat Map plot

Arguments

-
x
+ + +
x

a character string specifying the name of a numerical vector.

-
y
+
y

a character string specifying the name of a numerical vector.

-
type
+
type

a character string that represents the type of graph to display. -type argument can be set as 'combine' or 'split'. +type argument can be set as 'combine' or 'split'. Default 'combine'. For more information see Details.

-
show
-

a character string that represents where the plot should be focused. -show argument can be set as 'all' or 'zoomed'. -Default 'all'. +

show
+

a character string that represents where the plot should be focused. +show argument can be set as 'all' or 'zoomed'. +Default 'all'. For more information see Details.

-
numints
-

the number of intervals for a density grid object. +

numints
+

the number of intervals for a density grid object. Default numints value is 20.

-
method
-

a character string that defines which heat map will be created. -The method argument can be set as 'smallCellsRule', -'deterministic' or 'probabilistic'. -Default 'smallCellsRule'. +

method
+

a character string that defines which heat map will be created. +The method argument can be set as 'smallCellsRule', +'deterministic' or 'probabilistic'. +Default 'smallCellsRule'. For more information see Details.

-
k
-

the number of the nearest neighbours for which their centroid is calculated. -Default k value is 3. +

k
+

the number of the nearest neighbours for which their centroid is calculated. +Default k value is 3. For more information see Details.

-
noise
+
noise

the percentage of the initial variance that is used as the variance of the embedded -noise if the argument method is set to 'probabilistic'. +noise if the argument method is set to 'probabilistic'. Default noise value is 0.25. For more information see Details.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.heatmapPlot returns to the client-side a heat map plot and a message specifying +

ds.heatmapPlot returns to the client-side a heat map plot and a message specifying the number of invalid cells in each study.

Details

-

The ds.heatmapPlot function first generates a density grid +

The ds.heatmapPlot function first generates a density grid and uses it to plot the graph. Cells of the grid density matrix that hold a count of less than the filter set by DataSHIELD (usually 5) are considered invalid and turned into 0 to avoid potential @@ -132,53 +132,53 @@

Details

minimum and maximum value. This was done to reduce the risk of potential disclosure.

In the argument type can be specified two types of graphics to display:

'combine'

: a combined heat map plot is displayed

- +
'split'

: each heat map is plotted separately

- +

In the argument show can be specified two options:

'all'

: the ranges of the variables are used as plot limits

- +
'zoomed'

: the plot is zoomed to the region where the actual data are

- +

In the argument method can be specified 3 different heat map to be created:

'smallCellsRule'

: the heat map of the actual variables is created but grids with low counts are replaced with grids with zero counts

- +
'deterministic'
-

: the heat map of the scaled centroids of each +

: the heat map of the scaled centroids of each k nearest neighbours of the original variables are created, where the value of k is set by the user

- +
'probabilistic'
-

: the heat map of 'noisy' variables is generated. - The added noise follows a normal distribution with +

: the heat map of 'noisy' variables is generated. + The added noise follows a normal distribution with zero mean and variance equal to a percentage of - the initial variance of each input variable. + the initial variance of each input variable. This percentage is specified by the user in the argument noise

- - - -

In the k argument the user can choose any value for + + + +

In the k argument the user can choose any value for k equal to or greater than the pre-specified threshold used as a disclosure control for this method and lower than the number of observations minus the value of this threshold. By default the value of k is set to be equal to 3 (we suggest k to be equal to, or bigger than, 3). Note that the function fails if the user -uses the default value but the study has set a bigger threshold. +uses the default value but the study has set a bigger threshold. The value of k is used only -if the argument method is set to 'deterministic'. +if the argument method is set to 'deterministic'. Any value of k is ignored if the argument method is set to 'probabilistic' or 'smallCellsRule'.

-

The value of noise is used only if the argument +

The value of noise is used only if the argument method is set to 'probabilistic'. -Any value of noise is ignored if the argument -method is set to 'deterministic' or 'smallCellsRule'. -The user can choose any value for noise equal +Any value of noise is ignored if the argument +method is set to 'deterministic' or 'smallCellsRule'. +The user can choose any value for noise equal to or greater than the pre-specified threshold 'nfilter.noise'.

Server function called: heatmapPlotDS

@@ -189,7 +189,7 @@

Author

Examples

- +
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.hetcor.html b/docs/reference/ds.hetcor.html index f174cd12..5373fbae 100644 --- a/docs/reference/ds.hetcor.html +++ b/docs/reference/ds.hetcor.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Heterogeneous Correlation Matrix

- +
@@ -57,52 +57,52 @@

Heterogeneous Correlation Matrix

Arguments

-
data
+ + +
data

the name of a data frame consisting of factors, ordered factors, logical variables, character variables, and/or numeric variables, or the first of several variables.

-
ML
+
ML

if TRUE, compute maximum-likelihood estimates; if FALSE (default), compute quick two-step estimates.

-
std.err
+
std.err

if TRUE (default), compute standard errors.

-
bins
+
bins

number of bins to use for continuous variables in testing bivariate normality; the default is 4.

-
pd
+
pd

if TRUE (default) and if the correlation matrix is not positive-definite, an attempt will be made to adjust it to a positive-definite matrix, using the nearPD function in the Matrix package. Note that default arguments to nearPD are used (except corr=TRUE); for more control call nearPD directly.

-
use
+
use

if "complete.obs", remove observations with any missing data; if "pairwise.complete.obs", compute each correlation using all observations with valid data for that pair of variables.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

Returns an object of class "hetcor" from each study, with the following components: the +

Returns an object of class "hetcor" from each study, with the following components: the correlation matrix; the type of each correlation: "Pearson", "Polychoric", or "Polyserial"; the standard errors of the correlations, if requested; the number (or numbers) of observations on which -the correlations are based; p-values for tests of bivariate normality for each pair of variables; -the method by which any missing data were handled: "complete.obs" or "pairwise.complete.obs"; TRUE +the correlations are based; p-values for tests of bivariate normality for each pair of variables; +the method by which any missing data were handled: "complete.obs" or "pairwise.complete.obs"; TRUE for ML estimates, FALSE for two-step estimates.

@@ -128,15 +128,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.histogram.html b/docs/reference/ds.histogram.html index 3e03aeb0..777c4278 100644 --- a/docs/reference/ds.histogram.html +++ b/docs/reference/ds.histogram.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Generates a histogram plot

- +
@@ -58,63 +58,61 @@

Generates a histogram plot

Arguments

-
x
+ + +
x

a character string specifying the name of a numerical vector.

-
type
+
type

a character string that represents the type of graph to display. -The type argument can be set as 'combine' or 'split'. +The type argument can be set as 'combine' or 'split'. Default 'split'. For more information see Details.

-
num.breaks
+
num.breaks

a numeric specifying the number of breaks of the histogram. Default value is 10.

-
method
+
method

a character string that defines which histogram will be created. -The method argument can be set as 'smallCellsRule', -'deterministic' or 'probabilistic'. -Default 'smallCellsRule'. +The method argument can be set as 'smallCellsRule', +'deterministic' or 'probabilistic'. +Default 'smallCellsRule'. For more information see Details.

-
k
-

the number of the nearest neighbours for which their centroid is calculated. +

k
+

the number of the nearest neighbours for which their centroid is calculated. Default k value is 3. For more information see Details.

-
noise
+
noise

the percentage of the initial variance that is used as the variance of the embedded -noise if the argument method is set to 'probabilistic'. +noise if the argument method is set to 'probabilistic'. Default noise value is 0.25. For more information see Details.

-
vertical.axis,
+
vertical.axis,

a character string that defines what is shown in the vertical axis of the plot. The vertical.axis argument can be set as 'Frequency' or 'Density'. -Default 'Frequency'. +Default 'Frequency'. For more information see Details.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

one or more histogram objects and plots depending on the argument type

- - +

one or more histogram objects and plots depending on the argument type

Details

@@ -123,56 +121,56 @@

Details

the single plots.

In the argument type can be specified two types of graphics to display:

'combine'

: a histogram that merges the single plot is displayed.

- +
'split'

: each histogram is plotted separately.

- +

In the argument method can be specified 3 different histograms to be created:

'smallCellsRule'

: the histogram of the actual variable is created but bins with low counts are removed.

- +
'deterministic'
-

: the histogram of the scaled centroids of each +

: the histogram of the scaled centroids of each k nearest neighbours of the original variable where the value of k is set by the user.

- +
'probabilistic'
-

: the histogram shows the original distribution disturbed +

: the histogram shows the original distribution disturbed by the addition of random stochastic noise. The added noise follows a normal distribution with zero mean and - variance equal to a percentage of the initial variance of the input variable. + variance equal to a percentage of the initial variance of the input variable. This percentage is specified by the user in the argument noise.

- - - -

In the k argument the user can choose any value for k equal + + + +

In the k argument the user can choose any value for k equal to or greater than the pre-specified threshold used as a disclosure control for this method and lower than the number of observations minus the value of this threshold. By default the value of k is set to be equal to 3 (we suggest k to be equal to, or bigger than, 3). Note that the function fails if the user -uses the default value but the study has set a bigger threshold. -The value of k is used only if the argument -method is set to 'deterministic'. +uses the default value but the study has set a bigger threshold. +The value of k is used only if the argument +method is set to 'deterministic'. Any value of k is ignored if the argument method is set to 'probabilistic' or 'smallCellsRule'.

-

In the noise argument the percentage of the initial variance +

In the noise argument the percentage of the initial variance that is used as the variance of the embedded -noise if the argument method is set to 'probabilistic'. -Any value of noise is ignored if the argument -method is set to 'deterministic' or 'smallCellsRule'. -The user can choose any value for noise equal to or greater +noise if the argument method is set to 'probabilistic'. +Any value of noise is ignored if the argument +method is set to 'deterministic' or 'smallCellsRule'. +The user can choose any value for noise equal to or greater than the pre-specified threshold 'nfilter.noise'. By default the value of noise is set to be equal to 0.25.

In the argument vertical.axis can be specified two types of histograms:

'Frequency'

: the histogram of the frequencies is returned.

- +
'Density'

: the histogram of the densities is returned.

- +

Server function called: histogramDS2

@@ -182,7 +180,7 @@

Author

Examples

- +
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.igb_standards.html b/docs/reference/ds.igb_standards.html index e870b688..e59a5413 100644 --- a/docs/reference/ds.igb_standards.html +++ b/docs/reference/ds.igb_standards.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Converts birth measurements to intergrowth z-scores/centiles

- +
@@ -59,67 +59,67 @@

Converts birth measurements to intergrowth z-scores/centiles

Arguments

-
gagebrth
+ + +
gagebrth

the name of the "gestational age at birth in days" variable.

-
z
+
z

z-score(s) to convert (must be between 0 and 1). Default value is 0. This value is used only if fun is set to "igb_zscore2value".

-
p
-

centile(s) to convert (must be between 0 and 100). Default value is p=50. +

p
+

centile(s) to convert (must be between 0 and 100). Default value is p=50. This value is used only if fun is set to "igb_centile2value".

-
val
+
val

the name of the anthropometric variable to convert.

-
var
+
var

the name of the measurement to convert ("lencm", "wtkg", "hcircm", "wlr").

-
sex
+
sex

the name of the sex factor variable. The variable should be coded as Male/Female. -If it is coded differently (e.g. 0/1), then you can use the ds.recodeValues function to +If it is coded differently (e.g. 0/1), then you can use the ds.recodeValues function to recode the categories to Male/Female before the use of ds.igb_standards.

-
fun
+
fun

the name of the function to be used. This can be one of: "igb_centile2value", "igb_zscore2value", "igb_value2zscore" (default), "igb_value2centile".

-
newobj
+
newobj

a character string that provides the name for the output variable that is stored on the data servers. Default name is set to igb.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

assigns the converted measurement as a new object on the server-side

+

assigns the converted measurement as a new object on the server-side

Note

-

For gestational ages between 24 and 33 weeks, the INTERGROWTH very early preterm +

For gestational ages between 24 and 33 weeks, the INTERGROWTH very early preterm standard is used.

References

-

International standards for newborn weight, length, and head circumference by +

International standards for newborn weight, length, and head circumference by gestational age and sex: the Newborn Cross-Sectional Study of the INTERGROWTH-21st Project Villar, José et al. The Lancet, Volume 384, Issue 9946, 857-868 -INTERGROWTH-21st very preterm size at birth reference charts. Lancet 2016 +INTERGROWTH-21st very preterm size at birth reference charts. Lancet 2016 doi.org/10.1016/S0140-6736(16) 00384-6. Villar, José et al.

@@ -139,15 +139,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.isNA.html b/docs/reference/ds.isNA.html index 907810e8..9f81d806 100644 --- a/docs/reference/ds.isNA.html +++ b/docs/reference/ds.isNA.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Checks if a server-side vector is empty

- +
@@ -51,21 +51,21 @@

Checks if a server-side vector is empty

Arguments

-
x
+ + +
x

a character string specifying the name of the vector to check.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.isNA returns a boolean. If it is TRUE the vector is empty +

ds.isNA returns a boolean. If it is TRUE the vector is empty (all values are NA), FALSE otherwise.

@@ -82,7 +82,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -119,7 +119,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -135,15 +135,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.isValid.html b/docs/reference/ds.isValid.html index 66ccdcb0..d34ddbd6 100644 --- a/docs/reference/ds.isValid.html +++ b/docs/reference/ds.isValid.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Checks if a server-side object is valid

- +
@@ -51,21 +51,21 @@

Checks if a server-side object is valid

Arguments

-
x
+ + +
x

a character string specifying the name of a vector, dataframe or matrix.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.isValid returns a boolean. If it is TRUE input object is valid, FALSE otherwise.

+

ds.isValid returns a boolean. If it is TRUE input object is valid, FALSE otherwise.

Details

@@ -83,7 +83,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -119,7 +119,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -135,15 +135,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.kurtosis.html b/docs/reference/ds.kurtosis.html index 702f9d0e..896113ff 100644 --- a/docs/reference/ds.kurtosis.html +++ b/docs/reference/ds.kurtosis.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Calculates the kurtosis of a numeric variable

- +
@@ -49,39 +49,39 @@

Calculates the kurtosis of a numeric variable

Arguments

-
x
+ + +
x

a string character, the name of a numeric variable.

-
method
+
method

an integer between 1 and 3 selecting one of the algorithms for computing kurtosis detailed below. The default value is set to 1.

-
type
-

a character which represents the type of analysis to carry out. -If type is set to 'combine', 'combined', 'combines' or 'c', the global kurtosis is returned +

type
+

a character which represents the type of analysis to carry out. +If type is set to 'combine', 'combined', 'combines' or 'c', the global kurtosis is returned if type is set to 'split', 'splits' or 's', the kurtosis is returned separately for each study. if type is set to 'both' or 'b', both sets of outputs are produced. The default value is set to 'both'.

-
datasources
-

a list of DSConnection-class objects obtained after login. -If the datasources argument is not specified +

datasources
+

a list of DSConnection-class objects obtained after login. +If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

a matrix showing the kurtosis of the input numeric variable, the number of valid observations and +

a matrix showing the kurtosis of the input numeric variable, the number of valid observations and the validity message.

Details

-

The function calculates the kurtosis of an input variable x with three different methods. +

The function calculates the kurtosis of an input variable x with three different methods. The method is specified by the argument method. If x contains any missings, the function removes those before the calculation of the kurtosis. If method is set to 1 the following formula is used \( kurtosis= \frac{\sum_{i=1}^{N} (x_i - \bar(x))^4 /N}{(\sum_{i=1}^{N} ((x_i - \bar(x))^2) /N)^(2) } - 3\), @@ -107,15 +107,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.length.html b/docs/reference/ds.length.html index 2e3d15ed..fa6be208 100644 --- a/docs/reference/ds.length.html +++ b/docs/reference/ds.length.html @@ -1,11 +1,11 @@ Gets the length of an object in the server-side — ds.length • dsBaseClient - +
@@ -31,19 +31,19 @@
- +

Gets the length of an object in the server-side

- +

This function gets the length of a vector -or list that is stored on the server-side. +or list that is stored on the server-side. This function is similar to the R function length.

@@ -53,38 +53,38 @@

Gets the length of an object in the server-side

Arguments

-
x
+ + +
x

a character string specifying the name of a vector or list.

-
type
+
type

a character that represents the type of analysis to carry out. If type is set to 'combine', 'combined', 'combines' or 'c', a global length is returned -if type is set to 'split', 'splits' or 's', +if type is set to 'split', 'splits' or 's', the length is returned separately for each study. -if type is set to 'both' or 'b', -both sets of outputs are produced. +if type is set to 'both' or 'b', +both sets of outputs are produced. Default 'both'.

-
checks
-

logical. If TRUE the model components are checked. +

checks
+

logical. If TRUE the model components are checked. Default FALSE to save time. It is suggested that checks should only be undertaken once the function call has failed.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.length returns to the client-side the pooled length of a vector or a list, +

ds.length returns to the client-side the pooled length of a vector or a list, or the length of a vector or a list for each study separately.

@@ -98,7 +98,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -145,7 +145,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -161,15 +161,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.levels.html b/docs/reference/ds.levels.html index 68fca302..d4eda89f 100644 --- a/docs/reference/ds.levels.html +++ b/docs/reference/ds.levels.html @@ -1,11 +1,11 @@ Produces levels attributes of a server-side factor — ds.levels • dsBaseClient - +
@@ -31,19 +31,19 @@
- +

Produces levels attributes of a server-side factor

- +

This function provides access to the level attribute of -a factor variable stored on the server-side. +a factor variable stored on the server-side. This function is similar to R function levels.

@@ -53,21 +53,21 @@

Produces levels attributes of a server-side factor

Arguments

-
x
+ + +
x

a character string specifying the name of a factor variable.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.levels returns to the client-side the levels of a factor +

ds.levels returns to the client-side the levels of a factor class variable stored in the server-side.

@@ -81,7 +81,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -121,7 +121,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -137,15 +137,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.lexis.html b/docs/reference/ds.lexis.html index b47d3194..72b4fc78 100644 --- a/docs/reference/ds.lexis.html +++ b/docs/reference/ds.lexis.html @@ -5,7 +5,7 @@ - +
@@ -31,13 +31,13 @@
- +

Represents follow-up in multiple states on multiple time scales

- +
@@ -63,57 +63,57 @@

Represents follow-up in multiple states on multiple time scales

Arguments

-
data
+ + +
data

a character string specifying the name of a data frame containing the survival data to be expanded.

-
intervalWidth
+
intervalWidth

a numeric vector specifying the length of each interval. For more information see Details.

-
idCol
+
idCol

a character string denoting the column name that holds the individual IDs of the subjects. For more information see Details.

-
entryCol
+
entryCol

a character string denoting the column name that holds the entry times (i.e. start of follow up). For more information see Details.

-
exitCol
+
exitCol

a character string denoting the column name that holds the exit times (i.e. end of follow up). For more information see Details.

-
statusCol
+
statusCol

a character string denoting the column name that holds the failure/censoring status of each subject. For more information see Details.

-
variables
+
variables

a vector of character strings denoting the column names of additional variables to include in the final expanded table. For more information see Details.

-
expandDF
+
expandDF

a character string denoting the name of the new data frame containing the expanded data set. Default lexis.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. -If the datasources argument is not specified +

datasources
+

a list of DSConnection-class objects obtained after login. +If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.lexis returns to the server-side a data frame for each study with +

ds.lexis returns to the server-side a data frame for each study with the expanded version of the input table.

@@ -124,10 +124,10 @@

Details

interval in which a given individual is followed - regardless of how short or long that period may be. Each row includes:
(1) CENSOR: a variable indicating failure status for a particular -interval in that interval also known as censoring status. +interval in that interval also known as censoring status. This variable can take two values: 1 representing that the patient has died, relapsed or developed a -disease. 0 representing the lost-to-follow-up +disease. 0 representing the lost-to-follow-up or passed right through the interval without failing.
(2) SURVTIME an exposure-time variable indicating the duration of exposure-to-risk-of-failure the corresponding individual experienced in that interval before he/she failed or was censored.

@@ -140,11 +140,11 @@

Details

failure-status variable will take the value 0 in both intervals.
(3) UID.expanded the expanded data set also includes a unique ID in a form such as 77.13 which identifies that row of the -dataset as relating to the 77th individual in the input data set and his/her experience +dataset as relating to the 77th individual in the input data set and his/her experience (exposure-time and failure status)in the -14th interval. Note that .N indicates the (N+1)th interval because +14th interval. Note that .N indicates the (N+1)th interval because interval 1 has no suffix.
-(4) IDSEQ the first part of UID.expanded (before the '.'). +(4) IDSEQ the first part of UID.expanded (before the '.'). The value of this variable is repeated in every row to which the corresponding individual contributes data (i.e. to every row corresponding to an interval in which that individual was followed).
@@ -154,7 +154,7 @@

Details

the sum of the exposure times across all intervals) and the ultimate failure-status in the final interval to which they were exposed. The value of each of these variables is also repeated in every row corresponding to an interval in which that individual was followed.

