diff --git a/.Rbuildignore b/.Rbuildignore index dc588623..8f27db2f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,8 +17,8 @@ ^R/secure.global.ranking.md$ ^_pkgdown\.yml$ ^docs$ -^dsBase_6.3.1.tar.gz$ -^dsBase_6.3.1-permissive.tar.gz$ +^dsBase_6.3.2.tar.gz$ +^dsBase_6.3.2-permissive.tar.gz$ ^dsDanger_6.3.1.tar.gz$ ^\.circleci$ ^\.circleci/config\.yml$ diff --git a/.circleci/config.yml b/.circleci/config.yml index cff6767a..c96e0cce 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -5,7 +5,8 @@ version: 2.1 jobs: dsbaseclient: docker: - - image: cimg/base:current +# - image: cimg/base:current + - image: cimg/base:2024.11 resource_class: small steps: - checkout @@ -18,6 +19,10 @@ jobs: echo " Tag: " $CIRCLE_TAG - run: command: | + sudo apt-get install --no-install-recommends software-properties-common dirmngr + wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc + sudo add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" + sudo apt-get update -y sudo apt-get install -y r-base-core cmake - run: @@ -33,6 +38,9 @@ jobs: sudo apt-get install -y libjpeg-dev - run: command: | + sudo Rscript -e "install.packages('devtools', dependencies=TRUE)" + sudo Rscript -e "install.packages('covr', dependencies=TRUE)" + sudo Rscript -e "install.packages('fields', dependencies=TRUE)" sudo Rscript -e "install.packages('metafor', dependencies=TRUE)" sudo Rscript -e "install.packages('meta', dependencies=TRUE)" @@ -42,6 +50,15 @@ jobs: sudo Rscript -e "install.packages('panelaggregation', dependencies=TRUE)" sudo Rscript -e "install.packages('methods', dependencies=TRUE)" sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)" + + sudo Rscript -e "install.packages('DSI', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSOpal', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)" + sudo Rscript -e "install.packages('MolgenisAuth', dependencies=TRUE)" + sudo Rscript -e "install.packages('MolgenisArmadillo', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSMolgenisArmadillo', dependencies=TRUE)" + sudo Rscript -e "install.packages('DescTools', dependencies=TRUE)" + sudo Rscript -e "install.packages('e1071', dependencies=TRUE)" - run: command: | sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'", quiet=FALSE)' diff --git a/DESCRIPTION b/DESCRIPTION index 60af1d1c..815e10df 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,42 @@ Package: dsBaseClient Title: DataSHIELD Client Functions -Version: 6.3.1 -Author: DataSHIELD Developers -Maintainer: DataSHIELD Developers +Version: 6.3.2 +Authors@R: c(person(given = "Paul", + family = "Burton", + role = c("aut")), + person(given = "Rebecca", + family = "Wilson", + role = c("aut")), + person(given = "Olly", + family = "Butters", + role = c("aut")), + person(given = "Patricia", + family = "Ryser-Welch", + role = c("aut")), + person(given = "Alex", + family = "Westerberg", + role = c("aut")), + person(given = "Leire", + family = "Abarrategui", + role = c("aut")), + person(given = "Roberto", + family = "Villegas-Diaz", + role = c("aut"), + comment = c(ORCID = "0000-0001-5036-8661")), + person(given = "Demetris", + family = "Avraam", + role = c("aut"), + comment = c(ORCID = "0000-0001-8908-2441")), + person(given = "Yannick", + family = "Marcon", + role = c("aut"), + email = "yannick.marcon@obiba.org", + comment = c(ORCID = "0000-0003-0138-2023")), + person(given = "Stuart", + family = "Wheater", + role = c("aut", "cre"), + email = "stuart.wheater@arjuna.com", + comment = c(ORCID = "0009-0003-2419-1964"))) Description: DataSHIELD client functions for the client side. License: GPL-3 Depends: @@ -19,6 +53,14 @@ Imports: methods, dplyr Suggests: - testthat + lme4, + httr, + tibble, + testthat, + e1071, + DescTools, + DSOpal, + DSMolgenisArmadillo, + DSLite RoxygenNote: 7.3.2 Encoding: UTF-8 diff --git a/R/checkClass.R b/R/checkClass.R index 5cf86eac..779eca1e 100644 --- a/R/checkClass.R +++ b/R/checkClass.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details In DataSHIELD an object included in analysis must be of the same type in all #' the collaborating studies. If that is not the case the process is stopped -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param obj a string character, the name of the object to check for. #' @keywords internal #' @return a message or the class of the object if the object has the same class in all studies. diff --git a/R/ds.Boole.R b/R/ds.Boole.R index 1c5cf4f4..252346bf 100644 --- a/R/ds.Boole.R +++ b/R/ds.Boole.R @@ -34,9 +34,9 @@ #' Default \code{'NA'}. For more information see details. #' @param newobj a character string that provides the name for the output #' object that is stored on the data servers. Default \code{boole.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.Boole} returns the object specified by the \code{newobj} argument #' which is written to the server-side. Also, two validity messages are returned #' to the client-side indicating the name of the \code{newobj} which diff --git a/R/ds.abs.R b/R/ds.abs.R index 5b57b0ed..41c20455 100644 --- a/R/ds.abs.R +++ b/R/ds.abs.R @@ -10,9 +10,9 @@ #' @param x a character string providing the name of a numeric or an integer vector. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default name is set to \code{abs.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.abs} assigns a vector for each study that includes the absolute values of #' the input numeric or integer vector specified in the argument \code{x}. The created vectors #' are stored in the servers. diff --git a/R/ds.asCharacter.R b/R/ds.asCharacter.R index 72acbd45..c0bd4ce0 100644 --- a/R/ds.asCharacter.R +++ b/R/ds.asCharacter.R @@ -9,9 +9,9 @@ #' character. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{ascharacter.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{newobj} which has been created in each data source and if diff --git a/R/ds.asDataMatrix.R b/R/ds.asDataMatrix.R index 83b1037f..7b4833bb 100644 --- a/R/ds.asDataMatrix.R +++ b/R/ds.asDataMatrix.R @@ -8,9 +8,9 @@ #' a matrix. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{asdatamatrix.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.asFactor.R b/R/ds.asFactor.R index 7d6246d5..476f00f8 100644 --- a/R/ds.asFactor.R +++ b/R/ds.asFactor.R @@ -130,9 +130,9 @@ #' to be used in the creation of the matrix with dummy variables. #' If the \code{fixed.dummy.vars} is set to FALSE then any value of the baseline level is not taken #' into account. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.asFactorSimple.R b/R/ds.asFactorSimple.R index dce56a8a..313f7b40 100644 --- a/R/ds.asFactorSimple.R +++ b/R/ds.asFactorSimple.R @@ -14,9 +14,9 @@ #' the name of the variable to be converted to a factor. #' @param newobj.name a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{asfactor.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return 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(). @@ -109,4 +109,4 @@ return(list(return.info=return.info,return.message=return.message)) # } -#ds.asFactorSimple \ No newline at end of file +#ds.asFactorSimple diff --git a/R/ds.asInteger.R b/R/ds.asInteger.R index 139ceb6c..9b3b1a39 100644 --- a/R/ds.asInteger.R +++ b/R/ds.asInteger.R @@ -22,9 +22,9 @@ #' an integer. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{asinteger.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{newobj} which diff --git a/R/ds.asList.R b/R/ds.asList.R index 5383c506..d7366878 100644 --- a/R/ds.asList.R +++ b/R/ds.asList.R @@ -9,9 +9,9 @@ #' a list. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{aslist.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{newobj} which has been created in each data diff --git a/R/ds.asLogical.R b/R/ds.asLogical.R index de2920bf..2ddc33cf 100644 --- a/R/ds.asLogical.R +++ b/R/ds.asLogical.R @@ -8,9 +8,9 @@ #' input object to be coerced to a logical. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{aslogical.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{newobj} which diff --git a/R/ds.asMatrix.R b/R/ds.asMatrix.R index 04186109..1c5b0ced 100644 --- a/R/ds.asMatrix.R +++ b/R/ds.asMatrix.R @@ -11,9 +11,9 @@ #' a matrix. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{asmatrix.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{newobj} which diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R index 0c4e9a03..7b4da435 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -22,9 +22,9 @@ #' a numeric. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{asnumeric.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{newobj} which diff --git a/R/ds.assign.R b/R/ds.assign.R index 7c701726..25b71c74 100644 --- a/R/ds.assign.R +++ b/R/ds.assign.R @@ -10,9 +10,9 @@ #' @param toAssign a character string providing the object to assign. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{assign.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.assign} returns the R object assigned to a name #' that is written to the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.auc.R b/R/ds.auc.R index b971651a..ebfc5fc3 100644 --- a/R/ds.auc.R +++ b/R/ds.auc.R @@ -6,9 +6,9 @@ #' @param pred the name of the vector of the predicted values #' @param y the name of the outcome variable. Note that this variable should include #' the complete cases that are used in the regression model. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return returns the AUC and its standard error #' @author Demetris Avraam for DataSHIELD Development Team #' @export @@ -44,4 +44,4 @@ ds.auc <- function(pred=NULL, y=NULL, datasources=NULL){ return(output) -} \ No newline at end of file +} diff --git a/R/ds.boxPlot.R b/R/ds.boxPlot.R index ad2de1d8..5f113388 100644 --- a/R/ds.boxPlot.R +++ b/R/ds.boxPlot.R @@ -12,7 +12,7 @@ #' @param ylabel \code{caracter} (default \code{"y axis"}) Label to put on the y axis of the plot #' @param type \code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server #' \code{"split"}) -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return \code{ggplot} object #' @export diff --git a/R/ds.boxPlotGG.R b/R/ds.boxPlotGG.R index d35caba3..156e5714 100644 --- a/R/ds.boxPlotGG.R +++ b/R/ds.boxPlotGG.R @@ -17,7 +17,7 @@ #' @param ylabel \code{caracter} (default \code{"y axis"}) Label to put on the y axis of the plot #' @param type \code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server #' \code{"split"}) -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return \code{ggplot} object @@ -146,4 +146,4 @@ ds.boxPlotGG <- function(x, group = NULL, group2 = NULL, xlabel = "x axis", ylab return(plt) -} \ No newline at end of file +} diff --git a/R/ds.boxPlotGG_data_Treatment.R b/R/ds.boxPlotGG_data_Treatment.R index f27a9110..40f89730 100644 --- a/R/ds.boxPlotGG_data_Treatment.R +++ b/R/ds.boxPlotGG_data_Treatment.R @@ -6,7 +6,7 @@ #' @param variables \code{character vector} Name of the column(s) of the data frame to include on the boxplot #' @param group \code{character} (default \code{NULL}) Name of the first grouping variable. #' @param group2 \code{character} (default \code{NULL}) Name of the second grouping variable. -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return Does not return nothing, it creates the table \code{"boxPlotRawData"} on the server arranged to be passed to the #' ggplot boxplot function. Structure of the created table: \cr @@ -35,4 +35,4 @@ ds.boxPlotGG_data_Treatment <- function(table, variables, group = NULL, group2 = DSI::datashield.assign.expr(datasources, "boxPlotRawData", as.symbol(cally)) -} \ No newline at end of file +} diff --git a/R/ds.boxPlotGG_data_Treatment_numeric.R b/R/ds.boxPlotGG_data_Treatment_numeric.R index 04b33e04..0cf4b383 100644 --- a/R/ds.boxPlotGG_data_Treatment_numeric.R +++ b/R/ds.boxPlotGG_data_Treatment_numeric.R @@ -3,7 +3,7 @@ #' @description Internal function #' #' @param vector \code{character} Name of the table on the server side that holds the information to be plotted later -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return Does not return nothing, it creates the table \code{"boxPlotRawDataNumeric"} on the server arranged to be passed to the #' ggplot boxplot function. Structure of the created table: \cr diff --git a/R/ds.boxPlotGG_numeric.R b/R/ds.boxPlotGG_numeric.R index 7300c128..c1996628 100644 --- a/R/ds.boxPlotGG_numeric.R +++ b/R/ds.boxPlotGG_numeric.R @@ -5,7 +5,7 @@ #' @param ylabel \code{caracter} (default \code{"y axis"}) Label to put on the y axis of the plot #' @param type \code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server #' \code{"split"}) -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return \code{ggplot} object diff --git a/R/ds.boxPlotGG_table.R b/R/ds.boxPlotGG_table.R index fe6c158e..ebe9eb4c 100644 --- a/R/ds.boxPlotGG_table.R +++ b/R/ds.boxPlotGG_table.R @@ -10,7 +10,7 @@ #' @param ylabel \code{caracter} (default \code{"y axis"}) Label to put on the y axis of the plot #' @param type \code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server #' \code{"split"}) -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return \code{ggplot} object diff --git a/R/ds.bp_standards.R b/R/ds.bp_standards.R index 49374497..ae76c54c 100644 --- a/R/ds.bp_standards.R +++ b/R/ds.bp_standards.R @@ -16,9 +16,9 @@ #' blood pressure. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default name is set to \code{bp.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return 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. @@ -76,4 +76,4 @@ ds.bp_standards <- function(sex=NULL, age=NULL, height=NULL, bp=NULL, systolic=T cally <- call('bp_standardsDS', sex, age, height, bp, systolic) DSI::datashield.assign(datasources, newobj, cally) -} \ No newline at end of file +} diff --git a/R/ds.c.R b/R/ds.c.R index 01257aec..2093ac01 100644 --- a/R/ds.c.R +++ b/R/ds.c.R @@ -10,9 +10,9 @@ #' @param x a vector of character string providing the names of the objects to be combined. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{c.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.c} returns the vector of concatenating R #' objects which are written to the server-side. #' @examples diff --git a/R/ds.cbind.R b/R/ds.cbind.R index fdd1b34b..d943e017 100644 --- a/R/ds.cbind.R +++ b/R/ds.cbind.R @@ -32,9 +32,9 @@ #' For more information see \strong{Details}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Defaults \code{cbind.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default FALSE. #' @return \code{ds.cbind} returns a data frame combining the columns of the R diff --git a/R/ds.changeRefGroup.R b/R/ds.changeRefGroup.R index 1b8ad556..4bd5080a 100644 --- a/R/ds.changeRefGroup.R +++ b/R/ds.changeRefGroup.R @@ -22,9 +22,9 @@ #' @param 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). -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.changeRefGroup} returns a new vector with the specified level as a reference #' which is written to the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.class.R b/R/ds.class.R index 285b4045..036848ad 100644 --- a/R/ds.class.R +++ b/R/ds.class.R @@ -6,9 +6,9 @@ #' #' Server function called: \code{classDS} #' @param x a character string providing the name of the input R object. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.class} returns the type of the R object. #' @author DataSHIELD Development Team #' @seealso \code{\link{ds.exists}} to verify if an object is defined (exists) on the server-side. diff --git a/R/ds.colnames.R b/R/ds.colnames.R index 5950d99b..a4b98b1a 100644 --- a/R/ds.colnames.R +++ b/R/ds.colnames.R @@ -6,9 +6,9 @@ #' #' Server function called: \code{colnamesDS} #' @param x a character string providing the name of the input data frame or matrix. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.colnames} returns the column names of #' the specified server-side data frame or matrix. #' @author DataSHIELD Development Team diff --git a/R/ds.completeCases.R b/R/ds.completeCases.R index fed43208..ed95bf6d 100644 --- a/R/ds.completeCases.R +++ b/R/ds.completeCases.R @@ -14,9 +14,9 @@ #' 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" -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified, the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.contourPlot.R b/R/ds.contourPlot.R index 7973c1d1..4e195e48 100644 --- a/R/ds.contourPlot.R +++ b/R/ds.contourPlot.R @@ -50,9 +50,9 @@ #' see details. #' @param noise the percentage of the initial variance that is used as the variance of the embedded #' noise if the argument \code{method} is set to \code{'probabilistic'}. For more information see details. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.contourPlot} returns a contour plot to the client-side. #' @author DataSHIELD Development Team #' @examples diff --git a/R/ds.cor.R b/R/ds.cor.R index 1a5c86d6..53fb22db 100644 --- a/R/ds.cor.R +++ b/R/ds.cor.R @@ -27,9 +27,9 @@ #' Default NULL. #' @param type a character string that represents the type of analysis to carry out. #' This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. For more information see details. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.corTest.R b/R/ds.corTest.R index 7be1f992..38fffceb 100644 --- a/R/ds.corTest.R +++ b/R/ds.corTest.R @@ -19,9 +19,9 @@ #' This must be set to \code{'split'} or \code{'combine'}. Default is set to \code{'split'}. If #' \code{type} is set to "combine" then an approximated pooled correlation is estimated based on #' Fisher's z transformation. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.corTest} returns to the client-side the results of the correlation test. #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.cov.R b/R/ds.cov.R index 58aedc94..c67d2e13 100644 --- a/R/ds.cov.R +++ b/R/ds.cov.R @@ -35,9 +35,9 @@ #' \code{'pairwise.complete'}. Default \code{'pairwise.complete'}. For more information see details. #' @param type a character string that represents the type of analysis to carry out. #' This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. For more information see details. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{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 diff --git a/R/ds.dataFrame.R b/R/ds.dataFrame.R index e71c1daf..5837747c 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -32,9 +32,9 @@ #' are the same #' @param newobj a character string that provides the name for the output data frame #' that is stored on the data servers. Default \code{dataframe.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default is FALSE. #' @return \code{ds.dataFrame} returns the object specified by the \code{newobj} argument diff --git a/R/ds.dataFrameFill.R b/R/ds.dataFrameFill.R index eef95117..3de389b7 100644 --- a/R/ds.dataFrameFill.R +++ b/R/ds.dataFrameFill.R @@ -13,9 +13,9 @@ #' filled with extra columns of missing values. #' @param 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". -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.dataFrameFill} returns the object specified by the \code{newobj} argument which #' is written to the server-side. Also, two validity messages are returned to the #' client-side indicating the name of the \code{newobj} that has been created in each data source diff --git a/R/ds.dataFrameSort.R b/R/ds.dataFrameSort.R index d170dd87..de59d61e 100644 --- a/R/ds.dataFrameSort.R +++ b/R/ds.dataFrameSort.R @@ -33,9 +33,9 @@ #' @param newobj a character string that provides the name for the output data frame #' that is stored on the data servers. Default \code{dataframesort.newobj}. #' where \code{df.name} is the first argument of \code{ds.dataFrameSort()}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{newobj} which @@ -203,4 +203,4 @@ ds.dataFrameSort<-function(df.name=NULL, sort.key.name=NULL, sort.descending=FAL #END OF CHECK OBJECT CREATED CORRECTLY MODULE # ########################################################################################################### } -#ds.dataFrameSort \ No newline at end of file +#ds.dataFrameSort diff --git a/R/ds.dataFrameSubset.R b/R/ds.dataFrameSubset.R index 3b6dff97..46878520 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -28,9 +28,9 @@ #' If FALSE or NULL all rows with at least one missing values are removed from the subset. #' @param newobj a character string that provides the name for the output #' object that is stored on the data servers. Default \code{dataframesubset.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default FALSE. #' @return \code{ds.dataFrameSubset} returns diff --git a/R/ds.densityGrid.R b/R/ds.densityGrid.R index 33e1bb6d..b0766418 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -23,9 +23,9 @@ #' \code{'combine'}, a pooled grid density matrix is generated, #' instead if \code{type} is set to \code{'split'} #' one grid density matrix is generated. Default \code{'combine'}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.densityGrid} returns a grid density matrix. #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.dim.R b/R/ds.dim.R index 613bd984..4a6cd3a7 100644 --- a/R/ds.dim.R +++ b/R/ds.dim.R @@ -22,9 +22,9 @@ #' Default \code{'both'}. #' @param checks logical. If TRUE undertakes all DataSHIELD checks (time-consuming). #' Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. diff --git a/R/ds.elspline.R b/R/ds.elspline.R index 1fc4cffe..c4a2bbdd 100644 --- a/R/ds.elspline.R +++ b/R/ds.elspline.R @@ -17,9 +17,9 @@ #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{elspline.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the #' \code{newobj} argument (or its default name "elspline.newobj"), is assigned on the serverside. #' @author Demetris Avraam for DataSHIELD Development Team @@ -61,4 +61,4 @@ ds.elspline <- function(x, n, marginal = FALSE, names = NULL, newobj = NULL, dat calltext <- call("elsplineDS", x, n, marginal, names) DSI::datashield.assign(datasources, newobj, calltext) -} \ No newline at end of file +} diff --git a/R/ds.exists.R b/R/ds.exists.R index b6ef9e66..6dff8b4c 100644 --- a/R/ds.exists.R +++ b/R/ds.exists.R @@ -10,9 +10,9 @@ #' #' Server function called: \code{exists} #' @param x a character string providing the name of the object to look for. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.exists} returns a logical object. #' TRUE if the object is on the server-side and FALSE otherwise. #' @author DataSHIELD Development Team diff --git a/R/ds.exp.R b/R/ds.exp.R index 2fd9da3b..5bf325bd 100644 --- a/R/ds.exp.R +++ b/R/ds.exp.R @@ -9,9 +9,9 @@ #' @param x a character string providing the name of a numerical vector. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{exp.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.exp} returns a vector for each study of the exponential values for the numeric vector #' specified in the argument \code{x}. The created vectors are stored in the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.gamlss.R b/R/ds.gamlss.R index bd9d82f3..6a7622c7 100644 --- a/R/ds.gamlss.R +++ b/R/ds.gamlss.R @@ -64,9 +64,9 @@ #' only. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{gamlss_res}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return 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 diff --git a/R/ds.getWGSR.R b/R/ds.getWGSR.R index f883549a..ff4c60f5 100644 --- a/R/ds.getWGSR.R +++ b/R/ds.getWGSR.R @@ -52,9 +52,9 @@ #' by the formula $age_days=age_months*(365.25/12)$. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Defaults \code{getWGSR.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. #' @author Demetris Avraam for DataSHIELD Development Team diff --git a/R/ds.glm.R b/R/ds.glm.R index b96decd4..13cba2d9 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -17,7 +17,7 @@ #' #' Many GLMs can be fitted very simply using a formula such as: #' -#' \deqn{y~a+b+c+d} +#' \eqn{y~a+b+c+d} #' #' which simply means fit a GLM with \code{y} as the outcome variable and #' \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -26,7 +26,7 @@ #' Instead, if you need to fit a more complex #' model, for example: #' -#' \deqn{EVENT~1+TID+SEXF*AGE.60} +#' \eqn{EVENT~1+TID+SEXF*AGE.60} #' #' In the above model the outcome variable is \code{EVENT} #' and the covariates @@ -164,9 +164,9 @@ #' of parameter estimates is returned. Default FALSE. #' @param viewCor logical. If TRUE the correlation matrix of #' parameter estimates is returned. Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return Many of the elements of the output list returned by \code{ds.glm} are #' equivalent to those returned by the \code{glm()} function in native R. However, #' potentially disclosive elements diff --git a/R/ds.glmSLMA.R b/R/ds.glmSLMA.R index d3aa9167..7f3454bc 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -61,7 +61,7 @@ #' #' Many glms can be fitted very simply using a formula such as: #' -#' \deqn{y~a+b+c+d} +#' \eqn{y~a+b+c+d} #' #' which simply means fit a glm with \code{y} as the outcome variable and #' \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -70,7 +70,7 @@ #' Instead, if you need to fit a more complex #' model, for example: #' -#' \deqn{EVENT~1+TID+SEXF*AGE.60} +#' \eqn{EVENT~1+TID+SEXF*AGE.60} #' #' In the above model the outcome variable is \code{EVENT} #' and the covariates @@ -181,9 +181,9 @@ #' For more information see \strong{Details}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return The serverside aggregate functions \code{glmSLMADS1} and \code{glmSLMADS2} return #' output to the clientside, while the assign function \code{glmSLMADS.assign} simply writes #' the glm object to the serverside diff --git a/R/ds.glmerSLMA.R b/R/ds.glmerSLMA.R index efda6098..8bb8aa36 100644 --- a/R/ds.glmerSLMA.R +++ b/R/ds.glmerSLMA.R @@ -18,17 +18,17 @@ #' In \code{formula} most shortcut notation allowed by \code{glmer()} function is #' also allowed by \code{ds.glmerSLMA}. #' Many GLMEs can be fitted very simply using a formula like: -#' \deqn{y~a+b+(1|c)} +#' \eqn{y~a+b+(1|c)} #' which simply means fit an GLME with \code{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), \code{a} and \code{b} #' as fixed effects, and \code{c} as a random effect or grouping factor. #' #' It is also possible to fit models with random slopes by specifying a model such as -#' \deqn{y~a+b+(1+b|c)} +#' \eqn{y~a+b+(1+b|c)} #' where the effect of \code{b} can vary randomly between groups defined by \code{c}. #' Implicit nesting can be specified with formulas such as: \eqn{y~a+b+(1|c/d)} -#' or \eqn{y~a+b+(1|c)+(1|c:d)}. +#' or \eqn{y~a+b+(1|c)+(1|c:d)}. #' #' #' The \code{dataName} argument avoids you having to specify the name of the @@ -90,9 +90,9 @@ #' that contains all of the variables in the GLME formula. For more information see \strong{Details}. #' @param checks logical. If TRUE \code{ds.glmerSLMA} checks the structural integrity #' of the model. Default FALSE. For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param 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 \code{"binomial"} or \code{"poisson"}. diff --git a/R/ds.heatmapPlot.R b/R/ds.heatmapPlot.R index e2d656c1..262b1d70 100644 --- a/R/ds.heatmapPlot.R +++ b/R/ds.heatmapPlot.R @@ -82,9 +82,9 @@ #' noise if the argument \code{method} is set to \code{'probabilistic'}. #' Default \code{noise} value is \code{0.25}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.heatmapPlot} returns to the client-side a heat map plot and a message specifying #' the number of invalid cells in each study. #' @author DataSHIELD Development Team diff --git a/R/ds.hetcor.R b/R/ds.hetcor.R index 1b0e77f6..2b29be24 100644 --- a/R/ds.hetcor.R +++ b/R/ds.hetcor.R @@ -17,9 +17,9 @@ #' nearPD directly. #' @param 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. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return 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 @@ -53,4 +53,4 @@ ds.hetcor <- function(data=NULL, ML=TRUE, std.err=TRUE, bins=4, pd=TRUE, use="co return(output) -} \ No newline at end of file +} diff --git a/R/ds.histogram.R b/R/ds.histogram.R index 5b497758..0f5357b7 100644 --- a/R/ds.histogram.R +++ b/R/ds.histogram.R @@ -79,9 +79,9 @@ #' plot. The \code{vertical.axis} argument can be set as \code{'Frequency'} or \code{'Density'}. #' Default \code{'Frequency'}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return one or more histogram objects and plots depending on the argument \code{type} #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.igb_standards.R b/R/ds.igb_standards.R index c3d74f40..fb7953f1 100644 --- a/R/ds.igb_standards.R +++ b/R/ds.igb_standards.R @@ -15,9 +15,9 @@ #' "igb_zscore2value", "igb_value2zscore" (default), "igb_value2centile". #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default name is set to \code{igb.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @note 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 @@ -82,4 +82,4 @@ ds.igb_standards <- function(gagebrth=NULL, z=0, p=50, val=NULL, var=NULL, sex=N cally <- call('igb_standardsDS', gagebrth, z, p, val, var, sex, fun) DSI::datashield.assign(datasources, newobj, cally) -} \ No newline at end of file +} diff --git a/R/ds.isNA.R b/R/ds.isNA.R index 28ff808e..1d84577f 100644 --- a/R/ds.isNA.R +++ b/R/ds.isNA.R @@ -8,9 +8,9 @@ #' #' Server function called: \code{isNaDS} #' @param x a character string specifying the name of the vector to check. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.isNA} returns a boolean. If it is TRUE the vector is empty #' (all values are NA), FALSE otherwise. #' @author DataSHIELD Development Team diff --git a/R/ds.isValid.R b/R/ds.isValid.R index 34a94223..e43b61b1 100644 --- a/R/ds.isValid.R +++ b/R/ds.isValid.R @@ -10,9 +10,9 @@ #' #' Server function called: \code{isValidDS} #' @param x a character string specifying the name of a vector, dataframe or matrix. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.isValid} returns a boolean. If it is TRUE input object is valid, FALSE otherwise. #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.kurtosis.R b/R/ds.kurtosis.R index c262201b..974682bb 100644 --- a/R/ds.kurtosis.R +++ b/R/ds.kurtosis.R @@ -17,9 +17,9 @@ #' if \code{type} is set to 'split', 'splits' or 's', the kurtosis is returned separately for each study. #' if \code{type} is set to 'both' or 'b', both sets of outputs are produced. #' The default value is set to 'both'. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return a matrix showing the kurtosis of the input numeric variable, the number of valid observations and #' the validity message. #' @author Demetris Avraam, for DataSHIELD Development Team diff --git a/R/ds.length.R b/R/ds.length.R index a288de72..83cb5cae 100644 --- a/R/ds.length.R +++ b/R/ds.length.R @@ -17,9 +17,9 @@ #' @param 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. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. #' @author DataSHIELD Development Team diff --git a/R/ds.levels.R b/R/ds.levels.R index 1943ea0c..b32a5d1c 100644 --- a/R/ds.levels.R +++ b/R/ds.levels.R @@ -6,9 +6,9 @@ #' @details #' Server function called: \code{levelsDS} #' @param x a character string specifying the name of a factor variable. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.levels} returns to the client-side the levels of a factor #' class variable stored in the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.lexis.R b/R/ds.lexis.R index d692a65d..665a29ed 100644 --- a/R/ds.lexis.R +++ b/R/ds.lexis.R @@ -127,9 +127,9 @@ #' variables to include in the final expanded table. For more information see \strong{Details}. #' @param expandDF a character string denoting the name of the new data frame containing the #' expanded data set. Default \code{lexis.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.lexis} returns to the server-side a data frame for each study with #' the expanded version of the input table. #' diff --git a/R/ds.list.R b/R/ds.list.R index 239399db..b0847703 100644 --- a/R/ds.list.R +++ b/R/ds.list.R @@ -8,9 +8,9 @@ #' @param x a character string specifying the names of the objects to coerce into a list. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{list.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.list} returns a list of objects for each study that is stored on the server-side. #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.listDisclosureSettings.R b/R/ds.listDisclosureSettings.R index ec4546bb..33c73875 100644 --- a/R/ds.listDisclosureSettings.R +++ b/R/ds.listDisclosureSettings.R @@ -51,9 +51,9 @@ #' disclosure. #' #' Server function called: \code{listDisclosureSettingsDS} -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.listDisclosureSettings} returns a list containing the current settings of the #' \code{nfilters} in each study specified. #' @author DataSHIELD Development Team diff --git a/R/ds.listServersideFunctions.R b/R/ds.listServersideFunctions.R index fb5128a2..97188b28 100644 --- a/R/ds.listServersideFunctions.R +++ b/R/ds.listServersideFunctions.R @@ -1,6 +1,6 @@ #' @title Lists server-side functions #' @description Lists all current server-side functions -#' @details Uses \code{\link{datashield.methods}} function from \code{DSI} package to list all +#' @details Uses \code{\link[DSI]{datashield.methods}} function from \code{DSI} package to list all #' assign and aggregate functions on the available data repository servers. #' The only choice of arguments is in \code{datasources}; i.e. which studies to interrogate. #' Once the studies have @@ -8,9 +8,9 @@ #' of these studies and then all aggregate functions for all of them. #' #' This function does not call any server-side function. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. diff --git a/R/ds.lmerSLMA.R b/R/ds.lmerSLMA.R index 5619d55b..b6d05c9b 100644 --- a/R/ds.lmerSLMA.R +++ b/R/ds.lmerSLMA.R @@ -18,12 +18,12 @@ #' #' In \code{formula} most shortcut notation allowed by \code{lmer()} function is #' also allowed by \code{ds.lmerSLMA}. Many LMEs can be fitted very simply using a formula like: -#' \deqn{y ~ a + b + (1 | c)} +#' \eqn{y ~ a + b + (1 | c)} #' which simply means fit an LME with \code{y} as the outcome variable with \code{a} and \code{b} #' as fixed effects, and \code{c} as a random effect or grouping factor. #' #' It is also possible to fit models with random slopes by specifying a model such as -#' \deqn{y ~ a + b + (1 + b | c)} +#' \eqn{y ~ a + b + (1 + b | c)} #' where the effect of \code{b} can vary randomly between groups defined by \code{c}. #' Implicit nesting can be specified with formulae such as \eqn{y ~ a + b + (1 | c / d)} #' or \eqn{y ~ a + b + (1 | c) + (1 | c : d)}. @@ -84,9 +84,9 @@ #' For more information see \strong{Details}. #' @param checks logical. If TRUE \code{ds.lmerSLMA} checks the structural integrity #' of the model. Default FALSE. For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param 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. diff --git a/R/ds.log.R b/R/ds.log.R index faed3f10..8c0b2e5d 100644 --- a/R/ds.log.R +++ b/R/ds.log.R @@ -8,9 +8,9 @@ #' Default \code{exp(1)}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the server-side. Default \code{log.