-

In intervalWidth argument if the total sum of the duration across all intervals is less +

In intervalWidth argument if the total sum of the duration across all intervals is less than the maximum follow-up of any individual in any contributing study, a final interval will be added by ds.lexis extending from the end of the last interval specified to the maximum follow-up time. If a single numeric value is specified @@ -162,39 +162,39 @@

Details

maximum follow-up time in any single study is exceeded. This argument is subject to disclosure checks.

The idCol argument must be a numeric or character. Note that when a particular variable is -identified as being the main ID to the data repository when the data are first transferred +identified as being the main ID to the data repository when the data are first transferred to the data repository (i.e. before DataSHIELD is used), that ID often ends up being of class character and will then be sorted in -alphabetic order (treating each digit as a character) rather than numeric. +alphabetic order (treating each digit as a character) rather than numeric. For example, containing the sequential IDs 1-1000, the order of the IDs will be:
1,10,100,101,102,103,104,105,106,107,108,109,11 ...
In an alphabetic listing: NOT to the expected order:
1,2,3,4,5,6,7,8,9,10,11,12,13 ...

This alphabetic order or the ID listing will then carry forward to the -expanded dataset. But the nature and order of the original ID +expanded dataset. But the nature and order of the original ID variable held in idCol doesn't -matter to ds.lexis. Provided every individual appears only once -in the original data set (before expansion) the order does not matter because +matter to ds.lexis. Provided every individual appears only once +in the original data set (before expansion) the order does not matter because ds.lexis works on its unique numeric vector -that is allocated from 1:M (where there are M individuals) +that is allocated from 1:M (where there are M individuals) in whatever order they appear in the original dataset.

in entryCol argument rather than using a total survival time variable to identify the -intervals to which any given individual is exposed, ds.lexis -requires an initial entry time and a final exit time. If the data you wish to expand +intervals to which any given individual is exposed, ds.lexis +requires an initial entry time and a final exit time. If the data you wish to expand contain only a total survival time variable and every individual starts follow-up at time 0, the entry times should all -be specified as zero, and the exit times as the total survival time. -So, entryCol should either be the name of the column +be specified as zero, and the exit times as the total survival time. +So, entryCol should either be the name of the column holding the entry time of each individual or else if no entryCol is -specified it will be defaulted to zero anyway and put into a variable +specified it will be defaulted to zero anyway and put into a variable called starttime in the expanded data set.

-

In exitCol argument, if the entry times (entryCol) are set, +

In exitCol argument, if the entry times (entryCol) are set, or defaulted, to zero, the exitCol variable should contain the total survival times.

If variables argument is not set (is -null) but the data argument is set, the expanded data -set will contain all variables in the data frame identified by the data argument. -If neither the data or -variables arguments are set, the expanded data set will only include the ID, +null) but the data argument is set, the expanded data +set will contain all variables in the data frame identified by the data argument. +If neither the data or +variables arguments are set, the expanded data set will only include the ID, exposure time and failure/censoring status variables which may still be useful for plotting survival data once these become available.

This function is particularly meant to be used in preparing data for a piecewise @@ -207,10 +207,10 @@

Details

number of intervals will inevitably improve the approximation to the true baseline hazard, but the addition of many more unnecessary time intervals slows the analysis and can become disclosive and yet will not improve the fit of the model.

-

If the number of failures in one or more +

If the number of failures in one or more periods in a given study is less than the specified disclosure filter determining minimum -acceptable cell size in a table (nfilter.tab) -then the expanded data frame is not created in that study, and a study-side message +acceptable cell size in a table (nfilter.tab) +then the expanded data frame is not created in that study, and a study-side message to this effect is made available in that study via ds.message() function.

Server functions called: lexisDS1, lexisDS2 and lexisDS3

@@ -226,7 +226,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -286,7 +286,7 @@ 
Examples

            
   #Confirm expanded dataframe created
   ds.ls(datasources = connections) 
-}
+} # }
@@ -302,15 +302,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.list.html b/docs/reference/ds.list.html index 12c5d7e2..209dcb5b 100644 --- a/docs/reference/ds.list.html +++ b/docs/reference/ds.list.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Constructs a list of objects in the server-side

- +
@@ -49,26 +49,26 @@

Constructs a list of objects in the server-side

Arguments

-
x
+ + +
x

a character string specifying the names of the objects to coerce into a list.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default list.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.list returns a list of objects for each study that is stored on the server-side.

+

ds.list returns a list of objects for each study that is stored on the server-side.

Details

@@ -83,7 +83,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -117,7 +117,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -133,15 +133,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.listClientsideFunctions.html b/docs/reference/ds.listClientsideFunctions.html index 43aefc16..6f6570e6 100644 --- a/docs/reference/ds.listClientsideFunctions.html +++ b/docs/reference/ds.listClientsideFunctions.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Lists client-side functions

- +
@@ -49,9 +49,7 @@

Lists client-side functions

Value

- - -

ds.listClientsideFunctions returns a list containing +

ds.listClientsideFunctions returns a list containing all server-side functions.

@@ -68,7 +66,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   #Library with all DataSHIELD functions
@@ -77,7 +75,7 @@ 
Examples

   #Visualise all functions
   ds.listClientsideFunctions()
   
-}   
+} # }
@@ -92,15 +90,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.listDisclosureSettings.html b/docs/reference/ds.listDisclosureSettings.html index 4219844b..45969706 100644 --- a/docs/reference/ds.listDisclosureSettings.html +++ b/docs/reference/ds.listDisclosureSettings.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Lists disclosure settings

- +
@@ -49,17 +49,17 @@

Lists disclosure settings

Arguments

-
datasources
-

a list of DSConnection-class objects obtained after login. + + +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.listDisclosureSettings returns a list containing the current settings of the +

ds.listDisclosureSettings returns a list containing the current settings of the nfilters in each study specified.

@@ -113,7 +113,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
  
   ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -150,7 +150,7 @@ 
Examples

             
    # Clear the Datashield R sessions and logout  
    datashield.logout(connections) 
-}
+} # }
@@ -166,15 +166,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.listOpals.html b/docs/reference/ds.listOpals.html index b3f52513..5ab10679 100644 --- a/docs/reference/ds.listOpals.html +++ b/docs/reference/ds.listOpals.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Lists all Opal objects in the analytic environment

- +
@@ -51,9 +51,7 @@

Lists all Opal objects in the analytic environment

Value

- - -

Lists all of the sets of Opals currently found in the analytic environment and advises +

Lists all of the sets of Opals currently found in the analytic environment and advises the user how best to respond depending whether there are zero, one or multiple Opals detected.

@@ -86,15 +84,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.listServersideFunctions.html b/docs/reference/ds.listServersideFunctions.html index cb2ec475..757fbc03 100644 --- a/docs/reference/ds.listServersideFunctions.html +++ b/docs/reference/ds.listServersideFunctions.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Lists server-side functions

- +
@@ -49,25 +49,25 @@

Lists server-side functions

Arguments

-
datasources
-

a list of DSConnection-class objects obtained after login. + + +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.listServersideFunctions returns to the client-side -a list containing all server-side functions separately for each study. +

ds.listServersideFunctions returns to the client-side +a list containing all server-side functions separately for each study. Firstly lists assign and then aggregate functions.

Details

Uses datashield.methods function from DSI package to list all assign and aggregate functions on the available data repository servers. -The only choice of arguments is in datasources; i.e. which studies to interrogate. +The only choice of arguments is in datasources; i.e. which studies to interrogate. Once the studies have been selected ds.listServersideFunctions lists all assign functions for all of these studies and then all aggregate functions for all of them.

@@ -80,7 +80,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
  
   ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -113,7 +113,7 @@ 
Examples

             
   # Clear the Datashield R sessions and logout  
   datashield.logout(connections) 
-}
+} # }
@@ -128,15 +128,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.lmerSLMA.html b/docs/reference/ds.lmerSLMA.html index f54bc9ee..2c0444ed 100644 --- a/docs/reference/ds.lmerSLMA.html +++ b/docs/reference/ds.lmerSLMA.html @@ -5,7 +5,7 @@ - +
@@ -31,13 +31,13 @@
- +

Fits Linear Mixed-Effect model via Study-Level Meta-Analysis

- +
@@ -69,186 +69,148 @@

Fits Linear Mixed-Effect model via Study-Level Meta-Analysis

Arguments

-
formula
-

an object of class formula describing the model to be fitted. + + +

formula
+

an object of class formula describing the model to be fitted. For more information see Details.

-
offset
+
offset

a character string specifying the name of a variable to be used as an offset.

-
weights
+
weights

a character string specifying the name of a variable containing prior regression weights for the fitting process.

-
combine.with.metafor
+
combine.with.metafor

logical. If TRUE the estimates and standard errors for each regression coefficient are pooled across studies using random-effects meta-analysis under maximum likelihood (ML), restricted maximum likelihood (REML) or fixed-effects meta-analysis (FE). Default TRUE.

-
dataName
+
dataName

a character string specifying the name of an (optional) data frame -that contains all of the variables in the LME formula. +that contains all of the variables in the LME formula. For more information see Details.

-
checks
-

logical. If TRUE ds.lmerSLMA checks the structural integrity +

checks
+

logical. If TRUE ds.lmerSLMA checks the structural integrity of the model. Default FALSE. For more information see Details.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

-
REML
+
REML

logical. If TRUE the REstricted Maximum Likelihood (REML) -is used for parameter optimization. -If FALSE the parameters are optimized using standard ML (maximum likelihood). Default TRUE. +is used for parameter optimization. +If FALSE the parameters are optimized using standard ML (maximum likelihood). Default TRUE. For more information see Details.

-
control_type
+
control_type

an optional character string vector specifying the nature of a parameter (or parameters) to be modified in the convergence control options which can be viewed or -modified via the lmerControl function of the package lme4. +modified via the lmerControl function of the package lme4. For more information see Details.

-
control_value
+
control_value

numeric representing the new value which you want to allocate the -control parameter corresponding to the control-type. +control parameter corresponding to the control-type. For more information see Details.

-
optimizer
+
optimizer

specifies the parameter optimizer that lmer should use. For more information see Details.

-
verbose
+
verbose

an integer value. If \(verbose > 0\) the output is generated during the optimization of -the parameter estimates. If \(verbose > 1\) the output is generated during the individual penalized -iteratively reweighted least squares (PIRLS) steps. Default verbose +the parameter estimates. If \(verbose > 1\) the output is generated during the individual penalized +iteratively reweighted least squares (PIRLS) steps. Default verbose value is 0 which means no additional output.

-
notify.of.progress
+
notify.of.progress

specifies if console output should be produced to indicate progress. Default FALSE.

-
assign
+
assign

a logical, indicates whether the function will call a second server-side function (an assign) in order to save the regression outcomes (i.e. a lmerMod object) on each server. Default FALSE.

-
newobj
+
newobj

a character string specifying the name of the object to which the lmerMod object -representing the model fit on the serverside in each study is to be written. This argument is +representing the model fit on the serverside in each study is to be written. This argument is used only when the argument assign is set to TRUE. If no <newobj> argument is specified, the output object defaults to "new.lmer.obj".

Value

- - -

Many of the elements of the output list returned by ds.lmerSLMA are +

Many of the elements of the output list returned by ds.lmerSLMA are equivalent to those returned by the lmer() function in native R. However, potentially disclosive elements -such as individual-level residuals and linear predictor values are blocked. +such as individual-level residuals and linear predictor values are blocked. In this case, only non-disclosive elements are returned from each study separately.

- -

The list of elements returned by ds.lmerSLMA is mentioned below:

- - -

ds.lmerSLMA returns a list of elements mentioned +

ds.lmerSLMA returns a list of elements mentioned below separately for each study.

- - -

coefficients: a matrix with 5 columns:

-

-
First
+

coefficients: a matrix with 5 columns:

First

: the names of all of the regression parameters (coefficients) in the model

- +
second

: the estimated values

- +
third

: corresponding standard errors of the estimated values

- +
fourth

: the ratio of estimate/standard error

- +
fifth

: the p-value treating that as a standardised normal deviate

- - -

CorrMatrix: the correlation matrix of parameter estimates.

+

CorrMatrix: the correlation matrix of parameter estimates.

VarCovMatrix: the variance-covariance matrix of parameter estimates.

- -

weights: the vector (if any) holding regression weights.

- -

offset: the vector (if any) holding an offset.

- -

cov.scaled: equivalent to VarCovMatrix.

- -

Nmissing: the number of missing observations in the given study.

- -

Nvalid: the number of valid (non-missing) observations in the given study.

- - -

Ntotal: the total number of observations +

Ntotal: the total number of observations in the given study (Nvalid + Nmissing).

- -

data: equivalent to input parameter dataName (above).

- -

call: summary of key elements of the call to fit the model.

- -

There are a small number of more esoteric items of the information returned by ds.lmerSLMA. Additional information about these can be found in the help file for the lmer() function in the lme4 package.

- -

Once the study-specific output has been returned, the function returns several elements relating to the pooling of estimates across studies via study-level meta-analysis. These are as follows:

- -

input.beta.matrix.for.SLMA: a matrix containing the vector of coefficient estimates from each study.

- -

input.se.matrix.for.SLMA: a matrix containing the vector of standard error estimates for coefficients from each study.

- -

SLMA.pooled.estimates: a matrix containing pooled estimates for each regression coefficient across all studies with pooling under SLMA via random-effects meta-analysis under maximum likelihood (ML), restricted maximum likelihood (REML) or via fixed-effects meta-analysis (FE).

- -

convergence.error.message: reports for each study whether the model converged. If it did not some information about the reason for this is reported.

@@ -260,34 +222,34 @@

Details

When there are multiple data sources, the LME is fitted to convergence in each data source independently. The estimates and standard errors returned to the client-side which enable cross-study pooling -using Study-Level Meta-Analysis (SLMA). The SLMA used by default metafor package - but as the SLMA occurs on the client-side (a standard R environment), the user can choose - any approach to meta-analysis. Additional information about fitting -LMEs using the lmer function can be +using Study-Level Meta-Analysis (SLMA). The SLMA used by default metafor package + but as the SLMA occurs on the client-side (a standard R environment), the user can choose + any approach to meta-analysis. Additional information about fitting +LMEs using the lmer function can be obtained using R help for lmer and the lme4 package.

In formula most shortcut notation allowed by lmer() function is also allowed by ds.lmerSLMA. Many LMEs can be fitted very simply using a formula like: $$y~a+b+(1|c)$$ which simply means fit an LME with y as the outcome variable with a and b as fixed effects, and c as a random effect or grouping factor.

-

It is also possible to fit models with random slopes by specifying a model such as -$$y~a+b+(1+b|c)$$ +

It is also possible to fit models with random slopes by specifying a model such as +$$y~a+b+(1+b|c)$$ where the effect of b can vary randomly between groups defined by c. Implicit nesting can be specified with formulae such as \(y~a+b+(1|c/d)\) or \(y~a+b+(1|c)+(1|c:d)\).

The dataName argument avoids you having to specify the name of the -data frame in front of each covariate in the formula. -For example, if the data frame is called DataFrame you avoid having to write: +data frame in front of each covariate in the formula. +For example, if the data frame is called DataFrame you avoid having to write: \(DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)\).

-

The checks argument verifies that the variables in the model are all defined (exist) +

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study -and that they have the correct characteristics required to fit the model. +and that they have the correct characteristics required to fit the model. It is suggested to make checks argument TRUE if an unexplained problem in the model fit is encountered because the running process takes several minutes.

REML can help to mitigate bias associated with the fixed-effects. See help on the lmer() function for more details.

In control_type at present only one such parameter can be modified, -namely the tolerance of the convergence criterion to the gradient of the log-likelihood +namely the tolerance of the convergence criterion to the gradient of the log-likelihood at the maximum likelihood achieved. We have enabled this because our practical experience suggests that in situations where the model looks to have converged with sensible parameter values but formal convergence is not being declared if we allow the model to be more @@ -317,7 +279,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -355,7 +317,7 @@ 
Examples

   
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-  }
+  } # }
@@ -370,15 +332,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.log.html b/docs/reference/ds.log.html index f0bd58d7..30f10ae2 100644 --- a/docs/reference/ds.log.html +++ b/docs/reference/ds.log.html @@ -1,10 +1,10 @@ -Computes logarithms in the server-side — ds.log • dsBaseClientComputes logarithms in the server-side — ds.log • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Computes logarithms in the server-side

- +
-

Computes the logarithms for a specified numeric vector. +

Computes the logarithms for a specified numeric vector. This function is similar to the R log function. by default natural logarithms.

@@ -51,31 +51,31 @@

Computes logarithms in the server-side

Arguments

-
x
+ + +
x

a character string providing the name of a numerical vector.

-
base
+
base

a positive number, the base for which logarithms are computed. Default exp(1).

-
newobj
+
newobj

a character string that provides the name for the output variable that is stored on the server-side. Default log.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.log returns a vector for each study of the transformed values for the numeric vector +

ds.log returns a vector for each study of the transformed values for the numeric vector specified in the argument x. The created vectors are stored in the server-side.

@@ -89,7 +89,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki 
   # Connecting to the Opal servers
@@ -126,7 +126,7 @@ 
Examples

 
   # clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -142,15 +142,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.look.html b/docs/reference/ds.look.html index b4e803e9..ae0d0cc7 100644 --- a/docs/reference/ds.look.html +++ b/docs/reference/ds.look.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Performs direct call to a server-side aggregate function

- +
@@ -51,27 +51,27 @@

Performs direct call to a server-side aggregate function

Arguments

-
toAggregate
+ + +
toAggregate

a character string specifying the function call to be made. For more information see Details.

-
checks
-

logical. If TRUE the optional checks are undertaken. +

checks
+

logical. If TRUE the optional checks are undertaken. Default FALSE to save time.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

the output from the specified server-side aggregate function to the client-side.

+

the output from the specified server-side aggregate function to the client-side.

Details

@@ -95,7 +95,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -136,7 +136,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -151,15 +151,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.ls.html b/docs/reference/ds.ls.html index de0980a2..e0086831 100644 --- a/docs/reference/ds.ls.html +++ b/docs/reference/ds.ls.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

lists all objects on a server-side environment

- +
@@ -56,64 +56,58 @@

lists all objects on a server-side environment

Arguments

-
search.filter
-

character string (potentially including * symbol) specifying the filter + + +

search.filter
+

character string (potentially including * symbol) specifying the filter for the object name that you want to find in the enviroment. For more information see Details.

-
env.to.search
+

an integer (e.g. in 2 or 2L format) specifying the position in the search path of the environment to be explored. 1L is the current active analytic environment on the server-side and is the default value of env.to.search. For more information see Details.

-
search.GlobalEnv
+
search.GlobalEnv

Logical. If TRUE, ds.ls will list all objects in the .GlobalEnv R environment on the server-side. If FALSE and if env.to.search is also set as a valid integer, ds.ls will list all objects in the server-side R environment -identified by env.to.search in the search path. +identified by env.to.search in the search path. For more information see Details.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.ls returns to the client-side a list containing:

- - -

(1) the name/details of the server-side R environment which ds.ls has searched;

- - -

(2) a vector of character strings giving the names of +

ds.ls returns to the client-side a list containing:
+(1) the name/details of the server-side R environment which ds.ls has searched;
+(2) a vector of character strings giving the names of all objects meeting the naming criteria specified by the argument search.filter in this -specified R server-side environment;

- - -

(3) the nature of the search filter string as it was applied.

+specified R server-side environment;
+(3) the nature of the search filter string as it was applied.

Details

-

When running analyses one may want to know the objects already generated. This +

When running analyses one may want to know the objects already generated. This request is not disclosive as it only returns the names of the objects and not their contents.

By default, objects in DataSHIELD's Active Serverside Analytic Environment (.GlobalEnv) -will be listed. This is the environment that contains all of the objects that server-side DataSHIELD +will be listed. This is the environment that contains all of the objects that server-side DataSHIELD is using for the main analysis or has written out to the server-side during the process -of managing or undertaking the analysis (variables, scalars, matrices, data frames, etc).

+of managing or undertaking the analysis (variables, scalars, matrices, data frames, etc).

The environment to explore is specified by the argument env.to.search (i.e. environment -to search) to an integer value. The default environment +to search) to an integer value. The default environment which R names as .GlobalEnv is set by specifying env.to.search = 1 or 1L (1L is just an explicit way of writing the integer 1).

-

If the search.GlobalEnv argument is set to TRUE the env.to.search parameter +

If the search.GlobalEnv argument is set to TRUE the env.to.search parameter is set to 1L regardless of what value it is set in the call -or if it is set to NULL. +or if it is set to NULL. So, if search.GlobalEnv is set to TRUE, ds.ls will automatically search the .GlobalEnv R environment on the server-side which contains all of the variables, data frames and other objects read in at the start of the analysis, @@ -125,12 +119,12 @@

Details

env.to.search argument but you can specify search filters including * wildcards using the search.filter argument.

In search.filter you can use the symbol * to find all the object that contains -the specified characters. For example, search.filter = "Sd2*" +the specified characters. For example, search.filter = "Sd2*" will list the names of all objects in the specified -environment with names beginning capital S, lower case d and number 2. +environment with names beginning capital S, lower case d and number 2. Similarly, search.filter="*.ID" will return all objects with names ending with .ID, -for example Study.ID. -If a value is not specified for the search.filter argument or it is set as NULL, the names of +for example Study.ID. +If a value is not specified for the search.filter argument or it is set as NULL, the names of all objects in the specified environment will be returned.