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.log} returns a vector for each study of the transformed values for the numeric vector #' specified in the argument \code{x}. The created vectors are stored in the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.look.R b/R/ds.look.R index d45e5047..8dffa52f 100644 --- a/R/ds.look.R +++ b/R/ds.look.R @@ -20,9 +20,9 @@ #' For more information see \strong{Details}. #' @param checks logical. If TRUE the optional checks are undertaken. #' Default FALSE to save time. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return the output from the specified server-side aggregate function to the client-side. #' @author DataSHIELD Development Team #' diff --git a/R/ds.ls.R b/R/ds.ls.R index 8cfbf3ca..415c93f4 100644 --- a/R/ds.ls.R +++ b/R/ds.ls.R @@ -51,9 +51,9 @@ #' set as a valid integer, \code{ds.ls} will list all objects in the server-side R environment #' identified by \code{env.to.search} in the search path. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.ls} returns to the client-side a list containing: \cr #' (1) the name/details of the server-side R environment which \code{ds.ls} has searched;\cr #' (2) a vector of character strings giving the names of diff --git a/R/ds.lspline.R b/R/ds.lspline.R index 5c5cee79..9aca2397 100644 --- a/R/ds.lspline.R +++ b/R/ds.lspline.R @@ -14,9 +14,9 @@ #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{lspline.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the #' \code{newobj} argument (or its default name "lspline.newobj"), is assigned on the serverside. #' @author Demetris Avraam for DataSHIELD Development Team @@ -54,4 +54,4 @@ ds.lspline <- function(x, knots = NULL, marginal = FALSE, names = NULL, newobj = calltext <- call("lsplineDS", x, knots, marginal, names) DSI::datashield.assign(datasources, newobj, calltext) -} \ No newline at end of file +} diff --git a/R/ds.make.R b/R/ds.make.R index eb341d8e..07d14a83 100644 --- a/R/ds.make.R +++ b/R/ds.make.R @@ -64,9 +64,9 @@ #' @param toAssign a character string specifying the function or the arithmetic expression. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{make.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. diff --git a/R/ds.matrix.R b/R/ds.matrix.R index d2e8f611..6ee9bdfd 100644 --- a/R/ds.matrix.R +++ b/R/ds.matrix.R @@ -45,9 +45,9 @@ #' the row and column names respectively. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{matrix.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.matrixDet.R b/R/ds.matrixDet.R index 90ac58cf..5fcd81a5 100644 --- a/R/ds.matrixDet.R +++ b/R/ds.matrixDet.R @@ -13,9 +13,9 @@ #' variable that is stored on the data servers. Default \code{matrixdet.newobj}. #' @param logarithm logical. If TRUE the logarithm of the modulus of the determinant #' is calculated. Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.matrixDet.report.R b/R/ds.matrixDet.report.R index 126e48a7..be21aaa7 100644 --- a/R/ds.matrixDet.report.R +++ b/R/ds.matrixDet.report.R @@ -12,9 +12,9 @@ #' @param M1 a character string specifying the name of the matrix. #' @param logarithm logical. If TRUE the logarithm of the modulus of the determinant #' is calculated. Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixDet.report} returns to the client-side #' the determinant of a matrix that is stored on the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.matrixDiag.R b/R/ds.matrixDiag.R index 9c9ec6e9..f6edcbcd 100644 --- a/R/ds.matrixDiag.R +++ b/R/ds.matrixDiag.R @@ -53,9 +53,9 @@ #' For more information see \strong{Details}. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{matrixdiag.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.matrixDimnames.R b/R/ds.matrixDimnames.R index d8376210..6f4a37ea 100644 --- a/R/ds.matrixDimnames.R +++ b/R/ds.matrixDimnames.R @@ -11,9 +11,9 @@ #' An empty list is treated as NULL. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{matrixdimnames.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.matrixInvert.R b/R/ds.matrixInvert.R index f7745ebb..8cc3c447 100644 --- a/R/ds.matrixInvert.R +++ b/R/ds.matrixInvert.R @@ -9,9 +9,9 @@ #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. #' Default \code{matrixinvert.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.matrixMult.R b/R/ds.matrixMult.R index 89ce42ab..cf5349fe 100644 --- a/R/ds.matrixMult.R +++ b/R/ds.matrixMult.R @@ -12,9 +12,9 @@ #' @param M2 a character string specifying the name of the second matrix. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{matrixmult.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixMult} returns to the server-side #' the result of the two matrix multiplication. #' Also, two validity messages are returned to the client-side diff --git a/R/ds.matrixTranspose.R b/R/ds.matrixTranspose.R index 46556d46..bbd73a1a 100644 --- a/R/ds.matrixTranspose.R +++ b/R/ds.matrixTranspose.R @@ -12,9 +12,9 @@ #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. #' Default \code{matrixtranspose.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.mean.R b/R/ds.mean.R index e26ef636..f23356d5 100644 --- a/R/ds.mean.R +++ b/R/ds.mean.R @@ -38,9 +38,9 @@ #' the number of valid (non-missing) observations will be saved on the data servers. #' Default FALSE. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.mean} returns to the client-side a list including: \cr #' #' \code{Mean.by.Study}: estimated mean, \code{Nmissing} diff --git a/R/ds.meanByClass.R b/R/ds.meanByClass.R index 279bf891..538ef8c8 100644 --- a/R/ds.meanByClass.R +++ b/R/ds.meanByClass.R @@ -22,9 +22,9 @@ #' \code{type} can be set as: \code{'combine'} or \code{'split'}. #' Default \code{'combine'}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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). diff --git a/R/ds.meanSdGp.R b/R/ds.meanSdGp.R index 14a3fb91..1bd60936 100644 --- a/R/ds.meanSdGp.R +++ b/R/ds.meanSdGp.R @@ -61,9 +61,9 @@ #' are undertaken to ensure that the input objects are defined in all studies and that the #' variables are of equivalent class in each study. #' Default is FALSE to save time. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{type}. #' diff --git a/R/ds.merge.R b/R/ds.merge.R index ae7d9f00..4ac436fb 100644 --- a/R/ds.merge.R +++ b/R/ds.merge.R @@ -45,9 +45,9 @@ #' For more information see \code{match} in native R \code{merge} function. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{merge.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.message.R b/R/ds.message.R index 289c365b..eb88d8b9 100644 --- a/R/ds.message.R +++ b/R/ds.message.R @@ -19,9 +19,9 @@ #' Server function called: \code{messageDS} #' @param message.obj.name is a character string specifying the name of the list that #' contains the message. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.message} returns a list object from each study, #' containing the message that has been written by #' DataSHIELD into \code{$studysideMessage}. diff --git a/R/ds.metadata.R b/R/ds.metadata.R index 214bde6a..58f615b1 100644 --- a/R/ds.metadata.R +++ b/R/ds.metadata.R @@ -6,9 +6,9 @@ #' Server function \code{metadataDS} is called examines the attributes associated with the variable #' which are non-disclosive. #' @param x a character string specifying the name of the object. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.metadata} returns to the client-side the metadata of associated to an object #' held at the server. #' @author Stuart Wheater, DataSHIELD Development Team diff --git a/R/ds.mice.R b/R/ds.mice.R index f5e84f72..bcb473a4 100644 --- a/R/ds.mice.R +++ b/R/ds.mice.R @@ -38,9 +38,9 @@ #' that are stored on the data servers. Default \code{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. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return a list with three elements: the method, the predictorMatrix and the post. #' @author Demetris Avraam for DataSHIELD Development Team #' @export diff --git a/R/ds.names.R b/R/ds.names.R index 59af0990..97ebbdfd 100644 --- a/R/ds.names.R +++ b/R/ds.names.R @@ -11,11 +11,11 @@ #' using ds.glmSLMA. The resultant object saved on each server separately #' is formally of class "glm" and "ls" but responds TRUE to is.list(), #' @param xname a character string specifying the name of the list. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login that represent the particular data sources #' (studies) to be addressed by the function call. If the \code{datasources} #' argument is not specified the default set of connections will be used: -#' see \code{\link{datashield.connections_default}}. +#' see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.names} returns to the client-side the names #' of a list object stored on the server-side. #' @author Amadou Gaye, updated by Paul Burton for DataSHIELD development diff --git a/R/ds.ns.R b/R/ds.ns.R index cc11be6a..9c961fcf 100644 --- a/R/ds.ns.R +++ b/R/ds.ns.R @@ -22,9 +22,9 @@ #' are supplied, the basis parameters do not depend on x. Data can extend beyond Boundary.knots. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{ns.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return 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(). @@ -54,4 +54,4 @@ ds.ns <- function(x, df = NULL, knots = NULL, intercept = FALSE, Boundary.knots calltext <- call("nsDS", x, df, knots, intercept, Boundary.knots) DSI::datashield.assign(datasources, newobj, calltext) -} \ No newline at end of file +} diff --git a/R/ds.numNA.R b/R/ds.numNA.R index c1757c87..0bd75185 100644 --- a/R/ds.numNA.R +++ b/R/ds.numNA.R @@ -7,9 +7,9 @@ #' #' Server function called: \code{numNaDS} #' @param x a character string specifying the name of the vector. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.numNA} returns to the client-side the number of missing values #' on a server-side vector. #' @author DataSHIELD Development Team diff --git a/R/ds.qlspline.R b/R/ds.qlspline.R index 0302ccc4..45a3e2d3 100644 --- a/R/ds.qlspline.R +++ b/R/ds.qlspline.R @@ -22,9 +22,9 @@ #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{qlspline.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the #' \code{newobj} argument (or its default name "qlspline.newobj"), is assigned on the serverside. #' @author Demetris Avraam for DataSHIELD Development Team @@ -62,4 +62,4 @@ ds.qlspline <- function(x, q, na.rm = TRUE, marginal = FALSE, names = NULL, newo calltext <- call("qlsplineDS", x, q, na.rm, marginal, names) DSI::datashield.assign(datasources, newobj, calltext) -} \ No newline at end of file +} diff --git a/R/ds.quantileMean.R b/R/ds.quantileMean.R index 43e32696..48aa705b 100644 --- a/R/ds.quantileMean.R +++ b/R/ds.quantileMean.R @@ -15,9 +15,9 @@ #' @param type a character that represents the type of graph to display. #' This can be set as \code{'combine'} or \code{'split'}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.quantileMean} returns to the client-side the quantiles and statistical mean #' of a server-side numeric vector. #' @author DataSHIELD Development Team diff --git a/R/ds.rBinom.R b/R/ds.rBinom.R index be5d9220..2f39f8b1 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -41,9 +41,9 @@ #' @param 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. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. @@ -216,10 +216,11 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ cat("NO SEED SET IN STUDY",study.id,"\n\n") -} +} else { calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) } +} cat("\n\n") diff --git a/R/ds.rNorm.R b/R/ds.rNorm.R index 0f53ab92..6100c850 100644 --- a/R/ds.rNorm.R +++ b/R/ds.rNorm.R @@ -52,9 +52,9 @@ #' Default is FALSE. #' @param force.output.to.k.decimal.places an integer vector that #' forces the output random numbers vector to have k decimals. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. diff --git a/R/ds.rPois.R b/R/ds.rPois.R index 5fc262ff..2d2c7f01 100644 --- a/R/ds.rPois.R +++ b/R/ds.rPois.R @@ -38,9 +38,9 @@ #' 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. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. diff --git a/R/ds.rUnif.R b/R/ds.rUnif.R index 42691488..d98fa28f 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -58,9 +58,9 @@ #' an integer vector that forces the output random #' numbers vector to have k decimals. #' -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 @@ -234,9 +234,10 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ cat("NO SEED SET IN STUDY",study.id,"\n") -} +} else { calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) +} } diff --git a/R/ds.rbind.R b/R/ds.rbind.R index 85bca1d5..47e9165c 100644 --- a/R/ds.rbind.R +++ b/R/ds.rbind.R @@ -22,9 +22,9 @@ #' specifies column names of the output object. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Defaults \code{rbind.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default FALSE. #' @return \code{ds.rbind} returns a matrix combining the rows of the diff --git a/R/ds.reShape.R b/R/ds.reShape.R index 2a4840e9..f2214f55 100644 --- a/R/ds.reShape.R +++ b/R/ds.reShape.R @@ -29,9 +29,9 @@ #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. #' Default \code{reshape.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.recodeLevels.R b/R/ds.recodeLevels.R index 671401e4..a22d25b3 100644 --- a/R/ds.recodeLevels.R +++ b/R/ds.recodeLevels.R @@ -13,9 +13,9 @@ #' to the current number of levels. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{recodelevels.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.recodeLevels} returns to the server-side a variable of type factor #' with the replaces levels. #' @author DataSHIELD Development Team diff --git a/R/ds.recodeValues.R b/R/ds.recodeValues.R index 9643d33e..d44cc857 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -19,9 +19,9 @@ #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. #' Default \code{recodevalues.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress logical. If TRUE console output should be produced to indicate #' progress. Default FALSE. #' @return Assigns to each server a new variable with the recoded values. diff --git a/R/ds.rep.R b/R/ds.rep.R index 0e526149..2d2ce951 100644 --- a/R/ds.rep.R +++ b/R/ds.rep.R @@ -23,9 +23,9 @@ #' the \code{x1} is a character. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{seq.vect}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{newobj} that has been created diff --git a/R/ds.replaceNA.R b/R/ds.replaceNA.R index 3345b7de..28a51adb 100644 --- a/R/ds.replaceNA.R +++ b/R/ds.replaceNA.R @@ -19,9 +19,9 @@ #' The length of the list or vector must be equal to the number of servers (studies). #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{replacena.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. diff --git a/R/ds.rm.R b/R/ds.rm.R index 77b693db..e977afe5 100644 --- a/R/ds.rm.R +++ b/R/ds.rm.R @@ -14,9 +14,9 @@ #' #' Server function called: \code{rmDS} #' @param x.names a character string specifying the objects to be deleted. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return The \code{ds.rm} function deletes from the server-side #' the specified object. If this #' is successful the message \code{"Object(s) '' was deleted."} is returned @@ -94,4 +94,4 @@ ds.rm<-function(x.names=NULL, datasources=NULL){ return(output) } -#ds.rm \ No newline at end of file +#ds.rm diff --git a/R/ds.rowColCalc.R b/R/ds.rowColCalc.R index b63190bf..d531cce4 100644 --- a/R/ds.rowColCalc.R +++ b/R/ds.rowColCalc.R @@ -14,9 +14,9 @@ #' \code{"rowSums"}, \code{"colSums"}, \code{"rowMeans"} or \code{"colMeans"}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{rowcolcalc.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.rowColCalc} returns to the server-side rows and columns sums and means. #' @author DataSHIELD Development Team #' @examples diff --git a/R/ds.scatterPlot.R b/R/ds.scatterPlot.R index 81828648..827b3272 100644 --- a/R/ds.scatterPlot.R +++ b/R/ds.scatterPlot.R @@ -64,9 +64,9 @@ #' For more information see \strong{Details}. #' @param return.coords a logical. If TRUE the coordinates of the anonymised data points are return #' to the Console. Default value is FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.scatterPlot} returns to the client-side one or more scatter #' plots depending on the argument \code{type}. #' @author DataSHIELD Development Team diff --git a/R/ds.seq.R b/R/ds.seq.R index 1f0b722a..d21522a0 100644 --- a/R/ds.seq.R +++ b/R/ds.seq.R @@ -55,9 +55,9 @@ #' For more information see \strong{Details}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{seq.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.setSeed.R b/R/ds.setSeed.R index 20eabd5b..ee84a174 100644 --- a/R/ds.setSeed.R +++ b/R/ds.setSeed.R @@ -31,9 +31,9 @@ #' Server function called: \code{setSeedDS} #' @param seed.as.integer a numeric value or a NULL that primes the random seed #' in each data source. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return Sets the values of the vector of integers of length 626 known as #' \code{.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 diff --git a/R/ds.skewness.R b/R/ds.skewness.R index ed3b05d9..0ef8d93d 100644 --- a/R/ds.skewness.R +++ b/R/ds.skewness.R @@ -31,9 +31,9 @@ #' \code{type} can be set as: \code{'combine'}, \code{'split'} or \code{'both'}. For more information #' see \strong{Details}. #' The default value is set to \code{'both'}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.skewness} returns a matrix showing the skewness of the input numeric variable, #' the number of valid observations and the validity message. #' @author Demetris Avraam, for DataSHIELD Development Team diff --git a/R/ds.sqrt.R b/R/ds.sqrt.R index 22a03937..9193dbbc 100644 --- a/R/ds.sqrt.R +++ b/R/ds.sqrt.R @@ -10,9 +10,9 @@ #' @param x a character string providing the name of a numeric or an integer vector. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default name is set to \code{sqrt.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 \code{x}. The created vectors #' are stored in the servers. diff --git a/R/ds.subset.R b/R/ds.subset.R index 6f21bd08..40bd6ce0 100644 --- a/R/ds.subset.R +++ b/R/ds.subset.R @@ -19,8 +19,8 @@ #' operator. This parameter is ignored if the input data is not a vector. #' @param 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. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return no data are return to the user, the generated subset dataframe is stored on the server side. #' @author Gaye, A. #' @seealso \link{ds.subsetByClass} to subset by the classes of factor vector(s). diff --git a/R/ds.subsetByClass.R b/R/ds.subsetByClass.R index 2a2ab29a..5c6f92bb 100644 --- a/R/ds.subsetByClass.R +++ b/R/ds.subsetByClass.R @@ -11,8 +11,8 @@ #' @param variables a vector of string characters, the name(s) of the variables to subset by. #' @param 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'. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return a no data are return to the user but messages are printed out. #' @author Gaye, A. #' @seealso \link{ds.meanByClass} to compute mean and standard deviation across categories of a factor vectors. diff --git a/R/ds.summary.R b/R/ds.summary.R index b4d3061c..2d86287b 100644 --- a/R/ds.summary.R +++ b/R/ds.summary.R @@ -9,9 +9,9 @@ #' #' server functions called: \code{isValidDS}, \code{dimDS} and \code{colnamesDS} #' @param x a character string specifying the name of a numeric or factor variable. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. diff --git a/R/ds.table.R b/R/ds.table.R index f5a623d4..780f9f86 100644 --- a/R/ds.table.R +++ b/R/ds.table.R @@ -149,8 +149,8 @@ #' If no explicit name for the table object is specified, but #' is nevertheless TRUE, the name for the serverside table object defaults #' to \code{table.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' If the is to be specified, it should be set without #' inverted commas: e.g. datasources=connections.em or datasources=default.connections. If you wish to #' apply the function solely to e.g. the second connection server in a set of three, diff --git a/R/ds.table1D.R b/R/ds.table1D.R index 76e13199..07df60eb 100644 --- a/R/ds.table1D.R +++ b/R/ds.table1D.R @@ -16,8 +16,8 @@ #' @param 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. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return A list object containing the following items: #' \item{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 diff --git a/R/ds.table2D.R b/R/ds.table2D.R index c8b882ac..301a8993 100644 --- a/R/ds.table2D.R +++ b/R/ds.table2D.R @@ -17,8 +17,8 @@ #' @param 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. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return A list object containing the following items: #' \item{colPercent}{table(s) that hold column percentages for each level/category. Inner cells are reported as #' missing if one or more cells are 'invalid'.} diff --git a/R/ds.tapply.R b/R/ds.tapply.R index 457ecfe4..e9805e1d 100644 --- a/R/ds.tapply.R +++ b/R/ds.tapply.R @@ -68,9 +68,9 @@ #' \code{"N"} (or \code{"length"}), \code{"mean"},\code{"sd"}, \code{"sum"}, #' or \code{"quantile"}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.tapply} returns to the client-side an array of the summarized values. #' It has the same number of dimensions as INDEX. #' @examples diff --git a/R/ds.tapply.assign.R b/R/ds.tapply.assign.R index 6f506532..be7b7408 100644 --- a/R/ds.tapply.assign.R +++ b/R/ds.tapply.assign.R @@ -70,9 +70,9 @@ #' For more information see \strong{Details}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{tapply.assign.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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. diff --git a/R/ds.testObjExists.R b/R/ds.testObjExists.R index bf84065d..5b7e946a 100644 --- a/R/ds.testObjExists.R +++ b/R/ds.testObjExists.R @@ -8,9 +8,9 @@ #' #' Server function called: \code{testObjExistsDS} #' @param test.obj.name a character string specifying the name of the object to search. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.unList.R b/R/ds.unList.R index 773246fd..fa14a4f2 100644 --- a/R/ds.unList.R +++ b/R/ds.unList.R @@ -18,9 +18,9 @@ #' @param x.name a character string specifying the name of the input object to be unlisted. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{unlist.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{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 diff --git a/R/ds.unique.R b/R/ds.unique.R index 29797dee..327585bd 100644 --- a/R/ds.unique.R +++ b/R/ds.unique.R @@ -7,9 +7,9 @@ #' @param x.name a character string providing the name of the varable, in the server, to perform \code{unique} upon #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{unique.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.unique} returns the vector of unique R objects which are written to the server-side. #' @examples #' \dontrun{ diff --git a/R/ds.var.R b/R/ds.var.R index 0a74d4eb..178dc443 100644 --- a/R/ds.var.R +++ b/R/ds.var.R @@ -23,9 +23,9 @@ #' 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. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.var} returns to the client-side a list including:\cr #' #' \code{Variance.by.Study}: estimated variance, \code{Nmissing} diff --git a/R/ds.vectorCalc.R b/R/ds.vectorCalc.R index bc090a87..f019c7bc 100644 --- a/R/ds.vectorCalc.R +++ b/R/ds.vectorCalc.R @@ -13,8 +13,8 @@ #' @param calc a character, a symbol that indicates the mathematical operation to carry out: #' '+' for addition, '/' for division, *' for multiplication and '-' for subtraction. #' @param newobj the name of the output object. By default the name is 'vectorcalc.newobj'. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return no data are returned to user, the output vector is stored on the server side. #' @author Gaye, A. #' @export diff --git a/R/getPooledMean.R b/R/getPooledMean.R index ded7fae8..dba45bf3 100644 --- a/R/getPooledMean.R +++ b/R/getPooledMean.R @@ -4,8 +4,8 @@ #' @details This function is called to avoid calling the client function 'ds.mean' #' which may stop the process due to some checks not required when computing a mean inside #' a function. -#' @param dtsources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param x a character, the name of a numeric vector #' @keywords internal #' @return a pooled mean diff --git a/R/getPooledVar.R b/R/getPooledVar.R index 9fc9bbcd..0738d4bf 100644 --- a/R/getPooledVar.R +++ b/R/getPooledVar.R @@ -4,8 +4,8 @@ #' @details This function is called to avoid calling the client function 'ds.var' #' which may stop the process due to some checks not required when computing a mean inside #' a function. -#' @param dtsources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param x a character, the name of a numeric vector #' @keywords internal #' @return a pooled variance diff --git a/R/glmChecks.R b/R/glmChecks.R index 53576448..c720fa45 100644 --- a/R/glmChecks.R +++ b/R/glmChecks.R @@ -12,8 +12,8 @@ #' included in the linear predictor during fitting. #' @param 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. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @keywords internal #' @return an integer 0 if check was passed and 1 if failed #' @author Gaye, A. diff --git a/R/isAssigned.R b/R/isAssigned.R index c0f5150f..0460cb77 100644 --- a/R/isAssigned.R +++ b/R/isAssigned.R @@ -4,8 +4,8 @@ #' @details After calling an assign function it is important #' to know whether or not the action has been completed by #' checking if the output actually exists on the server side. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param newobj a character, the name the object to look for. #' @keywords internal #' @return nothing is return but the process is stopped if diff --git a/R/isDefined.R b/R/isDefined.R index a0206257..621b809a 100644 --- a/R/isDefined.R +++ b/R/isDefined.R @@ -3,9 +3,9 @@ #' @description This is an internal function. #' @details In DataSHIELD an object included in analysis must be defined (i.e. exists) #' in all the studies. If not the process should halt. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified, the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @param obj a character vector, the name of the object(s) to look for. #' @param 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 diff --git a/R/meanByClassHelper0a.R b/R/meanByClassHelper0a.R index d94898ff..21c6e90c 100644 --- a/R/meanByClassHelper0a.R +++ b/R/meanByClassHelper0a.R @@ -8,8 +8,8 @@ #' @param type a character which represents the type of analysis to carry out. If \code{type} is set to #' 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results #' is genrated for each study. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return 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). #' @keywords internal diff --git a/R/meanByClassHelper0b.R b/R/meanByClassHelper0b.R index 21b66d44..1419d53f 100644 --- a/R/meanByClassHelper0b.R +++ b/R/meanByClassHelper0b.R @@ -9,8 +9,8 @@ #' @param type a character which represents the type of analysis to carry out. If \code{type} is set to #' 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results #' is genrated for each study. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return 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). #' @keywords internal diff --git a/R/meanByClassHelper1.R b/R/meanByClassHelper1.R index 6010e58b..4b98201e 100644 --- a/R/meanByClassHelper1.R +++ b/R/meanByClassHelper1.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to break down #' the initial table by the specified categorical variables. -#' @param dtsource a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsource a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param tables a character vector, the tables to breakdown #' @param variable a character, the variable to subset on #' @param categories a character vector, the classes in the variables to subset on diff --git a/R/meanByClassHelper2.R b/R/meanByClassHelper2.R index a0b0dfef..9fac9125 100644 --- a/R/meanByClassHelper2.R +++ b/R/meanByClassHelper2.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to produce the final table #' if the user sets the parmater 'type' to combine (the default behaviour of 'ds.meanByClass'). -#' @param dtsources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param tablenames a character vector, the name of the subset tables #' @param variables a character vector, the names of the continuous variables to computes a mean for. #' @param invalidrecorder a list, holds informations about invalid subsets in each study. diff --git a/R/meanByClassHelper3.R b/R/meanByClassHelper3.R index 0b820033..61e61d1f 100644 --- a/R/meanByClassHelper3.R +++ b/R/meanByClassHelper3.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to produce the final tables #' if the user sets the parmater 'type' to 'split'. -#' @param dtsources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param tablenames a character vector, the name of the subset tables #' @param variables a character vector, the names of the continuous variables to computes a mean for. #' @param invalidrecorder a list, holds informations about invalid subsets in each study diff --git a/R/meanByClassHelper4.R b/R/meanByClassHelper4.R index 88e827fc..9597a7e8 100644 --- a/R/meanByClassHelper4.R +++ b/R/meanByClassHelper4.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to obtain 'loose' #' subset tables because the 'subsetByClass' function does not handle a table within a list. -#' @param dtsource a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsource a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param alist the name of the list that holds the final subset tables #' @param initialtable a character the name of the table that the subset were generated from #' @param variable a character, the variable to subset on diff --git a/R/subsetHelper.R b/R/subsetHelper.R index c01529ac..025a0680 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -7,9 +7,9 @@ #' This function is internal. #' #' Server function called: \code{dimDS} -#' @param dts a list of \code{\link{DSConnection-class}} +#' @param dts a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param data a character string specifying the name of the data frame or #' the factor vector and the range of the subset. #' @param rs a vector of two integers specifying the indices of the rows de extract. diff --git a/armadillo_azure-pipelines.yml b/armadillo_azure-pipelines.yml index 70788f76..595258a6 100644 --- a/armadillo_azure-pipelines.yml +++ b/armadillo_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -185,7 +185,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -235,7 +235,7 @@ jobs: curl -u admin:admin -X GET http://localhost:8080/packages - curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.1-permissive.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package sleep 60 docker container restart dsbaseclient_armadillo_1 @@ -263,7 +263,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -364,7 +364,7 @@ jobs: - bash: | curl -u admin:admin http://localhost:8080/whitelist - curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.1.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package docker container restart dsbaseclient_armadillo_1 sleep 60 @@ -387,7 +387,7 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' pwd mkdir $(Pipeline.Workspace)/logs diff --git a/azure-pipelines.yml b/azure-pipelines.yml index b9811a2a..691bd140 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -133,13 +133,14 @@ jobs: sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y + sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')" - sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)" + sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)" # XML grep for coverage report merging sudo apt-get install -qq xml-twig-tools -y @@ -185,7 +186,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -232,9 +233,11 @@ jobs: # Install dsBase. # If previous steps have failed then don't run. - bash: | - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - sleep 120 + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)" + + sleep 60 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)" @@ -258,7 +261,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -358,6 +361,8 @@ jobs: # If previous steps have failed then don't run - bash: | + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -374,9 +379,8 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' - pwd mkdir $(Pipeline.Workspace)/logs # run the coverage tool and output to coveragelist.csv diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 35b85108..cf5a1095 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -3,7 +3,7 @@ services: hostname: armadillo ports: - 8080:8080 - image: datashield/armadillo_citest:4.11.1 + image: datashield/armadillo_citest:5.1.2 environment: LOGGING_CONFIG: 'classpath:logback-file.xml' AUDIT_LOG_PATH: '/app/logs/audit.log' @@ -16,6 +16,6 @@ services: default: hostname: default - image: datashield/rock-knot-devel-permissive:latest + image: datashield/rserver-neutron-gypsum-permissive:latest environment: DEBUG: "FALSE" diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index fb233ea4..a55e8774 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -1,6 +1,6 @@ services: opal: - image: obiba/opal:5.0.1 + image: obiba/opal:5.1.4 ports: - "8443:8443" links: @@ -20,4 +20,4 @@ services: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar rock: - image: datashield/rock-knot-devel-permissive:latest + image: datashield/rock-margin-joule-permissive:latest diff --git a/docs/404.html b/docs/404.html index adefa480..7c81d5b9 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -73,12 +73,12 @@