Server function called: lsDS.

@@ -141,7 +135,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -192,7 +186,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -208,15 +202,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.lspline.html b/docs/reference/ds.lspline.html index e2583c7a..188e4632 100644 --- a/docs/reference/ds.lspline.html +++ b/docs/reference/ds.lspline.html @@ -6,7 +6,7 @@ - +
@@ -32,13 +32,13 @@
- +

Basis for a piecewise linear spline with meaningful coefficients

- +
@@ -62,38 +62,38 @@

Basis for a piecewise linear spline with meaningful coefficients

Arguments

-
x
+ + +
x

the name of the input numeric variable

-
knots
+
knots

numeric vector of knot positions

-
marginal
+
marginal

logical, how to parametrize the spline, see Details

-
names
+
names

character, vector of names for constructed variables

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default lspline.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

an object of class "lspline" and "matrix", which its name is specified by the +

an object of class "lspline" and "matrix", which its name is specified by the newobj argument (or its default name "lspline.newobj"), is assigned on the serverside.

@@ -120,15 +120,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.make.html b/docs/reference/ds.make.html index 694916d3..7d4ae3e2 100644 --- a/docs/reference/ds.make.html +++ b/docs/reference/ds.make.html @@ -5,7 +5,7 @@ - +
@@ -31,13 +31,13 @@
- +

Calculates a new object in the server-side

- +
@@ -53,26 +53,26 @@

Calculates a new object in the server-side

Arguments

-
toAssign
+ + +
toAssign

a character string specifying the function or the arithmetic expression.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default make.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.make returns the new object which is written to the +

ds.make returns the new object which is written to the server-side. Also a validity message is returned to the client-side indicating whether the new object has been correctly created at each source.

@@ -85,16 +85,16 @@

Details

details of the call to ds.make and the variables/objects which it invokes.

TROUBLESHOOTING: please note we have recently identified an error that makes ds.make fail and DataSHIELD crash.

-

The error arises from a call such as -ds.make(toAssign = '5.3 + beta*xvar', newobj = 'predvals'). +

The error arises from a call such as +ds.make(toAssign = '5.3 + beta*xvar', newobj = 'predvals'). This is a typical call you may make to get the predicted values from a simple linear regression model where -a y variable is regressed against an x variable (xvar) -where the estimated regression intercept is 5.3 +a y variable is regressed against an x variable (xvar) +where the estimated regression intercept is 5.3 and beta is the estimated regression slope.

This call appears to fail because in interpreting the arithmetic function which is its first argument -it first encounters the (length 1) scalar 5.3 +it first encounters the (length 1) scalar 5.3 and when it then encounters the xvar vector which has more than one element it fails - apparently because it does not recognise that you need to replicate the 5.3 value the appropriate number of times @@ -112,7 +112,7 @@

Details

vector of length equal to xvar with all elements 5.3. Finally, you can now issue a modified call to reflect what was originally needed: ds.make(toAssign = 'vect5.3+beta*xvar', 'predvals').

-

(2) Alternatively, if you simply swap the original call around: +

(2) Alternatively, if you simply swap the original call around: ds.make(toAssign = '(beta*xvar)+5.3', newobj = 'predvals') the error seems also to be circumvented. This is presumably because the first element of the arithmetic function is of length equal to xvar and it then knows to @@ -120,7 +120,7 @@

Details

The second work-around is easier, but it is worth knowing about the first trick because creating a vector of ones of equal length to another vector can be useful in other settings. Equally the call: -ds.make(toAssign = 'indID-indID',newobj = 'ZEROS') +ds.make(toAssign = 'indID-indID',newobj = 'ZEROS') to create a vector of zeros of that same length may also be useful.

Server function : messageDS

The ds.make function is a wrapper for the DSI package function datashield.assign

@@ -132,7 +132,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -189,7 +189,7 @@ 
Examples

        
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -205,15 +205,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.matrix.html b/docs/reference/ds.matrix.html index 75114c3e..0b7c0d61 100644 --- a/docs/reference/ds.matrix.html +++ b/docs/reference/ds.matrix.html @@ -1,12 +1,12 @@ -Creates a matrix on the server-side — ds.matrix • dsBaseClientCreates a matrix on the server-side — ds.matrix • dsBaseClient - +
@@ -32,20 +32,20 @@
- +

Creates a matrix on the server-side

- +
-

Creates a matrix on the server-side -with dimensions specified by nrows.scalar -and ncols.scalar arguments and assigns the +

Creates a matrix on the server-side +with dimensions specified by nrows.scalar +and ncols.scalar arguments and assigns the values of all its elements based on the mdata argument.

@@ -64,58 +64,58 @@

Creates a matrix on the server-side

Arguments

-
mdata
+ + +
mdata

a character string specifying the name of a server-side scalar or vector. Also, a numeric value representing a -scalar specified from the client-side can be speficied. +scalar specified from the client-side can be speficied. Zeros, negative values and NAs are all allowed. For more information see Details.

-
from
+
from

a character string specifying the source and nature of mdata. This can be set as "serverside.vector", "serverside.scalar" or "clientside.scalar". Default "clientside.scalar".

-
nrows.scalar
-

an integer or a character string that specifies the number +

nrows.scalar
+

an integer or a character string that specifies the number of rows in the matrix to be created. For more information see Details.

-
ncols.scalar
-

an integer or a character string that specifies +

ncols.scalar
+

an integer or a character string that specifies the number of columns in the matrix to be created.

-
byrow
+
byrow

logical. If TRUE and mdata is a vector the matrix -created should be filled row by row. If FALSE the matrix created should +created should be filled row by row. If FALSE the matrix created should be filled column by column. Default = FALSE.

-
dimnames
+
dimnames

a list of length 2 giving the row and column names respectively.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default matrix.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.matrix returns the created matrix which is written on the server-side. +

ds.matrix returns the created matrix which is written on the server-side. In addition, two validity messages are returned indicating whether the new matrix has been created in each data source and if so whether it is in a valid form.

@@ -123,20 +123,20 @@

Value

Details

This function is similar to the R native function matrix().

-

If in the mdata argument a vector is specified this should have +

If in the mdata argument a vector is specified this should have the same length as the total number of elements in the matrix. If this is not TRUE the values in mdata will be used repeatedly until all elements in the matrix are full. If mdata argument is a scalar, all elements in the matrix will take that value.

-

In the nrows.scalar argument can be a character string specifying -the name of a server-side scalar. For example, +

In the nrows.scalar argument can be a character string specifying +the name of a server-side scalar. For example, if a server-side scalar named ss.scalar exists and holds the value 23, then by specifying nrows.scalar = "ss.scalar", the matrix created will -have 23 rows. Also this argument can be +have 23 rows. Also this argument can be a numeric value from the -client-side. The same rules are applied to ncols.scalar argument but in this -case the column numbers are specified. +client-side. The same rules are applied to ncols.scalar argument but in this +case the column numbers are specified. In both arguments a zero, negative, NULL or missing value is not permitted.

Server function called: matrixDS

@@ -148,7 +148,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -234,7 +234,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -250,15 +250,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.matrixDet.html b/docs/reference/ds.matrixDet.html index e933346c..8d94a581 100644 --- a/docs/reference/ds.matrixDet.html +++ b/docs/reference/ds.matrixDet.html @@ -1,12 +1,12 @@ -Calculates de determinant of a matrix in the server-side — ds.matrixDet • dsBaseClientCalculates de determinant of a matrix in the server-side — ds.matrixDet • dsBaseClient - +
@@ -32,20 +32,20 @@
- +

Calculates de determinant of a matrix in the server-side

- +
-

Calculates the determinant of a square matrix that is -written on the server-side. -This operation is only +

Calculates the determinant of a square matrix that is +written on the server-side. +This operation is only possible if the number of columns and rows of the matrix are the same.

@@ -55,32 +55,32 @@

Calculates de determinant of a matrix in the server-side

Arguments

-
M1
+ + +
M1

a character string specifying the name of the matrix.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default matrixdet.newobj.

-
logarithm
+
logarithm

logical. If TRUE the logarithm of the modulus of the determinant is calculated. Default FALSE.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.matrixDet returns the determinant of an existing matrix on the server-side. -The created new object is stored on the server-side. +

ds.matrixDet returns the determinant of an existing matrix on the server-side. +The created new object is stored on the server-side. Also, two validity messages are returned indicating whether the matrix has been created in each data source and if so whether it is in a valid form.

@@ -98,7 +98,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -153,7 +153,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -168,15 +168,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.matrixDet.report.html b/docs/reference/ds.matrixDet.report.html index 531c7e44..f216c851 100644 --- a/docs/reference/ds.matrixDet.report.html +++ b/docs/reference/ds.matrixDet.report.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Returns matrix determinant to the client-side

- +
@@ -51,33 +51,33 @@

Returns matrix determinant to the client-side

Arguments

-
M1
+ + +
M1

a character string specifying the name of the matrix.

-
logarithm
+
logarithm

logical. If TRUE the logarithm of the modulus of the determinant is calculated. Default FALSE.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.matrixDet.report returns to the client-side +

ds.matrixDet.report returns to the client-side the determinant of a matrix that is stored on the server-side.

Details

Calculates and returns to the client-side -the determinant of a square matrix on the server-side. -This function is similar to the native R determinant function. +the determinant of a square matrix on the server-side. +This function is similar to the native R determinant function. This operation is only possible if the number of columns and rows of the matrix are the same.

Server function called: matrixDetDS1

@@ -89,7 +89,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -141,7 +141,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -156,15 +156,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.matrixDiag.html b/docs/reference/ds.matrixDiag.html index 33bb94d1..66e8c6c4 100644 --- a/docs/reference/ds.matrixDiag.html +++ b/docs/reference/ds.matrixDiag.html @@ -1,11 +1,11 @@ Calculates matrix diagonals in the server-side — ds.matrixDiag • dsBaseClient - +
@@ -31,19 +31,19 @@
- +

Calculates matrix diagonals in the server-side

- +

Extracts the diagonal vector from a square matrix or -creates a diagonal matrix based on a vector or a scalar value +creates a diagonal matrix based on a vector or a scalar value on the server-side.

@@ -59,54 +59,54 @@

Calculates matrix diagonals in the server-side

Arguments

-
x1
+ + +
x1

a character string specifying the name of a server-side scalar or vector. Also, a numeric value or vector -specified from the client-side can be speficied. This argument depends +specified from the client-side can be speficied. This argument depends on the value specified in aim. For more information see Details.

-
aim
+
aim

a character string specifying the behaviour of the function. -This can be set as: +This can be set as: "serverside.vector.2.matrix", "serverside.scalar.2.matrix", "serverside.matrix.2.vector", "clientside.vector.2.matrix" or "clientside.scalar.2.matrix". For more information see Details.

-
nrows.scalar
-

an integer specifying the dimensions of the matrix -note that the matrix is square (same number of rows and columns). -If this argument is not specified the matrix dimensions are -defined by the length of the vector. +

nrows.scalar
+

an integer specifying the dimensions of the matrix +note that the matrix is square (same number of rows and columns). +If this argument is not specified the matrix dimensions are +defined by the length of the vector. For more information see Details.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default matrixdiag.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.matrixDiag returns to the server-side the square matrix diagonal. +

ds.matrixDiag returns to the server-side the square matrix diagonal. Also, two validity messages are returned indicating whether the new object has been created in each data source and if so whether it is in a valid form.

Details

-

The function behaviour is different depending on the +

The function behaviour is different depending on the value specified in the aim argument:
(1) If aim = "serverside.vector.2.matrix" the function takes a server-side vector and writes out a square matrix with @@ -131,7 +131,7 @@

Details

and writes out a square matrix with all diagonal values equal to the value of the scalar. The dimensions of the square matrix are determined by the value of the nrows.scalar argument.

-

If x1 is a vector and the nrows.scalar +

If x1 is a vector and the nrows.scalar is set as k, the vector will be used repeatedly to fill up the diagonal. For example, the vector is of length 7 and nrows.scalar = 18, a square diagonal matrix with @@ -145,7 +145,7 @@

Author

Examples

- +
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.matrixDimnames.html b/docs/reference/ds.matrixDimnames.html index 9087a165..24230307 100644 --- a/docs/reference/ds.matrixDimnames.html +++ b/docs/reference/ds.matrixDimnames.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Specifies the dimnames of the server-side matrix

- +
@@ -56,35 +56,35 @@

Specifies the dimnames of the server-side matrix

Arguments

-
M1
+ + +
M1

a character string specifying the name of a server-side matrix.

-
dimnames
+
dimnames

a list of length 2 giving -the row and column names respectively. +the row and column names respectively. An empty list is treated as NULL.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default matrixdimnames.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.matrixDimnames returns to the server-side -the matrix with specified row and column names. -Also, two validity messages are returned to the client-side +

ds.matrixDimnames returns to the server-side +the matrix with specified row and column names. +Also, two validity messages are returned to the client-side indicating the new object that has been created in each data source and if so whether it is in a valid form.

@@ -100,7 +100,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -159,7 +159,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -174,15 +174,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.matrixInvert.html b/docs/reference/ds.matrixInvert.html index c0563dcc..07f7e00c 100644 --- a/docs/reference/ds.matrixInvert.html +++ b/docs/reference/ds.matrixInvert.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Inverts a server-side square matrix

- +
@@ -49,28 +49,28 @@

Inverts a server-side square matrix

Arguments

-
M1
+ + +
M1

A character string specifying the name of the matrix to be inverted.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default matrixinvert.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.matrixInvert returns to the server-side the inverts square matrix. -Also, two validity messages are returned to the client-side +

ds.matrixInvert returns to the server-side the inverts square matrix. +Also, two validity messages are returned to the client-side indicating whether the new object has been created in each data source and if so whether it is in a valid form.

@@ -88,7 +88,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -146,7 +146,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -161,15 +161,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.matrixMult.html b/docs/reference/ds.matrixMult.html index 7f09c8e1..55623b50 100644 --- a/docs/reference/ds.matrixMult.html +++ b/docs/reference/ds.matrixMult.html @@ -1,10 +1,10 @@ -Calculates tow matrix multiplication in the server-side — ds.matrixMult • dsBaseClientCalculates tow matrix multiplication in the server-side — ds.matrixMult • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Calculates tow matrix multiplication in the server-side

- +
-

Calculates the matrix product of two matrices and +

Calculates the matrix product of two matrices and writes output to the server-side.

@@ -51,41 +51,41 @@

Calculates tow matrix multiplication in the server-side

Arguments

-
M1
+ + +
M1

a character string specifying the name of the first matrix.

-
M2
+
M2

a character string specifying the name of the second matrix.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default matrixmult.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.matrixMult returns to the server-side +

ds.matrixMult returns to the server-side the result of the two matrix multiplication. -Also, two validity messages are returned to the client-side +Also, two validity messages are returned to the client-side indicating whether the new object has been created in each data source and if so whether it is in a valid form.

Details

-

Undertakes standard matrix multiplication wherewith input matrices -A and B with dimensions A: m x n and B: n x p +

Undertakes standard matrix multiplication wherewith input matrices +A and B with dimensions A: m x n and B: n x p the output matrix C has dimensions m x p. This calculation -is only valid if the number of columns of A +is only valid if the number of columns of A is the same as the number of rows of B.

Server function called: matrixMultDS

@@ -96,7 +96,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -163,7 +163,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -178,15 +178,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.matrixTranspose.html b/docs/reference/ds.matrixTranspose.html index c40b7865..524e7531 100644 --- a/docs/reference/ds.matrixTranspose.html +++ b/docs/reference/ds.matrixTranspose.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Transposes a server-side matrix

- +
@@ -49,37 +49,37 @@

Transposes a server-side matrix

Arguments

-
M1
+ + +
M1

a character string specifying the name of the matrix.

-
newobj
-

a character string that provides the name for the output -variable that is stored on the data servers. +

newobj
+

a character string that provides the name for the output +variable that is stored on the data servers. Default matrixtranspose.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.matrixTranspose returns to the server-side the transpose matrix. -Also, two validity messages are returned to the client-side +

ds.matrixTranspose returns to the server-side the transpose matrix. +Also, two validity messages are returned to the client-side indicating whether the new object has been created in each data source and if so whether it is in a valid form.

Details

This operation converts matrix -A to matrix C where element C[i,j] of +A to matrix C where element C[i,j] of matrix C equals element A[j,i] of matrix -A. Matrix A, therefore, has the same number +A. Matrix A, therefore, has the same number of rows as matrix C has columns and vice versa.

Server function called: matrixTransposeDS

@@ -90,7 +90,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -148,7 +148,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -163,15 +163,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.mean.html b/docs/reference/ds.mean.html index 7afa3258..301e391e 100644 --- a/docs/reference/ds.mean.html +++ b/docs/reference/ds.mean.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Computes server-side vector statistical mean

- +
@@ -57,68 +57,49 @@

Computes server-side vector statistical mean

Arguments

-
x
+ + +
x

a character specifying the name of a numerical vector.

-
type
+
type

a character string that represents the type of analysis to carry out. This can be set as 'combine', 'combined', 'combines', 'split', 'splits', 's', -'both' or 'b'. +'both' or 'b'. For more information see Details.

-
checks
+
checks

logical. If TRUE optional checks of model -components will be undertaken. Default is FALSE to save time. +components will be undertaken. Default is FALSE to save time. It is suggested that checks should only be undertaken once the function call has failed.

-
save.mean.Nvalid
-

logical. If TRUE generated values of the mean and -the number of valid (non-missing) observations will be saved on the data servers. -Default FALSE. +

save.mean.Nvalid
+

logical. If TRUE generated values of the mean and +the number of valid (non-missing) observations will be saved on the data servers. +Default FALSE. For more information see Details.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.mean returns to the client-side a list including:

- - - -

Mean.by.Study: estimated mean, Nmissing

- - -

(number of missing observations), Nvalid (number of valid observations) and -Ntotal (sum of missing and valid observations) -separately for each study (if type = split or type = both).

- - -

Global.Mean: estimated mean, Nmissing, Nvalid and Ntotal

- - -

across all studies combined (if type = combine or type = both).

- - -

Nstudies: number of studies being analysed.

- - -

ValidityMessage: indicates if the analysis was possible.

- - - -

If save.mean.Nvalid is set as TRUE, the objects +

ds.mean returns to the client-side a list including:

+

Mean.by.Study: estimated mean, Nmissing +(number of missing observations), Nvalid (number of valid observations) and +Ntotal (sum of missing and valid observations) +separately for each study (if type = split or type = both).
Global.Mean: estimated mean, Nmissing, Nvalid and Ntotal +across all studies combined (if type = combine or type = both).
Nstudies: number of studies being analysed.
ValidityMessage: indicates if the analysis was possible.

+

If save.mean.Nvalid is set as TRUE, the objects Nvalid.all.studies, Nvalid.study.specific, mean.all.studies and mean.study.specific are written to the server-side.

@@ -127,16 +108,16 @@

Details

This function is similar to the R function mean.

The function can carry out 3 types of analysis depending on the argument type:
-(1) If type is set to 'combine', 'combined', +(1) If type is set to 'combine', 'combined', 'combines' or 'c', a global mean is calculated.
(2) If type is set to 'split', 'splits' or 's', the mean is calculated separately for each study.
-(3) If type is set to 'both' or 'b', +(3) If type is set to 'both' or 'b', both sets of outputs are produced.

-

If the argument save.mean.Nvalid is set to TRUE +

If the argument save.mean.Nvalid is set to TRUE study-specific means and Nvalids -as well as the global equivalents across all studies combined -are saved in the server-side. +as well as the global equivalents across all studies combined +are saved in the server-side. Once the estimated means and Nvalids are written into the server-side R environments, they can be used directly to centralize the variable of interest around its global mean or its study-specific means. Finally, @@ -155,7 +136,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -192,7 +173,7 @@ 
Examples

              
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -208,15 +189,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.meanByClass.html b/docs/reference/ds.meanByClass.html index 9c7d8560..8b081930 100644 --- a/docs/reference/ds.meanByClass.html +++ b/docs/reference/ds.meanByClass.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Computes the mean and standard deviation across categories

- +
@@ -57,36 +57,36 @@

Computes the mean and standard deviation across categories

Arguments

-
x
+ + +
x

a character string specifying the name of the dataset or a text formula.

-
outvar
+
outvar

a character vector specifying the names of the continuous variables.

-
covar
+
covar

a character vector specifying the names of up to 3 categorical variables

-
type
+
type

a character string that represents the type of analysis to carry out. -type can be set as: 'combine' or 'split'. -Default 'combine'. +type can be set as: 'combine' or 'split'. +Default 'combine'. For more information see Details.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.meanByClass returns to the client-side a table or a list of tables that +

ds.meanByClass returns to the client-side a table or a list of tables that hold the length of the numeric variable(s) and their mean and standard deviation in each subgroup (subset).