Page not found (404)

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 3f1def72..8a0484d2 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -256,11 +256,11 @@

NA

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/authors.html b/docs/authors.html index feb204c7..bfe7a3c1 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -40,7 +40,43 @@

Authors and Citation

  • -

    DataSHIELD Developers. Maintainer. +

    Paul Burton. Author. +

    +
    • +
  • +

    Rebecca Wilson. Author. +

    +
    • +
  • +

    Olly Butters. Author. +

    +
    • +
  • +

    Patricia Ryser-Welch. Author. +

    +
    • +
  • +

    Alex Westerberg. Author. +

    +
    • +
  • +

    Leire Abarrategui. Author. +

    +
    • +
  • +

    Roberto Villegas-Diaz. Author. +

    +
    • +
  • +

    Demetris Avraam. Author. +

    +
    • +
  • +

    Yannick Marcon. Author. +

    +
    • +
  • +

    Stuart Wheater. Author, maintainer.

@@ -52,15 +88,15 @@

Citation

-

Developers D (2024). +

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Wheater S (2025). dsBaseClient: DataSHIELD Client Functions. -R package version 6.3.1. +R package version 6.3.2. 

@Manual{,
   title = {dsBaseClient: DataSHIELD Client Functions},
-  author = {DataSHIELD Developers},
-  year = {2024},
-  note = {R package version 6.3.1},
+  author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Stuart Wheater},
+  year = {2025},
+  note = {R package version 6.3.2},
 }
@@ -70,11 +106,11 @@

Citation

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/index.html b/docs/index.html index 94baefd3..46cf64d1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -117,7 +117,16 @@

Citation

Developers

    -
  • DataSHIELD Developers
    Maintainer
    • +
  • Paul Burton
    Author
    • +
  • Rebecca Wilson
    Author
    • +
  • Olly Butters
    Author
    • +
  • Patricia Ryser-Welch
    Author
    • +
  • Alex Westerberg
    Author
    • +
  • Leire Abarrategui
    Author
    • +
  • Roberto Villegas-Diaz
    Author
    • +
  • Demetris Avraam
    Author
    • +
  • Yannick Marcon
    Author
    • +
  • Stuart Wheater
    Author, maintainer
@@ -129,12 +138,12 @@

Developers

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 46a418da..901afc7f 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 3.1.3 -pkgdown: 2.1.1 +pkgdown: 2.1.3 pkgdown_sha: ~ articles: {} -last_built: 2024-11-11T14:56Z +last_built: 2025-06-10T15:10Z diff --git a/docs/reference/checkClass.html b/docs/reference/checkClass.html index 8a4483b3..9a8f7a17 100644 --- a/docs/reference/checkClass.html +++ b/docs/reference/checkClass.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -78,11 +78,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/colPercent.html b/docs/reference/colPercent.html index 4f2acdc8..49bb3dfe 100644 --- a/docs/reference/colPercent.html +++ b/docs/reference/colPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -76,11 +76,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.Boole.html b/docs/reference/ds.Boole.html index 2445ed80..247976e5 100644 --- a/docs/reference/ds.Boole.html +++ b/docs/reference/ds.Boole.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -200,11 +200,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.abs.html b/docs/reference/ds.abs.html index 65f8640c..3738979a 100644 --- a/docs/reference/ds.abs.html +++ b/docs/reference/ds.abs.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -150,11 +150,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asCharacter.html b/docs/reference/ds.asCharacter.html index df1c7cb9..79fa4660 100644 --- a/docs/reference/ds.asCharacter.html +++ b/docs/reference/ds.asCharacter.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -132,11 +132,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asDataMatrix.html b/docs/reference/ds.asDataMatrix.html index b8ceb870..6b11888e 100644 --- a/docs/reference/ds.asDataMatrix.html +++ b/docs/reference/ds.asDataMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -135,11 +135,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asFactor.html b/docs/reference/ds.asFactor.html index a75085f9..dfdd14ec 100644 --- a/docs/reference/ds.asFactor.html +++ b/docs/reference/ds.asFactor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -229,11 +229,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

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+

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Author

-

Developed by DataSHIELD Developers.

+

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-

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+

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Examples

-

Developed by DataSHIELD Developers.

+

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-

Site built with pkgdown 2.1.1.

+

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Examples

-

Developed by DataSHIELD Developers.

+

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-

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+

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

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+

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

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Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

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Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

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Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrame.html b/docs/reference/ds.dataFrame.html index f32cf6bc..990e6d2d 100644 --- a/docs/reference/ds.dataFrame.html +++ b/docs/reference/ds.dataFrame.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -199,11 +199,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrameSort.html b/docs/reference/ds.dataFrameSort.html index efa19b70..4c4ec611 100644 --- a/docs/reference/ds.dataFrameSort.html +++ b/docs/reference/ds.dataFrameSort.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -171,11 +171,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrameSubset.html b/docs/reference/ds.dataFrameSubset.html index f1559f19..30fa01af 100644 --- a/docs/reference/ds.dataFrameSubset.html +++ b/docs/reference/ds.dataFrameSubset.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -216,11 +216,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.densityGrid.html b/docs/reference/ds.densityGrid.html index 03906004..4cc1af0f 100644 --- a/docs/reference/ds.densityGrid.html +++ b/docs/reference/ds.densityGrid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -120,11 +120,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dmtC2S.html b/docs/reference/ds.dmtC2S.html index 3b453ecb..cf64782a 100644 --- a/docs/reference/ds.dmtC2S.html +++ b/docs/reference/ds.dmtC2S.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -120,11 +120,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.elspline.html b/docs/reference/ds.elspline.html index 102add33..514720b2 100644 --- a/docs/reference/ds.elspline.html +++ b/docs/reference/ds.elspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -119,11 +119,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.exists.html b/docs/reference/ds.exists.html index 08944f12..8665c79e 100644 --- a/docs/reference/ds.exists.html +++ b/docs/reference/ds.exists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -138,11 +138,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.exp.html b/docs/reference/ds.exp.html index 134f9743..5686927f 100644 --- a/docs/reference/ds.exp.html +++ b/docs/reference/ds.exp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -132,11 +132,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.extractQuantiles.html b/docs/reference/ds.extractQuantiles.html index 8056889b..3ba33a1c 100644 --- a/docs/reference/ds.extractQuantiles.html +++ b/docs/reference/ds.extractQuantiles.html @@ -26,7 +26,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -176,11 +176,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.forestplot.html b/docs/reference/ds.forestplot.html index a651872d..81f892b5 100644 --- a/docs/reference/ds.forestplot.html +++ b/docs/reference/ds.forestplot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -118,11 +118,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.gamlss.html b/docs/reference/ds.gamlss.html index 4e92d7c7..a86f96e0 100644 --- a/docs/reference/ds.gamlss.html +++ b/docs/reference/ds.gamlss.html @@ -23,7 +23,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -215,11 +215,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.getWGSR.html b/docs/reference/ds.getWGSR.html index 9f647c02..e33fb230 100644 --- a/docs/reference/ds.getWGSR.html +++ b/docs/reference/ds.getWGSR.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -204,11 +204,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glm.html b/docs/reference/ds.glm.html index 097d6a86..8a2fad81 100644 --- a/docs/reference/ds.glm.html +++ b/docs/reference/ds.glm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -196,13 +196,13 @@

Details

In formula most shortcut notation for formulas allowed under R's standard glm() function is also allowed by ds.glm.

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

-

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

+

\(y~a+b+c+d\)

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

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

-

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

+

\(EVENT~1+TID+SEXF*AGE.60\)

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), @@ -237,7 +237,7 @@

Details

The data 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: \(DataFrame$y ~ DataFrame$a + DataFrame$b + DataFrame$c + DataFrame$d\)

+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) on the server-side at every study and that they have the correct characteristics required to fit the model. @@ -427,11 +427,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmPredict.html b/docs/reference/ds.glmPredict.html index 228bed88..613b8268 100644 --- a/docs/reference/ds.glmPredict.html +++ b/docs/reference/ds.glmPredict.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -227,11 +227,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmSLMA.html b/docs/reference/ds.glmSLMA.html index b429327a..b9bd4795 100644 --- a/docs/reference/ds.glmSLMA.html +++ b/docs/reference/ds.glmSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -281,13 +281,13 @@

Details

In formula Most shortcut notation for formulas allowed under R's standard glm() function is also allowed by ds.glmSLMA.

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

-

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

+

\(y~a+b+c+d\)

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

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

-

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

+

\(EVENT~1+TID+SEXF*AGE.60\)

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), @@ -355,7 +355,7 @@

Details

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: \(DataFrame$y ~ DataFrame$a + DataFrame$b + DataFrame$c + DataFrame$d\)

+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) on the server-site at every study and that they have the correct characteristics required to fit the model. @@ -493,11 +493,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmSummary.html b/docs/reference/ds.glmSummary.html index 327060d8..45ada449 100644 --- a/docs/reference/ds.glmSummary.html +++ b/docs/reference/ds.glmSummary.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -154,11 +154,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmerSLMA.html b/docs/reference/ds.glmerSLMA.html index 8d8a3b6c..062bbae9 100644 --- a/docs/reference/ds.glmerSLMA.html +++ b/docs/reference/ds.glmerSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -235,13 +235,13 @@

Details

In formula most shortcut notation allowed by glmer() function is also allowed by ds.glmerSLMA. Many GLMEs can be fitted very simply using a formula like: -$$y~a+b+(1|c)$$ +\(y~a+b+(1|c)\) 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 -$$y~a+b+(1+b|c)$$ +\(y~a+b+(1+b|c)\) 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 \(y~a+b+(1|c)+(1|c:d)\).

@@ -249,7 +249,7 @@

Details

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: -\(DataFrame$y ~ DataFrame$a + DataFrame$b + (1 | DataFrame$c)\).

+\(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)\).