@@ -115,7 +115,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -157,7 +157,7 @@ 
Examples

              
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -173,15 +173,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.meanSdGp.html b/docs/reference/ds.meanSdGp.html index 214d6cb0..51702b22 100644 --- a/docs/reference/ds.meanSdGp.html +++ b/docs/reference/ds.meanSdGp.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Computes the mean and standard deviation across groups defined by one factor

- +
@@ -57,41 +57,41 @@

Computes the mean and standard deviation across groups defined by one factor

Arguments

-
x
+ + +
x

a character string specifying the name of a numeric continuous variable.

-
y
+
y

a character string specifying the name of a categorical variable of class factor.

-
type
+
type

a character string that represents the type of analysis to carry out. -This can be set as: "combine", "split" or "both". -Default "both". +This can be set as: "combine", "split" or "both". +Default "both". For more information see Details.

-
do.checks
+
do.checks

logical. If TRUE the administrative checks are undertaken to ensure that the input objects are defined in all studies and that the -variables are of equivalent class in each study. +variables are of equivalent class in each study. Default is FALSE to save time.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.meanSdGp returns to the client-side the mean, SD, Nvalid and SEM combined +

ds.meanSdGp returns to the client-side the mean, SD, Nvalid and SEM combined across studies and/or separately for each study, depending on the argument type.

@@ -99,7 +99,7 @@

Details

This function calculates the mean, standard deviation (SD), N (number of observations) and the standard error of the mean (SEM) of a continuous variable broken down into subgroups defined by a single factor.

-

There are important differences between ds.meanSdGp function compared to +

There are important differences between ds.meanSdGp function compared to the function ds.meanByClass:

(A) ds.meanSdGp does not actually subset the data it simply calculates the required statistics and reports them. This means you cannot use this function if you wish to physically break the @@ -117,13 +117,13 @@

Details

(4) sex = 1 and BMI = 1 -> newfactor = 4
(5) sex = 1 and BMI = 2 -> newfactor = 5
(6) sex = 1 and BMI = 3 -> newfactor = 6

-

(C) At present, ds.meanByClass calculates the sample size in each group to mean the +

(C) At present, ds.meanByClass calculates the sample size in each group to mean the total sample size (i.e. it includes all observations in each group regardless of whether or not they include missing values for the continuous variable or the factor). The calculation of sample size in each group by ds.meanSdGp always reports the number of observations that are non-missing both for the continuous variable and the factor. This makes sense - in the case of ds.meanByClass, -the total size of the physical subsets was important, +the total size of the physical subsets was important, but when it comes down only to ds.meanSdGp which undertakes analysis without physical subsetting, it is only the observations with non-missing values in both variables that contribute to the calculation of means and SDs within each group @@ -151,7 +151,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -202,7 +202,7 @@ 
Examples

              
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -218,15 +218,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.merge.html b/docs/reference/ds.merge.html index d80f86fd..87767638 100644 --- a/docs/reference/ds.merge.html +++ b/docs/reference/ds.merge.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@

- +

Merges two data frames in the server-side

- +
@@ -64,84 +64,84 @@

Merges two data frames in the server-side

Arguments

-
x.name
+ + +
x.name

a character string specifying the name of the -first data frame to be merged. The length of the string should be less than the -specified threshold for the nfilter.stringShort which is one of the disclosure +first data frame to be merged. The length of the string should be less than the +specified threshold for the nfilter.stringShort which is one of the disclosure prevention checks in DataSHIELD.

-
y.name
+
y.name

a character string specifying the name of the -second data frame to be merged. The length of the string should be less than the -specified threshold for the nfilter.stringShort which is one of the disclosure +second data frame to be merged. The length of the string should be less than the +specified threshold for the nfilter.stringShort which is one of the disclosure prevention checks in DataSHIELD.

-
by.x.names
-

a character string or a vector of names specifying +

by.x.names
+

a character string or a vector of names specifying of the column(s) in data frame x.name for merging.

-
by.y.names
-

a character string or a vector of names specifying +

by.y.names
+

a character string or a vector of names specifying of the column(s) in data frame y.name for merging.

-
all.x
+
all.x

logical. If TRUE then extra rows will be added to the output, -one for each row in x.name that has no matching row in y.name. +one for each row in x.name that has no matching row in y.name. If FALSE the rows with data from both data frames are included in the output. Default FALSE.

-
all.y
+
all.y

logical. If TRUE then extra rows will be added to the output, -one for each row in y.name that has no matching row in x.name. +one for each row in y.name that has no matching row in x.name. If FALSE the rows with data from both data frames are included in the output. Default FALSE.

-
sort
+
sort

logical. If TRUE the merged result is sorted on elements in the by.x.names and by.y.names columns. Default TRUE.

-
suffixes
+
suffixes

a character vector of length 2 specifying the suffixes to be used for making unique common column names in the two input data frames when they both appear in the merged data frame.

-
no.dups
+
no.dups

logical. Suffixes are appended in more cases to avoid duplicated column names in the merged data frame. Default TRUE (FALSE before R version 3.5.0).

-
incomparables
-

values that cannot be matched. This is intended to +

incomparables
+

values that cannot be matched. This is intended to be used for merging on one column, so these are incomparable values of that column. For more information see match in native R merge function.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default merge.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.merge returns the merged data frame that is written on the server-side. +

ds.merge returns the merged data frame that is written on the server-side. Also, two validity messages are returned to the client-side indicating whether the new object has been created in each data source and if so whether it is in a valid form.

@@ -149,7 +149,7 @@

Value

Details

This function is similar to the native R function merge. -There are some changes compared with the native R function +There are some changes compared with the native R function in choosing which variables to use to merge the data frames, the function merge is very flexible. For example, you can choose to merge using all vectors that appear in both data frames. However, for ds.merge @@ -165,7 +165,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -220,7 +220,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -236,15 +236,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.message.html b/docs/reference/ds.message.html index beb5af05..7c94b88e 100644 --- a/docs/reference/ds.message.html +++ b/docs/reference/ds.message.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Returns server-side messages to the client-side

- +
@@ -51,22 +51,22 @@

Returns server-side messages to the client-side

Arguments

-
message.obj.name
-

is a character string specifying the name of the list that + + +

message.obj.name
+

is a character string specifying the name of the list that contains the message.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.message returns a list object from each study, +

ds.message returns a list object from each study, containing the message that has been written by DataSHIELD into $studysideMessage.

@@ -82,7 +82,7 @@

Details

available are designed to be able to write the designated error message to the $serversideMessage object into the list that is saved on the server-side as the primary output of that function. So only valid server-side functions of -DataSHIELD can write a $studysideMessage. The error message is a string that +DataSHIELD can write a $studysideMessage. The error message is a string that cannot exceed a length of nfilter.string a default of 80 characters.

Server function called: messageDS

@@ -93,7 +93,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -133,7 +133,7 @@ 
Examples

   
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -148,15 +148,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.metadata.html b/docs/reference/ds.metadata.html index acd990df..0d807090 100644 --- a/docs/reference/ds.metadata.html +++ b/docs/reference/ds.metadata.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Gets the metadata associated with a variable held on the server

- +
@@ -51,21 +51,21 @@

Gets the metadata associated with a variable held on the server

Arguments

-
x
+ + +
x

a character string specifying the name of the object.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.metadata returns to the client-side the metadata of associated to an object +

ds.metadata returns to the client-side the metadata of associated to an object held at the server.

@@ -80,7 +80,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   # connecting to the Opal servers
 
@@ -110,7 +110,7 @@ 
Examples

 
   # clear the Datashield R sessions and logout
   DSI::datashield.logout(connections)
-}
+} # }
@@ -126,15 +126,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.mice.html b/docs/reference/ds.mice.html index 2c2a0d5f..871cd3c2 100644 --- a/docs/reference/ds.mice.html +++ b/docs/reference/ds.mice.html @@ -1,17 +1,17 @@ -Multivariate Imputation by Chained Equations — ds.mice • dsBaseClientMultivariate Imputation by Chained Equations — ds.mice • dsBaseClient - +
@@ -37,25 +37,25 @@
- +

Multivariate Imputation by Chained Equations

- +
-

This function calls the miceDS that is a wrapper function of the mice +

This function calls the miceDS that is a wrapper function of the mice from the mice R package. The function creates multiple imputations (replacement values) -for multivariate missing data. The method is based on Fully Conditional Specification, +for multivariate missing data. The method is based on Fully Conditional Specification, where each incomplete variable is imputed by a separate model. The MICE algorithm can impute mixes of continuous, binary, unordered categorical and ordered categorical data. In addition, MICE can impute continuous two-level data, and maintain consistency between imputations by means of passive imputation. It is recommended that the imputation is -done in each datasource separately. Otherwise the user should make sure that the input +done in each datasource separately. Otherwise the user should make sure that the input data have the same columns in all datasources and in the same order.

@@ -76,71 +76,71 @@

Multivariate Imputation by Chained Equations

Arguments

-
data
+ + +
data

a data frame or a matrix containing the incomplete data.

-
m
+
m

Number of multiple imputations. The default is m=5.

-
maxit
+
maxit

A scalar giving the number of iterations. The default is 5.

-
method
-

Can be either a single string, or a vector of strings with length -ncol(data), specifying the imputation method to be used for each column in data. If -specified as a single string, the same method will be used for all blocks. The default -imputation method (when no argument is specified) depends on the measurement level of -the target column, as regulated by the defaultMethod argument in native R mice function. +

method
+

Can be either a single string, or a vector of strings with length +ncol(data), specifying the imputation method to be used for each column in data. If +specified as a single string, the same method will be used for all blocks. The default +imputation method (when no argument is specified) depends on the measurement level of +the target column, as regulated by the defaultMethod argument in native R mice function. Columns that need not be imputed have the empty method "".

-
predictorMatrix
-

A numeric matrix of ncol(data) rows and ncol(data) columns, +

predictorMatrix
+

A numeric matrix of ncol(data) rows and ncol(data) columns, containing 0/1 data specifying the set of predictors to be used for each target column. -Each row corresponds to a variable to be imputed. A value of 1 means that the column +Each row corresponds to a variable to be imputed. A value of 1 means that the column variable is used as a predictor for the target variables (in the rows). By default, the -predictorMatrix is a square matrix of ncol(data) rows and columns with all 1's, except +predictorMatrix is a square matrix of ncol(data) rows and columns with all 1's, except for the diagonal.

-
post
-

A vector of strings with length ncol(data) specifying expressions as strings. -Each string is parsed and executed within the sampler() function to post-process imputed -values during the iterations. The default is a vector of empty strings, indicating no +

post
+

A vector of strings with length ncol(data) specifying expressions as strings. +Each string is parsed and executed within the sampler() function to post-process imputed +values during the iterations. The default is a vector of empty strings, indicating no post-processing. Multivariate (block) imputation methods ignore the post parameter.

-
seed
+
seed

either NA (default) or "fixed". If seed is set to "fixed" then a fixed seed random number generator which is study-specific is used.

-
newobj_mids
+
newobj_mids

a character string that provides the name for the output mids object that is stored on the data servers. Default mids_object.

-
newobj_df
-

a character string that provides the name for the output dataframes -that are stored on the data servers. Default imputationSet. For example, if m=5, and +

newobj_df
+

a character string that provides the name for the output dataframes +that are stored on the data servers. Default imputationSet. For example, if m=5, and newobj_df="imputationSet", then five imputed dataframes are saved on the servers with names imputationSet.1, imputationSet.2, imputationSet.3, imputationSet.4, imputationSet.5.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

a list with three elements: the method, the predictorMatrix and the post.

+

a list with three elements: the method, the predictorMatrix and the post.

Details

@@ -164,15 +164,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.names.html b/docs/reference/ds.names.html index 857e9a6a..69c83c36 100644 --- a/docs/reference/ds.names.html +++ b/docs/reference/ds.names.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Return the names of a list object

- +
@@ -49,11 +49,13 @@

Return the names of a list object

Arguments

-
xname
+ + +
xname

a character string specifying the name of the list.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login that represent the particular data sources (studies) to be addressed by the function call. If the datasources @@ -63,9 +65,7 @@

Arguments

Value

- - -

ds.names returns to the client-side the names +

ds.names returns to the client-side the names of a list object stored on the server-side.

@@ -88,7 +88,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
  
@@ -130,7 +130,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections)
 
-}
+} # }
@@ -146,15 +146,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.ns.html b/docs/reference/ds.ns.html index 2267fd5c..4cb30d13 100644 --- a/docs/reference/ds.ns.html +++ b/docs/reference/ds.ns.html @@ -5,7 +5,7 @@ - +
@@ -31,13 +31,13 @@
- +

Generate a Basis Matrix for Natural Cubic Splines

- +
@@ -61,48 +61,48 @@

Generate a Basis Matrix for Natural Cubic Splines

Arguments

-
x
+ + +
x

the predictor variable. Missing values are allowed.

-
df
-

degrees of freedom. One can supply df rather than knots; ns() then chooses +

df
+

degrees of freedom. One can supply df rather than knots; ns() then chooses df - 1 - intercept knots at suitably chosen quantiles of x (which will ignore missing values). The default, df = NULL, sets the number of inner knots as length(knots).

-
knots
+
knots

breakpoints that define the spline. The default is no knots; together with the natural boundary conditions this results in a basis for linear regression on x. Typical values are the mean or median for one knot, quantiles for more knots. See also Boundary.knots.

-
intercept
+
intercept

if TRUE, an intercept is included in the basis; default is FALSE.

-
Boundary.knots
+
Boundary.knots

boundary points at which to impose the natural boundary conditions and anchor the B-spline basis (default the range of the data). If both knots and Boundary.knots are supplied, the basis parameters do not depend on x. Data can extend beyond Boundary.knots.

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default ns.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

A matrix of dimension length(x) * df where either df was supplied or if knots were +

A matrix of dimension length(x) * df where either df was supplied or if knots were supplied, df = length(knots) + 1 + intercept. Attributes are returned that correspond to the arguments to ns, and explicitly give the knots, Boundary.knots etc for use by predict.ns(). The object is assigned at each serverside.

@@ -133,15 +133,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.numNA.html b/docs/reference/ds.numNA.html index b18ff79e..2bb4270f 100644 --- a/docs/reference/ds.numNA.html +++ b/docs/reference/ds.numNA.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Gets the number of missing values in a server-side vector

- +
@@ -51,21 +51,21 @@

Gets the number of missing values in a server-side vector

Arguments

-
x
+ + +
x

a character string specifying the name of the vector.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.numNA returns to the client-side the number of missing values +

ds.numNA returns to the client-side the number of missing values on a server-side vector.

@@ -80,7 +80,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
  ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -115,7 +115,7 @@ 
Examples

   datashield.logout(connections)
 
 
-}
+} # }
@@ -131,15 +131,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.qlspline.html b/docs/reference/ds.qlspline.html index 2135e271..d1a702dd 100644 --- a/docs/reference/ds.qlspline.html +++ b/docs/reference/ds.qlspline.html @@ -6,7 +6,7 @@ - +
@@ -32,13 +32,13 @@
- +

Basis for a piecewise linear spline with meaningful coefficients

- +
@@ -63,44 +63,44 @@

Basis for a piecewise linear spline with meaningful coefficients

Arguments

-
x
+ + +
x

the name of the input numeric variable

-
q
+
q

numeric, a single scalar greater or equal to 2 for a number of equal-frequency intervals along x or a vector of numbers in (0; 1) specifying the quantiles explicitly.

-
na.rm
+
na.rm

logical, whether NA should be removed when calculating quantiles, passed to na.rm of quantile. Default set to TRUE

-
marginal
+
marginal

logical, how to parametrize the spline, see Details

-
names
+
names

character, vector of names for constructed variables

-
newobj
-

a character string that provides the name for the output +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default qlspline.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

an object of class "lspline" and "matrix", which its name is specified by the +

an object of class "lspline" and "matrix", which its name is specified by the newobj argument (or its default name "qlspline.newobj"), is assigned on the serverside.

@@ -110,7 +110,7 @@

Details

the slope of the first segment. The consecutive coefficients correspond to the change in slope as compared to the previous segment. Function qlspline wraps lspline and calculates the knot positions to be at quantiles -of x. If q is a numerical scalar greater or equal to 2, the quantiles are computed at +of x. If q is a numerical scalar greater or equal to 2, the quantiles are computed at seq(0, 1, length.out = q + 1)[-c(1, q+1)], i.e. knots are at q-tiles of the distribution of x. Alternatively, q can be a vector of values in [0; 1] specifying the quantile probabilities directly (the vector is passed to argument probs of quantile).

@@ -132,15 +132,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.quantileMean.html b/docs/reference/ds.quantileMean.html index bb310d5e..bcc80bc5 100644 --- a/docs/reference/ds.quantileMean.html +++ b/docs/reference/ds.quantileMean.html @@ -1,10 +1,10 @@ -Computes the quantiles of a server-side variable — ds.quantileMean • dsBaseClientComputes the quantiles of a server-side variable — ds.quantileMean • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Computes the quantiles of a server-side variable

- +
-

This function calculates the mean and quantile values of a +

This function calculates the mean and quantile values of a server-side quantitative variable.

@@ -51,27 +51,27 @@

Computes the quantiles of a server-side variable

Arguments

-
x
+ + +
x

a character string specifying the name of the numeric vector.

-
type
+
type

a character that represents the type of graph to display. This can be set as 'combine' or 'split'. For more information see Details.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.quantileMean returns to the client-side the quantiles and statistical mean +

ds.quantileMean returns to the client-side the quantiles and statistical mean of a server-side numeric vector.

@@ -96,7 +96,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -134,7 +134,7 @@ 
Examples

   datashield.logout(connections)
 
 
-}
+} # }
@@ -150,15 +150,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.rBinom.html b/docs/reference/ds.rBinom.html index 8f5f31d1..63e174a8 100644 --- a/docs/reference/ds.rBinom.html +++ b/docs/reference/ds.rBinom.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates Binomial distribution in the server-side

- +
@@ -59,77 +59,77 @@

Generates Binomial distribution in the server-side

Arguments

-
samp.size
-

an integer value or an integer vector that defines the length of + + +

samp.size
+

an integer value or an integer vector that defines the length of the random numeric vector to be created in each source.

-
size
+
size

a positive integer that specifies the number of Bernoulli trials.

-
prob
+
prob

a numeric scalar value or vector in range 0 > prob > 1 which specifies the probability of a positive response (i.e. 1 rather than 0).

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default rbinom.newobj.

-
seed.as.integer
-

an integer or a NULL value which provides the +

seed.as.integer
+

an integer or a NULL value which provides the random seed in each data source.

-
return.full.seed.as.set
-

logical, if TRUE will return the full random number seed -in each data source (a numeric vector of length 626). If FALSE it will only return the +

return.full.seed.as.set
+

logical, if TRUE will return the full random number seed +in each data source (a numeric vector of length 626). If FALSE it will only return the trigger seed value you have provided. Default is FALSE.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.rBinom returns random number vectors -with a Binomial distribution for each study, +

ds.rBinom returns random number vectors +with a Binomial distribution for each study, taking into account the values specified in each parameter of the function. -The output vector is written to the server-side. -If requested, it also returned to the client-side the full 626 lengths -random seed vector generated in each source +The output vector is written to the server-side. +If requested, it also returned to the client-side the full 626 lengths +random seed vector generated in each source (see info for the argument return.full.seed.as.set).

Details

-

Creates a vector of random or pseudorandom non-negative integer values -distributed with a Binomial distribution. The ds.rBinom function's arguments specify -the number of trials, the success probability, the length and the seed of the output +

Creates a vector of random or pseudorandom non-negative integer values +distributed with a Binomial distribution. The ds.rBinom function's arguments specify +the number of trials, the success probability, the length and the seed of the output vector in each source.

-

To specify a different size in each source, you can use a character vector -(..., size="vector.of.sizes"...) +

To specify a different size in each source, you can use a character vector +(..., size="vector.of.sizes"...) or the datasources parameter to create the random vector for one source at a time, changing size as required. The default value for size = 1 which simulates binary outcomes (all observations 0 or 1).

-

To specify different prob in each source, you can use an integer or character vector -(..., prob="vector.of.probs"...) or the datasources parameter to create the random +

To specify different prob in each source, you can use an integer or character vector +(..., prob="vector.of.probs"...) or the datasources parameter to create the random vector for one source at a time, changing prob as required.

-

If seed.as.integer is an integer -e.g. 5 and there is more than one source (N) the seed is set as 5*N. -For example, in the first study the seed is set as 938*1, -in the second as 938*2 +

If seed.as.integer is an integer +e.g. 5 and there is more than one source (N) the seed is set as 5*N. +For example, in the first study the seed is set as 938*1, +in the second as 938*2 up to 938*N in the Nth study.

If seed.as.integer is set as 0 all sources will start with the seed value -0 and all the random number generators will, therefore, start from the same position. +0 and all the random number generators will, therefore, start from the same position. Besides, to use the same starting seed in all studies but do not wish it to -be 0, you can use datasources argument to generate the random number +be 0, you can use datasources argument to generate the random number vectors one source at a time.

Server functions called: rBinomDS and setSeedDS.

@@ -140,7 +140,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
 
@@ -187,7 +187,7 @@ 
Examples

             
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -202,15 +202,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.rNorm.html b/docs/reference/ds.rNorm.html index 82aaf359..164ac708 100644 --- a/docs/reference/ds.rNorm.html +++ b/docs/reference/ds.rNorm.html @@ -1,10 +1,10 @@ -Generates Normal distribution in the server-side — ds.rNorm • dsBaseClientGenerates Normal distribution in the server-side — ds.rNorm • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Generates Normal distribution in the server-side

- +
-

Generates normally distributed random (pseudorandom) scalar numbers. +

Generates normally distributed random (pseudorandom) scalar numbers. Besides, ds.rNorm allows creating different vector lengths in each server.

@@ -60,87 +60,87 @@

Generates Normal distribution in the server-side

Arguments

-
samp.size
+ + +
samp.size

an integer value or an integer vector that defines the length of the random numeric vector to be created in each source.

-
mean
+
mean

the mean value or vector of the Normal distribution to be created.

-
sd
+
sd

the standard deviation of the Normal distribution to be created.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default newObject.

-
seed.as.integer
-

an integer +

seed.as.integer
+

an integer or a NULL value which provides the random seed in each data source.

-
return.full.seed.as.set
-

logical, if TRUE will returns the full random number -seed in each data source (a numeric vector of length 626). -If FALSE it will only return the trigger seed value you have provided. +

return.full.seed.as.set
+

logical, if TRUE will returns the full random number +seed in each data source (a numeric vector of length 626). +If FALSE it will only return the trigger seed value you have provided. Default is FALSE.

-
force.output.to.k.decimal.places
-

an integer vector that +

force.output.to.k.decimal.places
+

an integer vector that forces the output random numbers vector to have k decimals.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.rNorm returns random number vectors with a normal distribution for each -study, taking into account the values specified in each parameter of the function. +

ds.rNorm returns random number vectors with a normal distribution for each +study, taking into account the values specified in each parameter of the function. The output vector is written to the server-side. If requested, it also returned to the client-side the full 626 lengths random seed vector generated in each source (see info for the argument return.full.seed.as.set).

Details

-

Creates a vector of pseudorandom numbers distributed -with a Normal distribution in each data source. -The ds.rNorm function's arguments specify the mean and the standard deviation -(sd) of the normal distribution and -the length and the seed of the output vector in each source.

+

Creates a vector of pseudorandom numbers distributed +with a Normal distribution in each data source. +The ds.rNorm function's arguments specify the mean and the standard deviation +(sd) of the normal distribution and +the length and the seed of the output vector in each source.

To specify a different mean value in each source, you can use a character vector (..., mean="vector.of.means"...) -or the datasources parameter to create the random vector for one source at a time, +or the datasources parameter to create the random vector for one source at a time, changing the mean as required. -Default value for mean = 0.

-

To specify different sd value in each source, +Default value for mean = 0.

+

To specify different sd value in each source, you can use a character vector (..., sd="vector.of.sds"... -or the datasources parameter to create the random vector for one source at a time, +or the datasources parameter to create the random vector for one source at a time, changing the <mean> as required. -Default value for sd = 0.

-

If seed.as.integer is an integer -e.g. 5 and there is more than one source (N) the seed is set as 5*N. -For example, in the first study the seed is set as 938*1, -in the second as 938*2 +Default value for sd = 0.

+

If seed.as.integer is an integer +e.g. 5 and there is more than one source (N) the seed is set as 5*N. +For example, in the first study the seed is set as 938*1, +in the second as 938*2 up to 938*N in the Nth study.

If seed.as.integer is set as 0 all sources will start with the seed value -0 and all the random number generators will, therefore, start from the same position. +0 and all the random number generators will, therefore, start from the same position. Also, to use the same starting seed in all studies but do not wish it to -be 0, you can use datasources argument to generate the random number +be 0, you can use datasources argument to generate the random number vectors one source at a time.

-

In force.output.to.k.decimal.places the range of k is 1-8 decimals. -If k = 0 the output random numbers are forced to integer. -If k = 9, no rounding of output numbers occurs. +

In force.output.to.k.decimal.places the range of k is 1-8 decimals. +If k = 0 the output random numbers are forced to integer. +If k = 9, no rounding of output numbers occurs. The default value of force.output.to.k.decimal.places = 9.

Server functions called: rNormDS and setSeedDS.

@@ -151,7 +151,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -202,7 +202,7 @@ 
Examples

            
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -217,15 +217,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.rPois.html b/docs/reference/ds.rPois.html index 915a3ff9..aaacd484 100644 --- a/docs/reference/ds.rPois.html +++ b/docs/reference/ds.rPois.html @@ -1,11 +1,11 @@ Generates Poisson distribution in the server-side — ds.rPois • dsBaseClient - +
@@ -31,19 +31,19 @@
- +

Generates Poisson distribution in the server-side

- +

Generates random (pseudorandom) non-negative integers -with a Poisson distribution. +with a Poisson distribution. Besides, ds.rPois allows creating different vector lengths in each server.

@@ -60,69 +60,69 @@

Generates Poisson distribution in the server-side

Arguments

-
samp.size
+ + +
samp.size

an integer value or an integer vector that defines the length of the random numeric vector to be created in each source.

-
lambda
+
lambda

the number of events mean per interval.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default newObject.

-
seed.as.integer
+
seed.as.integer

an integer or a NULL value which provides the random seed in each data source.

-
return.full.seed.as.set
+
return.full.seed.as.set

logical, if TRUE will return the full random number seed in each data source (a numeric vector of length 626). If -FALSE it will only return the trigger seed value you have provided. +FALSE it will only return the trigger seed value you have provided. Default is FALSE.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.rPois returns random number vectors with a Poisson distribution for each study, -taking into account the values specified in each parameter of the function. -The created vectors are stored in the server-side. +

ds.rPois returns random number vectors with a Poisson distribution for each study, +taking into account the values specified in each parameter of the function. +The created vectors are stored in the server-side. If requested, it also returned to the client-side the full -626 lengths random seed vector generated in each source +626 lengths random seed vector generated in each source (see info for the argument return.full.seed.as.set).

Details

-

Creates a vector of random or pseudorandom non-negative integer values -distributed with a Poisson distribution in each data source. -The ds.rPois function's arguments specify lambda, +

Creates a vector of random or pseudorandom non-negative integer values +distributed with a Poisson distribution in each data source. +The ds.rPois function's arguments specify lambda, the length and the seed of the output vector in each source.

-

To specify different lambda value in each source, you can use a character vector +

To specify different lambda value in each source, you can use a character vector (..., lambda = "vector.of.lambdas"...) or the datasources -parameter to create the random vector for one source at a time, +parameter to create the random vector for one source at a time, changing lambda as required. Default value for lambda> = 1.

-

If seed.as.integer is an integer -e.g. 5 and there is more than one source (N) the seed is set as 5*N. -For example, in the first study the seed is set as 938*1, -in the second as 938*2 +

If seed.as.integer is an integer +e.g. 5 and there is more than one source (N) the seed is set as 5*N. +For example, in the first study the seed is set as 938*1, +in the second as 938*2 up to 938*N in the Nth study.

If seed.as.integer is set as 0 all sources will start with the seed value -0 and all the random number generators will, therefore, start from the same position. +0 and all the random number generators will, therefore, start from the same position. Also, to use the same starting seed in all studies but do not wish it to -be 0, you can use datasources argument to generate the random number +be 0, you can use datasources argument to generate the random number vectors one source at a time.

Server functions called: rPoisDS and setSeedDS.

@@ -134,7 +134,7 @@

Author

Examples


-if (FALSE) {
+if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki 
   # Connecting to the Opal servers
@@ -177,7 +177,7 @@ 
Examples

         
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -192,15 +192,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.rUnif.html b/docs/reference/ds.rUnif.html index 81e77033..a9c582ce 100644 --- a/docs/reference/ds.rUnif.html +++ b/docs/reference/ds.rUnif.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates Uniform distribution in the server-side

- +
@@ -60,92 +60,92 @@

Generates Uniform distribution in the server-side

Arguments

-
samp.size
-

an integer value or an integer vector that defines the + + +

samp.size
+

an integer value or an integer vector that defines the length of the random numeric vector to be created in each source.

-
min
-

a numeric scalar that specifies the minimum value of the +

min
+

a numeric scalar that specifies the minimum value of the random numbers in the distribution.

-
max
-

a numeric scalar that specifies the maximum value of the +

max
+

a numeric scalar that specifies the maximum value of the random numbers in the distribution.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default newObject.

-
seed.as.integer
-

an integer or a NULL value which provides the random +

seed.as.integer
+

an integer or a NULL value which provides the random seed in each data source.

-
return.full.seed.as.set
-

logical, if TRUE will return the full random number -seed in each data source (a numeric vector of length 626). If FALSE it will only +

return.full.seed.as.set
+

logical, if TRUE will return the full random number +seed in each data source (a numeric vector of length 626). If FALSE it will only return the trigger seed value you have provided. Default is FALSE.

-
force.output.to.k.decimal.places
-

an integer or -an integer vector that forces the output random +

force.output.to.k.decimal.places
+

an integer or +an integer vector that forces the output random numbers vector to have k decimals.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.Unif returns random number vectors with a uniform distribution for each study, +

ds.Unif returns random number vectors with a uniform distribution for each study, taking into account the values specified in each parameter of the function. -The created vectors are stored in the server-side. If requested, it also returned to the +The created vectors are stored in the server-side. If requested, it also returned to the client-side the full 626 lengths random seed vector generated in each source (see info for the argument return.full.seed.as.set).

Details

-

It creates a vector of pseudorandom numbers distributed -with a uniform probability in each data source. -The ds.Unif function's arguments specify -the minimum and maximum of the uniform distribution +

It creates a vector of pseudorandom numbers distributed +with a uniform probability in each data source. +The ds.Unif function's arguments specify +the minimum and maximum of the uniform distribution and the length and the seed of the output vector in each source.

-

To specify different min values in each source, +

To specify different min values in each source, you can use a character vector (..., min="vector.of.mins"...) -or the datasources parameter to create the random vector for one source at a time, +or the datasources parameter to create the random vector for one source at a time, changing the min value as required. Default value for min = 0.

-

To specify different max values in each source, +

To specify different max values in each source, you can use a character vector (..., max="vector.of.maxs"...) -or the datasources parameter to create the random vector for one source at a time, +or the datasources parameter to create the random vector for one source at a time, changing the max value as required. Default value for max = 1.

-

If seed.as.integer is an integer -e.g. 5 and there is more than one source (N) the seed is set as 5*N. -For example, in the first study the seed is set as 938*1, -in the second as 938*2 +

If seed.as.integer is an integer +e.g. 5 and there is more than one source (N) the seed is set as 5*N. +For example, in the first study the seed is set as 938*1, +in the second as 938*2 up to 938*N in the Nth study.

If seed.as.integer is set as 0 all sources will start with the seed value -0 and all the random number generators will, therefore, start from the same position. +0 and all the random number generators will, therefore, start from the same position. Also, to use the same starting seed in all studies but do not wish it to -be 0, you can use datasources argument to generate +be 0, you can use datasources argument to generate the random number vectors one source at a time.

-

In force.output.to.k.decimal.places the range of k is 1-8 decimals. -If k = 0 the output random numbers are forced to an integer. -If k = 9, no rounding of output numbers occurs. +

In force.output.to.k.decimal.places the range of k is 1-8 decimals. +If k = 0 the output random numbers are forced to an integer. +If k = 9, no rounding of output numbers occurs. The default value of force.output.to.k.decimal.places = 9. If you wish to generate integers with equal probabilities in the range 1-10 -you should specify min = 0.5 and max = 10.5. +you should specify min = 0.5 and max = 10.5. Default value for k = 9.

Server functions called: rUnifDS and setSeedDS.

@@ -157,7 +157,7 @@

Author

Examples


-if (FALSE) {
+if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -207,7 +207,7 @@ 
Examples

            
   # Clear the Datashield R sessions and logout           
   datashield.logout(connections)
-}
+} # }
@@ -223,15 +223,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.ranksSecure.html b/docs/reference/ds.ranksSecure.html index 924ab94a..f29d764c 100644 --- a/docs/reference/ds.ranksSecure.html +++ b/docs/reference/ds.ranksSecure.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Secure ranking of a vector across all sources

- +
@@ -64,25 +64,27 @@

Secure ranking of a vector across all sources

Arguments

-
input.var.name
+ + +
input.var.name

a character string in a format that can pass through the DataSHIELD R parser which specifies the name of the vector to be ranked. Needs to have same name in each data source.

-
quantiles.for.estimation
+
quantiles.for.estimation

one of a restricted set of character strings. To mitigate disclosure risk only the following set of quantiles can be generated: c(0.025,0.05,0.10,0.20,0.25,0.30,0.3333,0.40,0.50,0.60,0.6667, 0.70,0.75,0.80,0.90,0.95,0.975). The allowable formats for the argument are of the general form: "0.025-0.975" where the first number is the lowest -quantile to be estimated and the second number is the equivalent highest +quantile to be estimated and the second number is the equivalent highest quantile to estimate. These two quantiles are then estimated along with all allowable quantiles in between. The allowable argument values are then: "0.025-0.975", "0.05-0.95", "0.10-0.90", "0.20-0.80". Two alternative values are "quartiles" i.e. c(0.25,0.50,0.75), and "median" i.e. c(0.50). The default value is "0.05-0.95". If the sample size is so small that an extreme -quartile could be disclosive the function will be terminated and an error +quartile could be disclosive the function will be terminated and an error message returned telling you that you might try using an argument with a narrower set of quantiles. This disclosure trap will be triggered if the total number of subjects across all studies divided by the total number @@ -90,7 +92,7 @@

Arguments

(the minimum cell size in a contingency table).

-
generate.quantiles
+
generate.quantiles

a logical value indicating whether the ds.ranksSecure function should carry on to estimate the key quantile values specified by argument <quantiles.for.estimation> or should stop @@ -114,7 +116,7 @@

Arguments

from "0.025-0.975" to "0.05-0.95".

-
output.ranks.df
+
output.ranks.df

a character string in a format that can pass through the DataSHIELD R parser which specifies an optional name for the data.frame written to the serverside on each data source that contains @@ -126,7 +128,7 @@

Arguments

information and cannot therefore be passed to the clientside.

-
summary.output.ranks.df
+
summary.output.ranks.df

a character string in a format that can pass through the DataSHIELD R parser which specifies an optional name for the summary data.frame written to the serverside on each data source that contains @@ -138,24 +140,24 @@

Arguments

information and cannot therefore be passed to the clientside.

-
ranks.sort.by
+
ranks.sort.by

a character string taking two possible values. These are "ID.orig" and "vals.orig". These define the order in which the output.ranks.df and summary.output.ranks.df data frames are presented. If the argument is set as "ID.orig" the order of rows in the output data frames are precisely the same as the order of original input vector that is being ranked (i.e. V2BR). This means the ranks can simply be cbinded to the -matrix, data frame or tibble that originally included V2BR so it also +matrix, data frame or tibble that originally included V2BR so it also includes the corresponding ranks. If it is set as "vals.orig" the output data frames are in order of increasing magnitude of the original values of V2BR. Default value is "ID.orig".

-
shared.seed.value
+
shared.seed.value

an integer value which is used to set the random seed generator in each study. Initially, the seed is set to be the same in all studies, so the order and parameters of the repeated -encryption procedures are precisely the same in each study. Then a +encryption procedures are precisely the same in each study. Then a study-specific modification of the seed in each study ensures that the procedures initially generating the masking pseudodata (which are then subject to the same encryption procedures as the real data) are different @@ -164,17 +166,17 @@

Arguments

header document.

-
synth.real.ratio
+
synth.real.ratio

an integer value specifying the ratio between the number of masking pseudodata values generated in each study compared to the number of real data values in V2BR.

-
NA.manage
+
NA.manage

character string taking three possible values: "NA.delete", "NA.low","NA.hi". This argument determines how missing values are managed before ranking. "NA.delete" results in all missing values being removed -prior to ranking. This means that the vector of ranks in each study is +prior to ranking. This means that the vector of ranks in each study is shorter than the original vector of V2BR values by an amount corresponding to the number of missing values in V2BR in that study. Any rows containing missing values in V2BR are simply removed before the ranking procedure is @@ -185,7 +187,7 @@

Arguments

for example, that if there are a total of M values of V2BR that are missing across all studies, there will be a total of M observations that are ranked lowest each with a rank of (M+1)/2. So if 7 are missing the lowest 7 ranks -will be 4,4,4,4,4,4,4 and if 4 are missing the first 4 ranks will be +will be 4,4,4,4,4,4,4 and if 4 are missing the first 4 ranks will be 2.5,2.5,2.5,2.5. "NA.hi" indicates that all missing values should be converted to a new value that has a meaningful magnitude that is higher(less negative or more positive)than the highest non-missing value of V2BR in any @@ -199,7 +201,7 @@

Arguments

2.5,2.5,2.5,2.5. The default value of the "NA.manage" argument is "NA.delete"

-
rm.residual.objects
+
rm.residual.objects

logical value. Default = TRUE: at the beginning and end of each run of ds.ranksSecure delete all extraneous objects that are otherwise left behind. These are not usually needed, but could be of value @@ -207,12 +209,12 @@

Arguments

the residual objects

-
monitor.progress
+
monitor.progress

logical value. Default = FALSE. If TRUE, function outputs information about its progress.

-
datasources
+
datasources

specifies the particular opal object(s) to use. If the <datasources> argument is not specified (NULL) the default set of opals will be used. If <datasources> is specified, it should be set without @@ -225,9 +227,7 @@

Arguments

Value

- - -

the data frame objects specified by the arguments output.ranks.df +

the data frame objects specified by the arguments output.ranks.df and summary.output.ranks.df. These are written to the serverside in each study. Provided the sort order is consistent these data frames can be cbinded to any other data frame, matrix or tibble object containing V2BR or to the @@ -262,7 +262,7 @@

Details

global quantiles are, in general, different to the mean or median of the equivalent quantiles calculated independently in each data source separately. For more details about the cluster of functions that collectively -enable secure global ranking and estimation of global quantiles see the +enable secure global ranking and estimation of global quantiles see the associated document entitled "secure.global.ranking.docx".

@@ -282,15 +282,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.rbind.html b/docs/reference/ds.rbind.html index 4b76cca8..30de9105 100644 --- a/docs/reference/ds.rbind.html +++ b/docs/reference/ds.rbind.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Combines R objects by rows in the server-side

- +
@@ -58,57 +58,55 @@

Combines R objects by rows in the server-side

Arguments

-
x
+ + +
x

a character vector with the name of the objects to be combined.

-
DataSHIELD.checks
+
DataSHIELD.checks

logical, if TRUE checks that all input objects exist and are of an appropriate class.

-
force.colnames
-

can be NULL or a vector of characters that +

force.colnames
+

can be NULL or a vector of characters that specifies column names of the output object.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Defaults rbind.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

-
notify.of.progress
+
notify.of.progress

specifies if console output should be produced to indicate progress. Default FALSE.

Value

- - -

ds.rbind returns a matrix combining the rows of the +

ds.rbind returns a matrix combining the rows of the R objects specified in the function -which is written to the server-side. -It also returns two messages to the client-side with the name of newobj

- - -

that has been created in each data source and DataSHIELD.checks result.

+which is written to the server-side. +It also returns two messages to the client-side with the name of newobj +that has been created in each data source and DataSHIELD.checks result.

Details

A sequence of vector, matrix or data-frame arguments is combined by rows to produce a matrix on the server-side.

-

In DataSHIELD.checks the checks are relatively slow. +

In DataSHIELD.checks the checks are relatively slow. Default DataSHIELD.checks value is FALSE.

If force.colnames is NULL column names are inferred from the names or column names of the first object specified in the x argument. -The vector of column names must have the same number of elements as +The vector of column names must have the same number of elements as the columns in the output object.

Server functions called: rbindDS.

@@ -120,7 +118,7 @@

Author

Examples


-if (FALSE) {
+if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki 
   
   # Connecting to the Opal servers
@@ -161,7 +159,7 @@ 
Examples

            
   # Clear the Datashield R sessions and logout  
   datashield.logout(connections) 
-  }
+  } # }
@@ -177,15 +175,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.reShape.html b/docs/reference/ds.reShape.html index 7b5acd9b..cbd97a29 100644 --- a/docs/reference/ds.reShape.html +++ b/docs/reference/ds.reShape.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Reshapes server-side grouped data

- +
@@ -62,42 +62,44 @@

Reshapes server-side grouped data

Arguments

-
data.name
+ + +
data.name

a character string specifying the name of the data frame to be reshaped.

-
varying
+
varying

names of sets of variables in the wide format that correspond to single variables in 'long' format.

-
v.names
+
v.names

the names of variables in the 'long' format that correspond to multiple variables in the 'wide' format.

-
timevar.name
+
timevar.name

the variable in 'long' format that differentiates multiple -records from the same group or individual. +records from the same group or individual. If more than one record matches, the first will be taken.

-
idvar.name
+
idvar.name

names of one or more variables in 'long' format that identify multiple records from the same group/individual. These variables may also be present in 'wide' format.

-
drop
+
drop

a vector of names of variables to drop before reshaping. This can simplify the resultant output.

-
direction
+
direction

a character string that partially matched to either 'wide' to reshape from 'long' to 'wide' format, or 'long' to reshape from 'wide' to 'long' format.

-
sep
+
sep

a character vector of length 1, indicating a separating character in the variable names in the 'wide' format. This is used for creating good v.names and times arguments based on the names in the varying argument. This is also used to create variable names @@ -105,24 +107,22 @@

Arguments

to 'wide' format.

-
newobj
+
newobj

a character string that provides the name for the output object -that is stored on the data servers. +that is stored on the data servers. Default reshape.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.reShape returns to the server-side a reshaped data frame -converted from 'long' to 'wide' format or from 'wide' to long' format. +

ds.reShape returns to the server-side a reshaped data frame +converted from 'long' to 'wide' format or from 'wide' to long' format. Also, two validity messages are returned to the client-side indicating whether the new object has been created in each data source and if so whether it is in a valid form.

@@ -133,7 +133,7 @@

Details

It reshapes a data frame containing longitudinal or otherwise grouped data between 'wide' format with repeated measurements in separate columns of the same record and 'long' format with the repeated -measurements in separate records. The reshaping can be in either direction. +measurements in separate records. The reshaping can be in either direction. Server function called: reShapeDS

@@ -143,7 +143,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see Wiki
   # Connecting to the Opal servers
@@ -182,7 +182,7 @@ 
Examples

   
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -198,15 +198,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.recodeLevels.html b/docs/reference/ds.recodeLevels.html index 9cf71a00..008e5014 100644 --- a/docs/reference/ds.recodeLevels.html +++ b/docs/reference/ds.recodeLevels.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Recodes the levels of a server-side factor vector

- +
@@ -54,31 +54,31 @@

Recodes the levels of a server-side factor vector

Arguments

-
x
+ + +
x

a character string specifying the name of a factor variable.

-
newCategories
+
newCategories

a character vector specifying the new levels. Its length must be equal or greater to the current number of levels.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default recodelevels.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.recodeLevels returns to the server-side a variable of type factor +

ds.recodeLevels returns to the server-side a variable of type factor with the replaces levels.

@@ -95,7 +95,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   
@@ -132,7 +132,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -148,15 +148,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.recodeValues.html b/docs/reference/ds.recodeValues.html index 3d8a6fbd..80bff411 100644 --- a/docs/reference/ds.recodeValues.html +++ b/docs/reference/ds.recodeValues.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Recodes server-side variable values

- +
@@ -59,49 +59,49 @@

Recodes server-side variable values

Arguments

-
var.name
+ + +
var.name

a character string providing the name of the variable to be recoded.

-
values2replace.vector
+
values2replace.vector

a numeric or character vector specifying the values in the variable var.name to be replaced.

-
new.values.vector
+
new.values.vector

a numeric or character vector specifying the new values.

-
missing
-

If supplied, any missing values in var.name will be replaced by this value. -Must be of length 1. If the analyst want to recode only missing values then it should also -specify an identical vector of values in both arguments values2replace.vector and +

missing
+

If supplied, any missing values in var.name will be replaced by this value. +Must be of length 1. If the analyst want to recode only missing values then it should also +specify an identical vector of values in both arguments values2replace.vector and new.values.vector. Otherwise please look the ds.replaceNA function.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default recodevalues.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

-
notify.of.progress
+
notify.of.progress

logical. If TRUE console output should be produced to indicate progress. Default FALSE.

Value

- - -

Assigns to each server a new variable with the recoded values. -Also, two validity messages are returned to the client-side +

Assigns to each server a new variable with the recoded values. +Also, two validity messages are returned to the client-side indicating whether the new object has been created in each data source and if so whether it is in a valid form.

@@ -122,7 +122,7 @@

Author

Examples

- +
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.rep.html b/docs/reference/ds.rep.html index 6df45922..56413642 100644 --- a/docs/reference/ds.rep.html +++ b/docs/reference/ds.rep.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Creates a repetitive sequence in the server-side

- +
@@ -63,64 +63,64 @@

Creates a repetitive sequence in the server-side

Arguments

-
x1
+ + +
x1

an scalar number, vector or list.

-
times
+
times

an integer from clientside or a serverside integer or vector.

-
length.out
+
length.out

a clientside integer or a serverside integer or vector.

-
each
+
each

a clientside or serverside integer.

-
source.x1
-

the source x1 argument. It can be "clientside" or "c" +

source.x1
+

the source x1 argument. It can be "clientside" or "c" and serverside or "s".

-
source.times
+
source.times

see source.x1

-
source.length.out
+
source.length.out

see source.x1

-
source.each
+
source.each

see source.x1

-
x1.includes.characters
-

Boolean parameter which specifies if +

x1.includes.characters
+

Boolean parameter which specifies if the x1 is a character.

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default seq.vect.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.rep returns in the server-side a vector with the specified repetitive sequence. +

ds.rep returns in the server-side a vector with the specified repetitive sequence. Also, two validity messages are returned to the client-side - the name of newobj that has been created + the name of newobj that has been created in each data source and if it is in a valid form.

@@ -137,7 +137,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -194,7 +194,7 @@ 
Examples

 
   # Clear the Datashield R sessions and logout  
   datashield.logout(connections) 
-} 
+} # }
@@ -210,15 +210,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.replaceNA.html b/docs/reference/ds.replaceNA.html index 84bb3886..144448a8 100644 --- a/docs/reference/ds.replaceNA.html +++ b/docs/reference/ds.replaceNA.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Replaces the missing values in a server-side vector

- +
@@ -51,31 +51,31 @@

Replaces the missing values in a server-side vector

Arguments

-
x
+ + +
x

a character string specifying the name of the vector.

-
forNA
-

a list or a vector that contains the replacement value(s), for each study. +

forNA
+

a list or a vector that contains the replacement value(s), for each study. The length of the list or vector must be equal to the number of servers (studies).

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default replacena.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.replaceNA returns to the server-side a new vector or table structure +

ds.replaceNA returns to the server-side a new vector or table structure with the missing values replaced by the specified values. The class of the vector is the same as the initial vector.

@@ -99,7 +99,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -158,7 +158,7 @@ 
Examples

  
   # Clear the Datashield R sessions and logout  
   datashield.logout(connections) 
-} 
+} # }
@@ -174,15 +174,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.rm.html b/docs/reference/ds.rm.html index f661d489..47cbcb7a 100644 --- a/docs/reference/ds.rm.html +++ b/docs/reference/ds.rm.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Deletes server-side R objects

- +
@@ -49,28 +49,28 @@

Deletes server-side R objects

Arguments

-
x.names
+ + +
x.names

a character string specifying the objects to be deleted.

-
datasources
-

a list of DSConnection-class objects obtained after login. -If the datasources argument is not specified +

datasources
+

a list of DSConnection-class objects obtained after login. +If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

The ds.rm function deletes from the server-side -the specified object. If this +

The ds.rm function deletes from the server-side +the specified object. If this is successful the message "Object(s) '<x.names>' was deleted." is returned to the client-side.

Details

-

This function is similar to the native R function +

This function is similar to the native R function rm().

The fact that it is an aggregate function may be surprising because it modifies an object @@ -89,7 +89,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -129,7 +129,7 @@ 
Examples

              
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -144,15 +144,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.rowColCalc.html b/docs/reference/ds.rowColCalc.html index 9ad7fe80..59560072 100644 --- a/docs/reference/ds.rowColCalc.html +++ b/docs/reference/ds.rowColCalc.html @@ -1,10 +1,10 @@ -Computes rows and columns sums and means in the server-side — ds.rowColCalc • dsBaseClientComputes rows and columns sums and means in the server-side — ds.rowColCalc • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Computes rows and columns sums and means in the server-side

- +
-

Computes sums and means of rows or columns +

Computes sums and means of rows or columns of a numeric matrix or data frame on the server-side.

@@ -51,31 +51,31 @@

Computes rows and columns sums and means in the server-side

Arguments

-
x
+ + +
x

a character string specifying the name of a matrix or a data frame.

-
operation
+
operation

a character string that indicates the operation to carry out: "rowSums", "colSums", "rowMeans" or "colMeans".

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default rowcolcalc.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.rowColCalc returns to the server-side rows and columns sums and means.

+

ds.rowColCalc returns to the server-side rows and columns sums and means.

Details

@@ -92,7 +92,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki 
   # Connecting to the Opal servers
@@ -132,7 +132,7 @@ 
Examples

   #Clear the Datashield R sessions and logout
   datashield.logout(connections) 
 
-}
+} # }
@@ -147,15 +147,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.sample.html b/docs/reference/ds.sample.html index 2f469a5d..8ebc307c 100644 --- a/docs/reference/ds.sample.html +++ b/docs/reference/ds.sample.html @@ -5,7 +5,7 @@ - +
@@ -31,13 +31,13 @@
- +

Performs random sampling and permuting of vectors, dataframes and matrices

- +
@@ -62,7 +62,9 @@

Performs random sampling and permuting of vectors, dataframes and matrices

Arguments

-
x
+ + +
x

Either a character string providing the name for the serverside vector, matrix or data.frame to be sampled or permuted, or an integer/numeric scalar (e.g. 923) indicating that one should create a new vector on the serverside @@ -77,7 +79,7 @@

Arguments

only.

-
size
+
size

a numeric/integer scalar indicating the size of the sample to be drawn. If the [x] argument is a vector, matrix or data.frame on the serverside and if the [size] argument is set either to 0 or to the length of @@ -90,7 +92,7 @@

Arguments

this is violated an error message will be returned.

-
seed.as.integer
+
seed.as.integer

this is precisely equivalent to the [seed.as.integer] arguments for the pseudo-random number generating functions (e.g. also see help for ds.rBinom, ds.rNorm, ds.rPois and ds.rUnif). @@ -113,14 +115,14 @@

Arguments

each source

-
replace
+
replace

a Boolean indicator (TRUE or FALSE) specifying whether the sample should be drawn with or without replacement. Default is FALSE so the sample is drawn without replacement. For further details see help for sample in native R.

-
prob
+
prob

a character string containing the name of a numeric vector of probability weights on the serverside that is associated with each of the elements of the vector to be sampled enabling the drawing of a sample @@ -128,12 +130,12 @@

Arguments

For further details see help for sample in native R.

-
newobj
+
newobj

This a character string providing a name for the output data.frame which defaults to 'newobj.sample' if no name is specified.

-
datasources
+
datasources

specifies the particular opal object(s) to use. If the <datasources> argument is not specified the default set of opals will be used. The default opals are called default.opals and the default can be set using the function @@ -145,16 +147,14 @@

Arguments

e.g. datasources=opals.em[c(1,3)]

-
notify.of.progress
+
notify.of.progress

specifies if console output should be produce to indicate progress. The default value for notify.of.progress is FALSE.

Value

- - -

the object specified by the <newobj> argument (or default name +

the object specified by the <newobj> argument (or default name 'newobj.sample') which is written to the serverside. In addition, two validity messages are returned indicating whether <newobj> has been created in each data source and if so whether @@ -179,7 +179,7 @@

Details

or a matrix it is first coerced to a data.frame on the serverside and so is dealt with in the same way (i.e. random selection of 10 rows). If x is an integer not expressed as a character string, it is dealt with in exactly the same way -as in native R. That is, if x = 923 and size=117, DataSHIELD will draw a +as in native R. That is, if x = 923 and size=117, DataSHIELD will draw a random sample in random order of size 117 from the vector 1:923 (i.e. 1, 2, ... ,923) with or without replacement depending whether [replace] is TRUE or FALSE. If the [x] argument is numeric (e.g. 923) and size is either undefined @@ -195,9 +195,9 @@

Details

1 whenever a row enters the sample and as a QA test, all values in that column in the output object should be 1. 'ID.seq' is a sequential numeric ID appended to the right of the object to be sampled during the running of ds.sample that runs from -1 to the length of the object and will be appended even if there is already +1 to the length of the object and will be appended even if there is already an equivalent sequential ID in the object. The output object is stored in -the same original order as it was before sampling, and so if the first +the same original order as it was before sampling, and so if the first four elements of 'ID.seq' are 3,4, 6, 15 ... then it means that rows 1 and 2 were not included in the random sample, but rows 3, 4 were. Row 5 was not included, 6 was included and rows 7-14 were not etc. The 'sampling.order' vector is @@ -238,15 +238,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.scatterPlot.html b/docs/reference/ds.scatterPlot.html index 8f9537a6..5c792f45 100644 --- a/docs/reference/ds.scatterPlot.html +++ b/docs/reference/ds.scatterPlot.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates non-disclosive scatter plots

- +
@@ -60,58 +60,58 @@

Generates non-disclosive scatter plots

Arguments

-
x
+ + +
x

a character string specifying the name of the explanatory variable, a numeric vector.

-
y
+
y

a character string specifying the name of the response variable, a numeric vector.

-
method
-

a character string that specifies the +

method
+

a character string that specifies the method that is used to generated non-disclosive -coordinates to be displayed in a scatter plot. +coordinates to be displayed in a scatter plot. This argument can be set as 'deteministic' or 'probabilistic'. -Default 'deteministic'. +Default 'deteministic'. For more information see Details.

-
k
+
k

the number of the nearest neighbors for which their centroid is calculated. -Default 3. +Default 3. For more information see Details.

-
noise
+
noise

the percentage of the initial variance that is used as the variance of the embedded noise if the argument method is set to 'probabilistic'. For more information see Details.

-
type
+
type

a character that represents the type of graph to display. -This can be set as 'combine' or 'split'. -Default 'split'. +This can be set as 'combine' or 'split'. +Default 'split'. For more information see Details.

-
return.coords
-

a logical. If TRUE the coordinates of the anonymised data points are return +

return.coords
+

a logical. If TRUE the coordinates of the anonymised data points are return to the Console. Default value is FALSE.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.scatterPlot returns to the client-side one or more scatter +

ds.scatterPlot returns to the client-side one or more scatter plots depending on the argument type.

@@ -119,24 +119,24 @@

Details

As the generation of a scatter plot from original data is disclosive and is not permitted in DataSHIELD, this function allows the user to plot non-disclosive scatter plots.

If the argument method is set to 'deterministic', the server-side function searches -for the k-1 nearest neighbors of each single data point and calculates the centroid -of such k points. +for the k-1 nearest neighbors of each single data point and calculates the centroid +of such k points. The proximity is defined by the minimum Euclidean distances of z-score transformed data.

When the coordinates of all centroids are estimated the function applies scaling to expand the centroids back to the dispersion of the original data. The scaling is achieved by multiplying the centroids with a scaling factor that is equal to the ratio between the standard deviation of the original variable and the standard deviation of the calculated centroids. The coordinates of the scaled centroids are then returned to the client-side.

-

The value of k is specified by the user. +

The value of k is specified by the user. The suggested and default value is equal to 3 which is also the suggested minimum threshold that is used to prevent disclosure which is specified in the -protection filter nfilter.kNN. When the value of k increases, +protection filter nfilter.kNN. When the value of k increases, the disclosure risk decreases but the utility loss increases. The value of k is used only -if the argument method is set to 'deterministic'. +if the argument method is set to 'deterministic'. Any value of k is ignored if the argument method is set to 'probabilistic'.

-

If the argument method is set to 'probabilistic', +

If the argument method is set to 'probabilistic', the server-side function generates a random normal noise of zero mean and variance equal to 10% of the variance of each x and y variable. The noise is added to each x and y variable and the disturbed by the addition of @@ -160,7 +160,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki 
   # Connecting to the Opal servers
@@ -210,7 +210,7 @@ 
Examples

   #Clear the Datashield R sessions and logout
   datashield.logout(connections) 
 
-}
+} # }
@@ -226,15 +226,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.seq.html b/docs/reference/ds.seq.html index 3e9aa41f..2235f610 100644 --- a/docs/reference/ds.seq.html +++ b/docs/reference/ds.seq.html @@ -1,10 +1,10 @@ -Generates a sequence in the server-side — ds.seq • dsBaseClientGenerates a sequence in the server-side — ds.seq • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Generates a sequence in the server-side

- +
-

This function generates a sequence for given parameters +

This function generates a sequence for given parameters on the server-side.

@@ -59,89 +59,89 @@

Generates a sequence in the server-side

Arguments

-
FROM.value.char
-

an integer or a number in character from specifying -the starting value for the sequence. + + +

FROM.value.char
+

an integer or a number in character from specifying +the starting value for the sequence. Default "1".

-
BY.value.char
-

an integer or a number in character from specifying +

BY.value.char
+

an integer or a number in character from specifying the value to increment each step in the sequence. Default "1".

-
TO.value.char
-

an integer or a number in character from specifying +

TO.value.char
+

an integer or a number in character from specifying the terminal value for the sequence. -Default NULL. +Default NULL. For more information see Details.

-
LENGTH.OUT.value.char
-

an integer or a number in character from specifying +

LENGTH.OUT.value.char
+

an integer or a number in character from specifying the length of the sequence at which point its extension should be stopped. -Default NULL. +Default NULL. For more information see Details.

-
ALONG.WITH.name
-

a character string specifying the name of a standard vector -to generate a vector of the same length. +

ALONG.WITH.name
+

a character string specifying the name of a standard vector +to generate a vector of the same length. For more information see Details.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default seq.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.seq returns to the server-side the generated sequence. -Also, two validity messages are returned to the client-side +

ds.seq returns to the server-side the generated sequence. +Also, two validity messages are returned to the client-side indicating whether the new object has been created in each data source and if so whether it is in a valid form.

Details

-

This function is similar to a native R function seq(). +

This function is similar to a native R function seq(). It creates a flexible range of sequence vectors that can then be used to help manage and analyse data.

Note: the combinations of arguments that are not allowed -for the function seq in native R are also prohibited in ds.seq.

-

To be specific, FROM.value.char argument +for the function seq in native R are also prohibited in ds.seq.

+

To be specific, FROM.value.char argument defines the start of the sequence and BY.value.char defines how the sequence is incremented (or decremented) at each step. But where the sequence stops can be defined in three different ways:
-(1) TO.value.char indicates the terminal value of the sequence. +(1) TO.value.char indicates the terminal value of the sequence. For example, ds.seq(FROM.value.char = "3", BY.value.char = "2", TO.value.char = "7") creates the sequence 3,5,7 on the server-side.
-(2) LENGTH.OUT.value.char indicates the length of the sequence. -For example, ds.seq(FROM.value.char = "3", BY.value.char = "2", -LENGTH.OUT.value.char = "7") +(2) LENGTH.OUT.value.char indicates the length of the sequence. +For example, ds.seq(FROM.value.char = "3", BY.value.char = "2", +LENGTH.OUT.value.char = "7") creates the sequence 3,5,7,9,11,13,15 on the server-side.
(3) ALONG.WITH.name specifies the name of a variable on the server-side, such that the sequence in each study will be equal in length to that variable. -For example, ds.seq(FROM.value.char = "3", BY.value.char = "2", +For example, ds.seq(FROM.value.char = "3", BY.value.char = "2", ALONG.WITH.name = "var.x") creates a sequence such that if var.x is of length 100 in study 1 the sequence written to study 1 will be 3,5,7,...,197,199,201 and if var.x is of length 4 in study 2, the sequence written to study 2 will be 3,5,7,9.
Only one of the three arguments: TO.value.char, LENGTH.OUT.value.char and ALONG.WITH.name can be non-null in any one call.

-

In LENGTH.OUT.value.char argument if you specify a number with a decimal point but +

In LENGTH.OUT.value.char argument if you specify a number with a decimal point but in character form this result in a sequence length(integer) + 1. -For example, LENGTH.OUT.value.char = "1000.0001" +For example, LENGTH.OUT.value.char = "1000.0001" generates a sequence of length 1001.

Server function called: seqDS

@@ -152,7 +152,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki
   # Connecting to the Opal servers
@@ -202,7 +202,7 @@ 
Examples

          
   # Clear the Datashield R sessions and logout
   datashield.logout(connections) 
-}
+} # }
@@ -217,15 +217,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.setDefaultOpals.html b/docs/reference/ds.setDefaultOpals.html index 35d166f2..2753f52a 100644 --- a/docs/reference/ds.setDefaultOpals.html +++ b/docs/reference/ds.setDefaultOpals.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Creates a default set of Opal objects called 'default.opals'

- +
@@ -49,9 +49,7 @@

Creates a default set of Opal objects called 'default.opals'

Value

- - -

Copies a specified set of Opals (on the client-side server) +

Copies a specified set of Opals (on the client-side server) and calls the copy 'default.opals'

@@ -99,15 +97,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.setSeed.html b/docs/reference/ds.setSeed.html index 87ca5b5f..f20baffa 100644 --- a/docs/reference/ds.setSeed.html +++ b/docs/reference/ds.setSeed.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Server-side random number generation

- +
@@ -49,22 +49,22 @@

Server-side random number generation

Arguments

-
seed.as.integer
+ + +
seed.as.integer

a numeric value or a NULL that primes the random seed in each data source.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

Sets the values of the vector of integers of length 626 known as +

Sets the values of the vector of integers of length 626 known as .Random.seed on each data source that is the true current state of the random seed in each source. It also returns the value of the trigger integer that has primed the random seed vector (.Random.seed) in @@ -77,9 +77,9 @@

Details

the full pseudorandom number seed that is a vector of integers of length 626 called .Random.seed, this vector is written to the server-side.

This function is similar to a native R function set.seed().

-

In seed.as.integer argument +

In seed.as.integer argument the current limitation on the value of the integer that -can be specified is -2147483647 up to +2147483647 +can be specified is -2147483647 up to +2147483647 (this is +/- ([2^31]-1)).

Because you only specify one integer in the call to ds.setSeed (i.e. the value for the seed.as.integer argument) that value will be @@ -88,7 +88,7 @@

Details

the same position and if a vector of pseudorandom number values is requested based on one of DataSHIELD's pseudorandom number generating functions precisely the same random vector will be generated in each source. If you want to avoid this -you can specify a different priming value in each source by using +you can specify a different priming value in each source by using the datasources argument to generate the random number vectors one source at a time with a different integer in each case.

Furthermore, if you use any one @@ -105,7 +105,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki 
   
   # Connecting to the Opal servers
@@ -144,7 +144,7 @@ 
Examples

                    
   # Clear the Datashield R sessions and logout  
   datashield.logout(connections) 
-  }
+  } # }
@@ -160,15 +160,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.skewness.html b/docs/reference/ds.skewness.html index 3c731a0b..86ff4c8c 100644 --- a/docs/reference/ds.skewness.html +++ b/docs/reference/ds.skewness.html @@ -1,10 +1,10 @@ -Calculates the skewness of a server-side numeric variable — ds.skewness • dsBaseClientCalculates the skewness of a server-side numeric variable — ds.skewness • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Calculates the skewness of a server-side numeric variable

- +
-

This function calculates the skewness of a numeric variable +

This function calculates the skewness of a numeric variable that is stored on the server-side (Opal server).

@@ -51,39 +51,39 @@

Calculates the skewness of a server-side numeric variable

Arguments

-
x
+ + +
x

a character string specifying the name of a numeric variable.

-
method
-

an integer value between 1 and 3 selecting one of the algorithms for computing skewness. +

method
+

an integer value between 1 and 3 selecting one of the algorithms for computing skewness. For more information see Details. The default value is set to 1.

-
type
-

a character string which represents the type of analysis to carry out. +

type
+

a character string which represents the type of analysis to carry out. type can be set as: 'combine', 'split' or 'both'. For more information -see Details. +see Details. The default value is set to 'both'.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.skewness returns a matrix showing the skewness of the input numeric variable, +

ds.skewness returns a matrix showing the skewness of the input numeric variable, the number of valid observations and the validity message.

Details

This function is similar to the function skewness in R package e1071.

-

The function calculates the skewness of an input variable x +

The function calculates the skewness of an input variable x with three different methods:
(1) If method is set to 1 the following formula is used \( skewness= \frac{\sum_{i=1}^{N} (x_i - \bar(x))^3 /N}{(\sum_{i=1}^{N} ((x_i - \bar(x))^2) /N)^(3/2) }\), where \( \bar{x} \) is the mean of x and \(N\) is the number of observations.
@@ -91,9 +91,9 @@

Details

the following formula is used \( skewness= \frac{\sum_{i=1}^{N} (x_i - \bar(x))^3 /N}{(\sum_{i=1}^{N} ((x_i - \bar(x))^2) /N)^(3/2) } * \frac{\sqrt(N(N-1)}{n-2}\).
(3) If method is set to 3 the following formula is used \( skewness= \frac{\sum_{i=1}^{N} (x_i - \bar(x))^3 /N}{(\sum_{i=1}^{N} ((x_i - \bar(x))^2) /N)^(3/2) } * (\frac{N-1}{N})^(3/2)\).

The type argument can be set as follows:
-(1) If type is set to 'combine', 'combined', 'combines' or 'c', +(1) If type is set to 'combine', 'combined', 'combines' or 'c', the global skewness is returned.
-(2) If type is set to 'split', 'splits' or 's', +(2) If type is set to 'split', 'splits' or 's', the skewness is returned separately for each study.
(3) If type is set to 'both' or 'b', both sets of outputs are produced.

If x contains any missing value, the function removes those before @@ -107,7 +107,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -143,7 +143,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   DSI::datashield.logout(connections) 
   
-} 
+} # }
@@ -158,15 +158,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.sqrt.html b/docs/reference/ds.sqrt.html index 6254ae2e..46c711cb 100644 --- a/docs/reference/ds.sqrt.html +++ b/docs/reference/ds.sqrt.html @@ -1,10 +1,10 @@ -Computes the square root values of a variable — ds.sqrt • dsBaseClientComputes the square root values of a variable — ds.sqrt • dsBaseClient - +
@@ -30,18 +30,18 @@
- +

Computes the square root values of a variable

- +
-

Computes the square root values for a specified numeric or integer vector. +

Computes the square root values for a specified numeric or integer vector. This function is similar to R function sqrt.

@@ -51,34 +51,34 @@

Computes the square root values of a variable

Arguments

-
x
+ + +
x

a character string providing the name of a numeric or an integer vector.

-
newobj
+
newobj

a character string that provides the name for the output variable that is stored on the data servers. Default name is set to sqrt.newobj.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.sqrt assigns a vector for each study that includes the square root values of +

ds.sqrt assigns a vector for each study that includes the square root values of the input numeric or integer vector specified in the argument x. The created vectors are stored in the servers.

Details

-

The function calls the server-side function sqrtDS that computes the -square root values of the elements of a numeric or integer vector and assigns a new vector -with those square root values on the server-side. The name of the new generated vector is +

The function calls the server-side function sqrtDS that computes the +square root values of the elements of a numeric or integer vector and assigns a new vector +with those square root values on the server-side. The name of the new generated vector is specified by the user through the argument newobj, otherwise is named by default to sqrt.newobj.

@@ -89,7 +89,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   # Connecting to the Opal servers
 
@@ -134,7 +134,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(connections) 
 
-}
+} # }
@@ -150,15 +150,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.subset.html b/docs/reference/ds.subset.html index 2306f5c8..69240cf0 100644 --- a/docs/reference/ds.subset.html +++ b/docs/reference/ds.subset.html @@ -5,7 +5,7 @@ - +
@@ -31,13 +31,13 @@
- +

Generates a valid subset of a table or a vector

- +
@@ -62,47 +62,47 @@

Generates a valid subset of a table or a vector

Arguments

-
x
+ + +
x

a character, the name of the dataframe or the factor vector and the range of the subset.

-
subset
+
subset

the name of the output object, a list that holds the subset object. If set to NULL the default name of this list is 'subsetObject'

-
completeCases
+
completeCases

a character that tells if only complete cases should be included or not.

-
rows
+
rows

a vector of integers, the indices of the rows to extract.

-
cols
+
cols

a vector of integers or a vector of characters; the indices of the columns to extract or their names.

-
logicalOperator
+
logicalOperator

a boolean, the logical parameter to use if the user wishes to subset a vector using a logical operator. This parameter is ignored if the input data is not a vector.

-
threshold
+
threshold

a numeric, the threshold to use in conjunction with the logical parameter. This parameter is ignored if the input data is not a vector.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

Value

- - -

no data are return to the user, the generated subset dataframe is stored on the server side.

+

no data are return to the user, the generated subset dataframe is stored on the server side.

Details

@@ -125,7 +125,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   # load the login data
   data(logindata)
@@ -168,7 +168,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(conns)
 
-}
+} # }
@@ -184,15 +184,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.subsetByClass.html b/docs/reference/ds.subsetByClass.html index 8429941e..8a8fad3b 100644 --- a/docs/reference/ds.subsetByClass.html +++ b/docs/reference/ds.subsetByClass.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates valid subset(s) of a data frame or a factor

- +
@@ -56,29 +56,29 @@

Generates valid subset(s) of a data frame or a factor

Arguments

-
x
+ + +
x

a character, the name of the dataframe or the vector to generate subsets from.

-
subsets
+
subsets

the name of the output object, a list that holds the subset objects. If set to NULL the default name of this list is 'subClasses'.

-
variables
+
variables

a vector of string characters, the name(s) of the variables to subset by.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

Value

- - -

a no data are return to the user but messages are printed out.

+

a no data are return to the user but messages are printed out.

Details

@@ -100,7 +100,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   # load the login data
   data(logindata)
@@ -130,7 +130,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(conns)
 
-}
+} # }
@@ -146,15 +146,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.summary.html b/docs/reference/ds.summary.html index 0ed05ce4..309c6a0d 100644 --- a/docs/reference/ds.summary.html +++ b/docs/reference/ds.summary.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Generates the summary of a server-side object

- +
@@ -49,34 +49,34 @@

Generates the summary of a server-side object

Arguments

-
x
+ + +
x

a character string specifying the name of a numeric or factor variable.

-
datasources
-

a list of DSConnection-class objects obtained after login. +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.summary returns to the client-side the class and -size of the server-side object. +

ds.summary returns to the client-side the class and +size of the server-side object. Also other information is returned depending on the class of the object. For example, potentially disclosive information -such as the minimum and maximum values of numeric vectors are not returned. +such as the minimum and maximum values of numeric vectors are not returned. The summary is given for each study separately.

Details

-

This function provides some insight about an object. Unlike the similar native R +

This function provides some insight about an object. Unlike the similar native R summary function only a limited class of objects can be used as input to reduce the risk of disclosure. For example, the minimum and the maximum values of a numeric vector - are not given to the client because they are potentially disclosive.

+ are not given to the client because they are potentially disclosive.

server functions called: isValidDS, dimDS and colnamesDS

@@ -86,7 +86,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   ## Version 6, for version 5 see the Wiki 
   
@@ -127,7 +127,7 @@ 
Examples

   # Clear the Datashield R sessions and logout  
   datashield.logout(connections) 
 
-}
+} # }
@@ -143,15 +143,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.table.html b/docs/reference/ds.table.html index de9855d7..4c524ddd 100644 --- a/docs/reference/ds.table.html +++ b/docs/reference/ds.table.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates 1-, 2-, and 3-dimensional contingency tables with option of assigning to serverside only and producing chi-squared statistics

- +
@@ -63,7 +63,9 @@

Generates 1-, 2-, and 3-dimensional contingency tables with option of assign

Arguments

-
rvar
+ + +
rvar

is a character string (in inverted commas) specifying the name of the variable defining the rows in all of the 2 dimensional tables that form the output. Please see 'details' above for more @@ -71,25 +73,25 @@

Arguments

by <rvar> but <cvar> and <stvar> are both NULL

-
cvar
+
cvar

is a character string specifying the name of the variable defining the columns in all of the 2 dimensional tables that form the output.

-
stvar
+
stvar

is a character string specifying the name of the variable that indexes the separate two dimensional tables in the output if the call specifies a 3 dimensional table.

-
report.chisq.tests
+
report.chisq.tests

if TRUE, chi-squared tests are applied to every 2 dimensional table in the output and reported as "chisq.test_table.name". Default = FALSE.

-
exclude
+
exclude

this argument is passed through to the table function in native R which is called by tableDS. The help for table in native R indicates that 'exclude' specifies any levels that should be deleted for @@ -114,15 +116,15 @@

Arguments

the 3s by deleting rows of data, or converting the 3s to a different value.

-
useNA
+
useNA

this argument is passed through to the table function in -native R which is called by tableDS. In DataSHIELD, this argument can take +native R which is called by tableDS. In DataSHIELD, this argument can take two values: "no" or "always" which indicate whether to include NA values in the table. For further information, please see the help for the <exclude> argument (above) and/or the help for the table function in native R. Default value is set to "always".

-
suppress.chisq.warnings
+
suppress.chisq.warnings

if set to TRUE, the default warnings are suppressed that would otherwise be produced by the table function in native R whenever an expected cell count in one or more cells is less than 5. @@ -130,7 +132,7 @@

Arguments

help provided for the <report.chisq.tests> argument (above).

-
table.assign
+
table.assign

is a Boolean argument set by default to FALSE. If it is FALSE the ds.table function acts as a standard aggregate function - it returns the table that is specified in its call to the clientside @@ -143,7 +145,7 @@

Arguments

to the clientside because it fails disclosure rules.

-
newobj
+
newobj

this a character string providing a name for the output table object to be written to the serverside if <table.assign> is TRUE. If no explicit name for the table object is specified, but <table.assign> @@ -151,7 +153,7 @@

Arguments

to table.newobj.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default. If the <datasources> is to be specified, it should be set without @@ -162,7 +164,7 @@

Arguments

e.g. datasources=connections.em[c(1,3)].

-
force.nfilter
+
force.nfilter

if <force.nfilter> is non-NULL it must be specified as a positive integer represented as a character string: e.g. "173". This the has the effect of the standard value of 'nfilter.tab' (often 1, 3, 5 or 10 @@ -178,21 +180,15 @@

Arguments

Value

- - -

Having created the requested table based on serverside data +

Having created the requested table based on serverside data it is returned to the clientside for the analyst to visualise (unless it is blocked because it fails the disclosure control criteria or there is an error for some other reason).

- -

The clientside output from ds.table includes error messages that identify when the creation of a table from a particular study has failed and why. If table.assign=TRUE, ds.table also writes the requested table as an object named by the <newobj> argument or set to 'newObj' by default.

- -

Further information about the visible material passed to the clientside, and the optional table object written to the serverside can be seen under 'details' (above).

@@ -223,7 +219,7 @@

Details

The true counts in the studyside vector are replaced by a sequential set of cell-IDs running from 1:n (where n is the total number of cells in the table) in the empty -representation of the structure of the potentially disclosive table +representation of the structure of the potentially disclosive table that is returned to the clientside. These cell-IDs reflect the order of the counts in the true counts vector on the serverside. In consequence, if the number 13 appears in a cell of the empty @@ -292,15 +288,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.table1D.html b/docs/reference/ds.table1D.html index c511e7d9..cd8e6c28 100644 --- a/docs/reference/ds.table1D.html +++ b/docs/reference/ds.table1D.html @@ -5,7 +5,7 @@ - +
@@ -31,13 +31,13 @@
- +

Generates 1-dimensional contingency tables

- +
@@ -58,32 +58,32 @@

Generates 1-dimensional contingency tables

Arguments

-
x
+ + +
x

a character, the name of a numerical vector with discrete values - usually a factor.

-
type
+
type

a character which represent the type of table to ouput: pooled table or one table for each data source. If type is set to 'combine', a pooled 1-dimensional table is returned; if If type is set to 'split' a 1-dimensional table is returned for each data source.

-
warningMessage
+
warningMessage

a boolean, if set to TRUE (deafult) a warning is displayed if any returned table is invalid. Warning messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information which are stored in the output object 'validity' - see the list of output objects.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

Value

- - -

A list object containing the following items:

+

A list object containing the following items:

counts

table(s) that hold counts for each level/category. If some cells counts are invalid (see 'Details' section) only the total (outer) cell counts are displayed in the returned individual study tables or in the pooled @@ -118,7 +118,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   # load the file that contains the login details
   data(logindata)
@@ -148,7 +148,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(conns)
 
-}
+} # }
@@ -164,15 +164,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.table2D.html b/docs/reference/ds.table2D.html index d22b9dda..96270839 100644 --- a/docs/reference/ds.table2D.html +++ b/docs/reference/ds.table2D.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Generates 2-dimensional contingency tables

- +
@@ -57,37 +57,37 @@

Generates 2-dimensional contingency tables

Arguments

-
x
+ + +
x

a character, the name of a numerical vector with discrete values - usually a factor.

-
y
+
y

a character, the name of a numerical vector with discrete values - usually a factor.

-
type
+
type

a character which represent the type of table to ouput: pooled table or one table for each data source or both. If type is set to 'combine', a pooled 2-dimensional table is returned; If type is set to 'split' a 2-dimensional table is returned for each data source. If type is set to 'both' (default) a pooled 2-dimensional table plus a 2-dimensional table for each data source are returned.

-
warningMessage
+
warningMessage

a boolean, if set to TRUE (deafult) a warning is displayed if any returned table is invalid. Warning messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information which are stored in the output object 'validity' - see the list of output objects.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

Value

- - -

A list object containing the following items:

+

A list object containing the following items:

colPercent

table(s) that hold column percentages for each level/category. Inner cells are reported as missing if one or more cells are 'invalid'.

@@ -129,7 +129,7 @@

Author

Examples

- +
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.tapply.assign.html b/docs/reference/ds.tapply.assign.html index 654fca22..c65eeacf 100644 --- a/docs/reference/ds.tapply.assign.html +++ b/docs/reference/ds.tapply.assign.html @@ -5,7 +5,7 @@ - +
@@ -31,13 +31,13 @@
- +

Applies a Function Over a Ragged Array on the server-side

- +
@@ -59,47 +59,47 @@

Applies a Function Over a Ragged Array on the server-side

Arguments

-
X.name
+ + +
X.name

a character string specifying the name of the variable to be summarized.

-
INDEX.names
-

a character string specifying the name of a single factor -or a vector of names of up to two factors to index the variable to be summarized. +

INDEX.names
+

a character string specifying the name of a single factor +or a vector of names of up to two factors to index the variable to be summarized. For more information see Details.

-
FUN.name
-

a character string specifying the name of one of the allowable -summarizing functions. This can be set as: +

FUN.name
+

a character string specifying the name of one of the allowable +summarizing functions. This can be set as: "N" (or "length"), "mean","sd", "sum", -or "quantile". +or "quantile". For more information see Details.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default tapply.assign.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.tapply.assign returns an array of the summarized values. +

ds.tapply.assign returns an array of the summarized values. The array is written to the server-side. It has the same number of dimensions as INDEX.

Details

This function applies one of -a selected range of functions to each cell of a ragged array, +a selected range of functions to each cell of a ragged array, that is to each (non-empty) group of values given by each unique combination of a series of indexing factors.

The range of allowable summarizing functions for DataSHIELD ds.tapply function @@ -111,7 +111,7 @@

Details

team could work on them if requested.

To protect against disclosure the number of observations in each summarizing group in each source is calculated -and if any of these falls below the value of nfilter.tab +and if any of these falls below the value of nfilter.tab (the minimum allowable non-zero count in a contingency table) the tapply analysis of that source will return only an error message. The value of nfilter.tab is can be set and modified only by the data custodian. If an @@ -123,14 +123,14 @@

Details

which individuals have got at least one positive value for a binary outcome variable, then that flagging does not have to be overtly returned to the client-side. Rather, it can be written as a vector to the server-side at each source (which, like any other server-side -object, cannot then be seen, abstracted or copied). This can be done using -ds.tapply.assign which writes the results as a newobj to the server-side -and does not test the number of observations in each group against nfilter.tab. +object, cannot then be seen, abstracted or copied). This can be done using +ds.tapply.assign which writes the results as a newobj to the server-side +and does not test the number of observations in each group against nfilter.tab. For more information see the help option of ds.tapply.assign function.

The native R tapply function has optional arguments such as na.rm = TRUE for FUN = mean -which will exclude any NAs from the outcome variable to be summarized. -However, in order to keep DataSHIELD's ds.tapply and ds.tapply.assign +which will exclude any NAs from the outcome variable to be summarized. +However, in order to keep DataSHIELD's ds.tapply and ds.tapply.assign functions straightforward, the server-side functions tapplyDS and tapplyDS.assign both starts by stripping any observations which have missing (NA) values in either the outcome variable or in @@ -138,7 +138,7 @@

Details

on complete cases.

In INDEX.names argument the native R tapply function can coerce non-factor vectors into factors. However, this does not always work when -using the DataSHIELD ds.tapply or ds.tapply.assign +using the DataSHIELD ds.tapply or ds.tapply.assign functions so if you are concerned that an indexing vector is not being treated correctly as a factor, please first declare it explicitly as a factor using ds.asFactor.

@@ -155,7 +155,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -201,7 +201,7 @@ 
Examples

                  
   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
-  }
+  } # }
@@ -216,15 +216,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.tapply.html b/docs/reference/ds.tapply.html index 878b0a75..d1d6d8d8 100644 --- a/docs/reference/ds.tapply.html +++ b/docs/reference/ds.tapply.html @@ -1,11 +1,11 @@ Applies a Function Over a Server-Side Ragged Array — ds.tapply • dsBaseClient - +
@@ -31,19 +31,19 @@
- +

Applies a Function Over a Server-Side Ragged Array

- +

Apply one of a selected range of functions to summarize an -outcome variable over one or more indexing factors. +outcome variable over one or more indexing factors. The resultant summary is written to the client-side.

@@ -58,41 +58,41 @@

Applies a Function Over a Server-Side Ragged Array

Arguments

-
X.name
+ + +
X.name

a character string specifying the name of the variable to be summarized.

-
INDEX.names
-

a character string specifying the name of a single factor -or a list or vector of names of up to two factors to index the variable to be summarized. +

INDEX.names
+

a character string specifying the name of a single factor +or a list or vector of names of up to two factors to index the variable to be summarized. For more information see Details.

-
FUN.name
-

a character string specifying the name of one of the allowable -summarizing functions. This can be set as: +

FUN.name
+

a character string specifying the name of one of the allowable +summarizing functions. This can be set as: "N" (or "length"), "mean","sd", "sum", -or "quantile". +or "quantile". For more information see Details.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.tapply returns to the client-side an array of the summarized values. +

ds.tapply returns to the client-side an array of the summarized values. It has the same number of dimensions as INDEX.

Details

This function is similar to a native R function tapply(). -It applies one of a selected range of functions to each cell +It applies one of a selected range of functions to each cell of a ragged array, that is to each (non-empty) group of values given by each unique combination of a series of indexing factors.

The range of allowable summarizing functions for DataSHIELD ds.tapply function @@ -104,7 +104,7 @@

Details

team could work on them if requested.

To protect against disclosure the number of observations in each summarizing group in each source is calculated -and if any of these falls below the value of nfilter.tab +and if any of these falls below the value of nfilter.tab (the minimum allowable non-zero count in a contingency table) the tapply analysis of that source will return only an error message. The value of nfilter.tab is can be set and modified only by the data custodian. If an @@ -116,14 +116,14 @@

Details

which individuals have got at least one positive value for a binary outcome variable, then that flagging does not have to be overtly returned to the client-side. Rather, it can be written as a vector to the server-side at each source (which, like any other server-side -object, cannot then be seen, abstracted or copied). This can be done using -ds.tapply.assign which writes the results as a newobj to the server-side -and does not test the number of observations in each group against nfilter.tab. +object, cannot then be seen, abstracted or copied). This can be done using +ds.tapply.assign which writes the results as a newobj to the server-side +and does not test the number of observations in each group against nfilter.tab. For more information see the help option of ds.tapply.assign function.

The native R tapply function has optional arguments such as na.rm = TRUE for FUN = mean -which will exclude any NAs from the outcome variable to be summarized. -However, in order to keep DataSHIELD's ds.tapply and ds.tapply.assign +which will exclude any NAs from the outcome variable to be summarized. +However, in order to keep DataSHIELD's ds.tapply and ds.tapply.assign functions straightforward, the server-side functions tapplyDS and tapplyDS.assign both starts by stripping any observations which have missing (NA) values in either the outcome variable or in @@ -131,7 +131,7 @@

Details

on complete cases.

In INDEX.names argument the native R tapply function can coerce non-factor vectors into factors. However, this does not always work when -using the DataSHIELD ds.tapply or ds.tapply.assign +using the DataSHIELD ds.tapply or ds.tapply.assign functions so if you are concerned that an indexing vector is not being treated correctly as a factor, please first declare it explicitly as a factor using ds.asFactor.

@@ -148,7 +148,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -192,7 +192,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-} 
+} # }
@@ -207,15 +207,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.testObjExists.html b/docs/reference/ds.testObjExists.html index 1d1053f0..2dc6b97d 100644 --- a/docs/reference/ds.testObjExists.html +++ b/docs/reference/ds.testObjExists.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Checks if an R object exists on the server-side

- +
@@ -51,23 +51,23 @@

Checks if an R object exists on the server-side

Arguments

-
test.obj.name
+ + +
test.obj.name

a character string specifying the name of the object to search.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.testObjExists returns a list of messages specifying that the object exists +

ds.testObjExists returns a list of messages specifying that the object exists on the server-side. -If the specified object does not exist in at least one +If the specified object does not exist in at least one of the specified data sources or it exists but is of class NULL, the function returns an error message specifying that the object does not exist in all data sources.

@@ -86,7 +86,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -120,7 +120,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -135,15 +135,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.unList.html b/docs/reference/ds.unList.html index 609a7dc0..1a0b9c55 100644 --- a/docs/reference/ds.unList.html +++ b/docs/reference/ds.unList.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Flattens Server-Side Lists

- +
@@ -51,27 +51,27 @@

Flattens Server-Side Lists

Arguments

-
x.name
+ + +
x.name

a character string specifying the name of the input object to be unlisted.

-
newobj
-

a character string that provides the name for the output variable +

newobj
+

a character string that provides the name for the output variable that is stored on the data servers. Default unlist.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.unList returns to the server-side the unlist object. -Also, two validity messages are returned to the client-side +

ds.unList returns to the server-side the unlist object. +Also, two validity messages are returned to the client-side indicating whether the new object has been created in each data source and if so whether it is in a valid form.

@@ -97,7 +97,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   ## Version 6, for version 5 see the Wiki
   
   # connecting to the Opal servers
@@ -138,7 +138,7 @@ 
Examples

   # Clear the Datashield R sessions and logout                 
   datashield.logout(connections) 
   
-}   
+} # }
@@ -153,15 +153,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.unique.html b/docs/reference/ds.unique.html index 296893e3..5d1cd79b 100644 --- a/docs/reference/ds.unique.html +++ b/docs/reference/ds.unique.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Perform 'unique' on a variable on the server-side

- +
@@ -49,26 +49,26 @@

Perform 'unique' on a variable on the server-side

Arguments

-
x.name
+ + +
x.name

a character string providing the name of the varable, in the server, to perform unique upon

-
newobj
+
newobj

a character string that provides the name for the output object that is stored on the data servers. Default unique.newobj.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.unique returns the vector of unique R objects which are written to the server-side.

+

ds.unique returns the vector of unique R objects which are written to the server-side.

Details

@@ -82,7 +82,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
   # connecting to the Opal servers
 
   require('DSI')
@@ -111,7 +111,7 @@ 
Examples

 
   # Clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -126,15 +126,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.var.html b/docs/reference/ds.var.html index bfbc7f56..030dc4cd 100644 --- a/docs/reference/ds.var.html +++ b/docs/reference/ds.var.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Computes server-side vector variance

- +
@@ -49,70 +49,52 @@

Computes server-side vector variance

Arguments

-
x
+ + +
x

a character specifying the name of a numerical vector.

-
type
+
type

a character string that represents the type of analysis to carry out. This can be set as 'combine', 'combined', 'combines', 'split', 'splits', 's', -'both' or 'b'. +'both' or 'b'. For more information see Details.

-
checks
+
checks

logical. If TRUE optional checks of model -components will be undertaken. Default is FALSE to save time. +components will be undertaken. Default is FALSE to save time. It is suggested that checks should only be undertaken once the function call has failed.

-
datasources
-

a list of DSConnection-class +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Value

- - -

ds.var returns to the client-side a list including:

- - -

-

Variance.by.Study: estimated variance, Nmissing

- - -

(number of missing observations), Nvalid (number of valid observations) and -Ntotal (sum of missing and valid observations) -separately for each study (if type = split or type = both).

- - -

Global.Variance: estimated variance, Nmissing, Nvalid and Ntotal

- - -

across all studies combined (if type = combine or type = both).

- - -

Nstudies: number of studies being analysed.

- - -

ValidityMessage: indicates if the analysis was possible.

- - +

ds.var returns to the client-side a list including:

+

Variance.by.Study: estimated variance, Nmissing +(number of missing observations), Nvalid (number of valid observations) and +Ntotal (sum of missing and valid observations) +separately for each study (if type = split or type = both).
Global.Variance: estimated variance, Nmissing, Nvalid and Ntotal +across all studies combined (if type = combine or type = both).
Nstudies: number of studies being analysed.
ValidityMessage: indicates if the analysis was possible.

Details

This function is similar to the R function var.

The function can carry out 3 types of analysis depending on the argument type:
-(1) If type is set to 'combine', 'combined', +(1) If type is set to 'combine', 'combined', 'combines' or 'c', a global variance is calculated.
(2) If type is set to 'split', 'splits' or 's', the variance is calculated separately for each study.
-(3) If type is set to 'both' or 'b', +(3) If type is set to 'both' or 'b', both sets of outputs are produced.

Server function called: varDS

@@ -123,7 +105,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -159,7 +141,7 @@ 
Examples

              
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -175,15 +157,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/ds.vectorCalc.html b/docs/reference/ds.vectorCalc.html index bb8eb5ab..43e81df9 100644 --- a/docs/reference/ds.vectorCalc.html +++ b/docs/reference/ds.vectorCalc.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Performs a mathematical operation on two or more vectors

- +
@@ -51,29 +51,29 @@

Performs a mathematical operation on two or more vectors

Arguments

-
x
+ + +
x

a vector of characters, the names of the vectors to include in the operation.

-
calc
+
calc

a character, a symbol that indicates the mathematical operation to carry out: '+' for addition, '/' for division, *' for multiplication and '-' for subtraction.

-
newobj
+
newobj

the name of the output object. By default the name is 'vectorcalc.newobj'.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

Value

- - -

no data are returned to user, the output vector is stored on the server side.

+

no data are returned to user, the output vector is stored on the server side.

Details

@@ -92,7 +92,7 @@

Author

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
   # load the file that contains the login details
   data(logindata)
@@ -108,7 +108,7 @@ 
Examples

   # clear the Datashield R sessions and logout
   datashield.logout(conns)
 
-}
+} # }
@@ -124,15 +124,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/extract.html b/docs/reference/extract.html index 9e302939..eacb3fcf 100644 --- a/docs/reference/extract.html +++ b/docs/reference/extract.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Splits character by '$' and returns the single characters

- +
@@ -49,15 +49,15 @@

Splits character by '$' and returns the single characters

Arguments

-
input
+ + +
input

a vector or a list of characters

Value

- - -

a vector of characters

+

a vector of characters

Details

@@ -76,15 +76,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/getPooledMean.html b/docs/reference/getPooledMean.html index a0242324..4986842d 100644 --- a/docs/reference/getPooledMean.html +++ b/docs/reference/getPooledMean.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Gets a pooled statistical mean

- +
@@ -49,20 +49,20 @@

Gets a pooled statistical mean

Arguments

-
dtsources
+ + +
dtsources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

-
x
+
x

a character, the name of a numeric vector

Value

- - -

a pooled mean

+

a pooled mean

Details

@@ -83,15 +83,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/getPooledVar.html b/docs/reference/getPooledVar.html index 3f9718a7..0286fd8e 100644 --- a/docs/reference/getPooledVar.html +++ b/docs/reference/getPooledVar.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Gets a pooled variance

- +
@@ -49,20 +49,20 @@

Gets a pooled variance

Arguments

-
dtsources
+ + +
dtsources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

-
x
+
x

a character, the name of a numeric vector

Value

- - -

a pooled variance

+

a pooled variance

Details

@@ -83,15 +83,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/glmChecks.html b/docs/reference/glmChecks.html index 36e7f1a2..5a944f9e 100644 --- a/docs/reference/glmChecks.html +++ b/docs/reference/glmChecks.html @@ -4,7 +4,7 @@ - +
@@ -30,13 +30,13 @@
- +

Checks if the elements in the glm model have the right characteristics

- +
@@ -51,35 +51,35 @@

Checks if the elements in the glm model have the right characteristics

Arguments

-
formula
+ + +
formula

a character, a regression formula given as a string character

-
data
+
data

a character, the name of an optional data frame containing the variables in in the formula.

-
offset
+
offset

null or a numreric vector that can be used to specify an a priori known component to be included in the linear predictor during fitting.

-
weights
+
weights

a character, the name of an optional vector of 'prior weights' to be used in the fitting process. Should be NULL or a numeric vector.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

Value

- - -

an integer 0 if check was passed and 1 if failed

+

an integer 0 if check was passed and 1 if failed

Details

@@ -104,15 +104,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 3a2ee0bc..0ceeb7bf 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • dsBaseClientPackage index • dsBaseClient - +
@@ -29,7 +29,7 @@
- +
@@ -538,15 +538,15 @@

All functions
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/isAssigned.html b/docs/reference/isAssigned.html index ed8f6b9c..b3d66e75 100644 --- a/docs/reference/isAssigned.html +++ b/docs/reference/isAssigned.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Checks an object has been generated on the server side

- +
@@ -49,20 +49,20 @@

Checks an object has been generated on the server side

Arguments

-
datasources
+ + +
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

-
newobj
+
newobj

a character, the name the object to look for.

Value

- - -

nothing is return but the process is stopped if +

nothing is return but the process is stopped if the object was not generated in any one server.

@@ -84,15 +84,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/isDefined.html b/docs/reference/isDefined.html index e97303c7..54184020 100644 --- a/docs/reference/isDefined.html +++ b/docs/reference/isDefined.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Checks if the objects are defined in all studies

- +
@@ -49,17 +49,19 @@

Checks if the objects are defined in all studies

Arguments

-
datasources
-

a list of DSConnection-class objects obtained after login. + + +

datasources
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified, the default set of connections will be used: see datashield.connections_default.

-
obj
+
obj

a character vector, the name of the object(s) to look for.

-
error.message
+
error.message

a Boolean which specifies if the function should stop and return an error message when the input object is not defined in one or more studies or to return a list of TRUE/FALSE indicating in which studies the object is defined

@@ -67,9 +69,7 @@

Arguments

Value

- - -

returns an error message if error.message argument is set to TRUE (default) +

returns an error message if error.message argument is set to TRUE (default) and if the input object is not defined in one or more studies, or a Boolean value if error.message argument is set to FALSE.

@@ -95,15 +95,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/logical2int.html b/docs/reference/logical2int.html index 57c6fe54..ac52dac1 100644 --- a/docs/reference/logical2int.html +++ b/docs/reference/logical2int.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Turns a logical operator into an integer

- +
@@ -49,20 +49,20 @@

Turns a logical operator into an integer

Arguments

-
obj
+ + +
obj

a character, the logical parameter to turn into an integer

Value

- - -

an integer

+

an integer

Details

-

This function is called to turn a logical oprator given as a -character into an integer: '>' is turned into 1, '>=' into 2, '<' into 3, +

This function is called to turn a logical oprator given as a +character into an integer: '>' is turned into 1, '>=' into 2, '<' into 3, '<=' into 4, '==' into 5 and '!=' into 6.

@@ -78,15 +78,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/meanByClassHelper0a.html b/docs/reference/meanByClassHelper0a.html index 7a1be3e4..8d6cfebe 100644 --- a/docs/reference/meanByClassHelper0a.html +++ b/docs/reference/meanByClassHelper0a.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Computes the mean values of a numeric vector across a factor vector

- +
@@ -49,30 +49,30 @@

Computes the mean values of a numeric vector across a factor vector

Arguments

-
a
+ + +
a

a character, the name of a numeric vector.

-
b
+
b

a character, the name of a factor vector.

-
type
+
type

a character which represents the type of analysis to carry out. If type is set to 'combine', a pooled table of results is generated. If type is set to 'split', a table of results is genrated for each study.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

Value

- - -

a table or a list of tables that hold the length of the numeric variable and its mean +

a table or a list of tables that hold the length of the numeric variable and its mean and standard deviation in each subgroup (subset).

@@ -97,15 +97,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/meanByClassHelper0b.html b/docs/reference/meanByClassHelper0b.html index 8489c53d..f35054ef 100644 --- a/docs/reference/meanByClassHelper0b.html +++ b/docs/reference/meanByClassHelper0b.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Runs the computation if variables are within a table structure

- +
@@ -49,34 +49,34 @@

Runs the computation if variables are within a table structure

Arguments

-
x
+ + +
x

a character, the name of the dataset to get the subsets from.

-
outvar
+
outvar

a character vector, the names of the continuous variables

-
covar
+
covar

a character vector, the names of up to 3 categorical variables

-
type
+
type

a character which represents the type of analysis to carry out. If type is set to 'combine', a pooled table of results is generated. If type is set to 'split', a table of results is genrated for each study.

-
datasources
+
datasources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

Value

- - -

a table or a list of tables that hold the length of the numeric variable(s) and their mean +

a table or a list of tables that hold the length of the numeric variable(s) and their mean and standard deviation in each subgroup (subset).

@@ -101,15 +101,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/meanByClassHelper1.html b/docs/reference/meanByClassHelper1.html index a5f59892..810f46d7 100644 --- a/docs/reference/meanByClassHelper1.html +++ b/docs/reference/meanByClassHelper1.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Generates subset tables

- +
@@ -49,28 +49,28 @@

Generates subset tables

Arguments

-
dtsource
+ + +
dtsource

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

-
tables
+
tables

a character vector, the tables to breakdown

-
variable
+
variable

a character, the variable to subset on

-
categories
+
categories

a character vector, the classes in the variables to subset on

Value

- - -

a character the names of the new subset tables.

+

a character the names of the new subset tables.

Details

@@ -94,15 +94,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/meanByClassHelper2.html b/docs/reference/meanByClassHelper2.html index 36275c16..7540f66f 100644 --- a/docs/reference/meanByClassHelper2.html +++ b/docs/reference/meanByClassHelper2.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Generates a table for pooled results

- +
@@ -49,28 +49,28 @@

Generates a table for pooled results

Arguments

-
dtsources
+ + +
dtsources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

-
tablenames
+
tablenames

a character vector, the name of the subset tables

-
variables
+
variables

a character vector, the names of the continuous variables to computes a mean for.

-
invalidrecorder
+
invalidrecorder

a list, holds informations about invalid subsets in each study.

Value

- - -

a matrix, a table which contains the length, mean and standard deviation of each of the +

a matrix, a table which contains the length, mean and standard deviation of each of the specified 'variables' in each subset table.

@@ -95,15 +95,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/meanByClassHelper3.html b/docs/reference/meanByClassHelper3.html index 318a6aad..c5eb79f5 100644 --- a/docs/reference/meanByClassHelper3.html +++ b/docs/reference/meanByClassHelper3.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Generates results tables for each study separately

- +
@@ -49,28 +49,28 @@

Generates results tables for each study separately

Arguments

-
dtsources
+ + +
dtsources

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

-
tablenames
+
tablenames

a character vector, the name of the subset tables

-
variables
+
variables

a character vector, the names of the continuous variables to computes a mean for.

-
invalidrecorder
+
invalidrecorder

a list, holds informations about invalid subsets in each study

Value

- - -

a list which one results table for each study.

+

a list which one results table for each study.

Details

@@ -94,15 +94,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/meanByClassHelper4.html b/docs/reference/meanByClassHelper4.html index 7ac0ab41..ef479e86 100644 --- a/docs/reference/meanByClassHelper4.html +++ b/docs/reference/meanByClassHelper4.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Gets the subset tables out of the list (i.e. unlist)

- +
@@ -55,32 +55,32 @@

Gets the subset tables out of the list (i.e. unlist)

Arguments

-
dtsource
+ + +
dtsource

a list of DSConnection-class objects obtained after login. If the <datasources> the default set of connections will be used: see datashield.connections_default.

-
alist
+
alist

the name of the list that holds the final subset tables

-
initialtable
+
initialtable

a character the name of the table that the subset were generated from

-
variable
+
variable

a character, the variable to subset on

-
categories
+
categories

a character vector, the classes in the variables to subset on

Value

- - -

the 'loose' subset tables are stored on the server side

+

the 'loose' subset tables are stored on the server side

Details

@@ -104,15 +104,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/rowPercent.html b/docs/reference/rowPercent.html index 1fdb136c..da5df3fd 100644 --- a/docs/reference/rowPercent.html +++ b/docs/reference/rowPercent.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Produces row percentages

- +
@@ -49,15 +49,15 @@

Produces row percentages

Arguments

-
dataframe
+ + +
dataframe

a data frame

Value

- - -

a data frame

+

a data frame

Details

@@ -80,15 +80,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/reference/subsetHelper.html b/docs/reference/subsetHelper.html index 5f752cd8..33f96c87 100644 --- a/docs/reference/subsetHelper.html +++ b/docs/reference/subsetHelper.html @@ -3,7 +3,7 @@ - +
@@ -29,13 +29,13 @@
- +

Ensures that the requested subset is not larger than the original object

- +
@@ -49,30 +49,30 @@

Ensures that the requested subset is not larger than the original object

Arguments

-
dts
-

a list of DSConnection-class + + +

dts
+

a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

-
data
+
data

a character string specifying the name of the data frame or the factor vector and the range of the subset.

-
rs
+
rs

a vector of two integers specifying the indices of the rows de extract.

-
cs
+
cs

a vector of two integers or one or more characters.

Value

- - -

subsetHelper returns a message or the class of the object if the +

subsetHelper returns a message or the class of the object if the object has the same class in all studies.

@@ -85,7 +85,7 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
  ## Version 6, for version 5 see the Wiki
   
@@ -119,7 +119,7 @@ 
Examples

                       
   # clear the Datashield R sessions and logout
   datashield.logout(connections)
-}
+} # }
@@ -135,15 +135,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 99412924..e67315a8 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,438 +1,148 @@ - - - - /404.html - - - /LICENSE.html - - - /authors.html - - - /index.html - - - /reference/checkClass.html - - - /reference/colPercent.html - - - /reference/ds.Boole.html - - - /reference/ds.abs.html - - - /reference/ds.asCharacter.html - - - /reference/ds.asDataMatrix.html - - - /reference/ds.asFactor.html - - - /reference/ds.asFactorSimple.html - - - /reference/ds.asInteger.html - - - /reference/ds.asList.html - - - /reference/ds.asLogical.html - - - /reference/ds.asMatrix.html - - - /reference/ds.asNumeric.html - - - /reference/ds.assign.html - - - /reference/ds.auc.html - - - /reference/ds.boxPlot.html - - - /reference/ds.boxPlotGG.html - - - /reference/ds.boxPlotGG_data_Treatment.html - - - /reference/ds.boxPlotGG_data_Treatment_numeric.html - - - /reference/ds.boxPlotGG_numeric.html - - - /reference/ds.boxPlotGG_table.html - 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