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. @@ -379,11 +379,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.heatmapPlot.html b/docs/reference/ds.heatmapPlot.html index dd26dbd3..98404a7d 100644 --- a/docs/reference/ds.heatmapPlot.html +++ b/docs/reference/ds.heatmapPlot.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -199,11 +199,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.hetcor.html b/docs/reference/ds.hetcor.html index 5373fbae..0711ef7b 100644 --- a/docs/reference/ds.hetcor.html +++ b/docs/reference/ds.hetcor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -124,11 +124,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.histogram.html b/docs/reference/ds.histogram.html index 777c4278..53a41bf2 100644 --- a/docs/reference/ds.histogram.html +++ b/docs/reference/ds.histogram.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -190,11 +190,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.igb_standards.html b/docs/reference/ds.igb_standards.html index e59a5413..19b5bab9 100644 --- a/docs/reference/ds.igb_standards.html +++ b/docs/reference/ds.igb_standards.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -135,11 +135,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.isNA.html b/docs/reference/ds.isNA.html index 9f81d806..faf59b21 100644 --- a/docs/reference/ds.isNA.html +++ b/docs/reference/ds.isNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.isValid.html b/docs/reference/ds.isValid.html index d34ddbd6..7937930b 100644 --- a/docs/reference/ds.isValid.html +++ b/docs/reference/ds.isValid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.kurtosis.html b/docs/reference/ds.kurtosis.html index 896113ff..0b8a2155 100644 --- a/docs/reference/ds.kurtosis.html +++ b/docs/reference/ds.kurtosis.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -103,11 +103,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.length.html b/docs/reference/ds.length.html index fa6be208..16db9aab 100644 --- a/docs/reference/ds.length.html +++ b/docs/reference/ds.length.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -157,11 +157,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.levels.html b/docs/reference/ds.levels.html index d4eda89f..784dc51c 100644 --- a/docs/reference/ds.levels.html +++ b/docs/reference/ds.levels.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -133,11 +133,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lexis.html b/docs/reference/ds.lexis.html index 72b4fc78..73c5d66c 100644 --- a/docs/reference/ds.lexis.html +++ b/docs/reference/ds.lexis.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -298,11 +298,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.list.html b/docs/reference/ds.list.html index 209dcb5b..ff3cc73a 100644 --- a/docs/reference/ds.list.html +++ b/docs/reference/ds.list.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -129,11 +129,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listClientsideFunctions.html b/docs/reference/ds.listClientsideFunctions.html index 6f6570e6..cbada273 100644 --- a/docs/reference/ds.listClientsideFunctions.html +++ b/docs/reference/ds.listClientsideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -86,11 +86,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listDisclosureSettings.html b/docs/reference/ds.listDisclosureSettings.html index 45969706..97fa567e 100644 --- a/docs/reference/ds.listDisclosureSettings.html +++ b/docs/reference/ds.listDisclosureSettings.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -162,11 +162,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listOpals.html b/docs/reference/ds.listOpals.html index 5ab10679..023b6198 100644 --- a/docs/reference/ds.listOpals.html +++ b/docs/reference/ds.listOpals.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -80,11 +80,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listServersideFunctions.html b/docs/reference/ds.listServersideFunctions.html index 757fbc03..78d28e12 100644 --- a/docs/reference/ds.listServersideFunctions.html +++ b/docs/reference/ds.listServersideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -124,11 +124,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lmerSLMA.html b/docs/reference/ds.lmerSLMA.html index efd0e6f9..5df6ed8a 100644 --- a/docs/reference/ds.lmerSLMA.html +++ b/docs/reference/ds.lmerSLMA.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -229,18 +229,18 @@

Details

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: -$$y ~ a + b + (1 | c)$$ +\(y ~ a + b + (1 | c)\) 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 -$$y ~ a + b + (1 + b | c)$$ +\(y ~ a + b + (1 + b | c)\) 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: -\(DataFrame$y ~ DataFrame$a + DataFrame$b + (1 | DataFrame$c)\).

+\(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)\).

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. @@ -328,11 +328,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.log.html b/docs/reference/ds.log.html index 30f10ae2..0aa19bb8 100644 --- a/docs/reference/ds.log.html +++ b/docs/reference/ds.log.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -138,11 +138,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.look.html b/docs/reference/ds.look.html index ae0d0cc7..22c0bd25 100644 --- a/docs/reference/ds.look.html +++ b/docs/reference/ds.look.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -147,11 +147,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.ls.html b/docs/reference/ds.ls.html index e0086831..47cbb941 100644 --- a/docs/reference/ds.ls.html +++ b/docs/reference/ds.ls.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -198,11 +198,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lspline.html b/docs/reference/ds.lspline.html index 188e4632..2305a2e8 100644 --- a/docs/reference/ds.lspline.html +++ b/docs/reference/ds.lspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -116,11 +116,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.make.html b/docs/reference/ds.make.html index 7d4ae3e2..45279a12 100644 --- a/docs/reference/ds.make.html +++ b/docs/reference/ds.make.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -201,11 +201,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrix.html b/docs/reference/ds.matrix.html index 0b7c0d61..98033ed0 100644 --- a/docs/reference/ds.matrix.html +++ b/docs/reference/ds.matrix.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -246,11 +246,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.mean.html b/docs/reference/ds.mean.html index 301e391e..4edfce1d 100644 --- a/docs/reference/ds.mean.html +++ b/docs/reference/ds.mean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -185,11 +185,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.meanSdGp.html b/docs/reference/ds.meanSdGp.html index 51702b22..8dec44ec 100644 --- a/docs/reference/ds.meanSdGp.html +++ b/docs/reference/ds.meanSdGp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -214,11 +214,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.merge.html b/docs/reference/ds.merge.html index 87767638..aa606fef 100644 --- a/docs/reference/ds.merge.html +++ b/docs/reference/ds.merge.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -232,11 +232,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.message.html b/docs/reference/ds.message.html index 7c94b88e..bc64c1c3 100644 --- a/docs/reference/ds.message.html +++ b/docs/reference/ds.message.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -144,11 +144,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.metadata.html b/docs/reference/ds.metadata.html index 0d807090..577bbced 100644 --- a/docs/reference/ds.metadata.html +++ b/docs/reference/ds.metadata.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -122,11 +122,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.mice.html b/docs/reference/ds.mice.html index 871cd3c2..185c5498 100644 --- a/docs/reference/ds.mice.html +++ b/docs/reference/ds.mice.html @@ -25,7 +25,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -160,11 +160,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.names.html b/docs/reference/ds.names.html index 69c83c36..6fdf0eeb 100644 --- a/docs/reference/ds.names.html +++ b/docs/reference/ds.names.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -142,11 +142,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.ns.html b/docs/reference/ds.ns.html index 4cb30d13..a13f66b9 100644 --- a/docs/reference/ds.ns.html +++ b/docs/reference/ds.ns.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -129,11 +129,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.numNA.html b/docs/reference/ds.numNA.html index 2bb4270f..23591561 100644 --- a/docs/reference/ds.numNA.html +++ b/docs/reference/ds.numNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -127,11 +127,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.qlspline.html b/docs/reference/ds.qlspline.html index d1a702dd..1b27ef91 100644 --- a/docs/reference/ds.qlspline.html +++ b/docs/reference/ds.qlspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -128,11 +128,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.quantileMean.html b/docs/reference/ds.quantileMean.html index bcc80bc5..5cd60d55 100644 --- a/docs/reference/ds.quantileMean.html +++ b/docs/reference/ds.quantileMean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -146,11 +146,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rBinom.html b/docs/reference/ds.rBinom.html index 63e174a8..9811d02c 100644 --- a/docs/reference/ds.rBinom.html +++ b/docs/reference/ds.rBinom.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -198,11 +198,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rNorm.html b/docs/reference/ds.rNorm.html index 164ac708..f9113a66 100644 --- a/docs/reference/ds.rNorm.html +++ b/docs/reference/ds.rNorm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -213,11 +213,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rPois.html b/docs/reference/ds.rPois.html index aaacd484..fce73327 100644 --- a/docs/reference/ds.rPois.html +++ b/docs/reference/ds.rPois.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -188,11 +188,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rUnif.html b/docs/reference/ds.rUnif.html index a9c582ce..e3056eee 100644 --- a/docs/reference/ds.rUnif.html +++ b/docs/reference/ds.rUnif.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -219,11 +219,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.ranksSecure.html b/docs/reference/ds.ranksSecure.html index f29d764c..1af4c1a2 100644 --- a/docs/reference/ds.ranksSecure.html +++ b/docs/reference/ds.ranksSecure.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -278,11 +278,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rbind.html b/docs/reference/ds.rbind.html index 30de9105..f871a139 100644 --- a/docs/reference/ds.rbind.html +++ b/docs/reference/ds.rbind.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -171,11 +171,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.reShape.html b/docs/reference/ds.reShape.html index cbd97a29..481ee1b5 100644 --- a/docs/reference/ds.reShape.html +++ b/docs/reference/ds.reShape.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -194,11 +194,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.recodeLevels.html b/docs/reference/ds.recodeLevels.html index 008e5014..629a4d2b 100644 --- a/docs/reference/ds.recodeLevels.html +++ b/docs/reference/ds.recodeLevels.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -144,11 +144,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.recodeValues.html b/docs/reference/ds.recodeValues.html index 80bff411..8a627075 100644 --- a/docs/reference/ds.recodeValues.html +++ b/docs/reference/ds.recodeValues.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -132,11 +132,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rep.html b/docs/reference/ds.rep.html index 56413642..858e2f7e 100644 --- a/docs/reference/ds.rep.html +++ b/docs/reference/ds.rep.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -206,11 +206,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.replaceNA.html b/docs/reference/ds.replaceNA.html index 144448a8..1740298f 100644 --- a/docs/reference/ds.replaceNA.html +++ b/docs/reference/ds.replaceNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -170,11 +170,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rm.html b/docs/reference/ds.rm.html index 47cbcb7a..f57042a8 100644 --- a/docs/reference/ds.rm.html +++ b/docs/reference/ds.rm.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -140,11 +140,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rowColCalc.html b/docs/reference/ds.rowColCalc.html index 59560072..0163eb67 100644 --- a/docs/reference/ds.rowColCalc.html +++ b/docs/reference/ds.rowColCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -143,11 +143,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.sample.html b/docs/reference/ds.sample.html index 8ebc307c..1bf8b883 100644 --- a/docs/reference/ds.sample.html +++ b/docs/reference/ds.sample.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -234,11 +234,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.scatterPlot.html b/docs/reference/ds.scatterPlot.html index 5c792f45..6ca8eb68 100644 --- a/docs/reference/ds.scatterPlot.html +++ b/docs/reference/ds.scatterPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -222,11 +222,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.seq.html b/docs/reference/ds.seq.html index 2235f610..43c8c8ae 100644 --- a/docs/reference/ds.seq.html +++ b/docs/reference/ds.seq.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -213,11 +213,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.setDefaultOpals.html b/docs/reference/ds.setDefaultOpals.html index 2753f52a..20a68bac 100644 --- a/docs/reference/ds.setDefaultOpals.html +++ b/docs/reference/ds.setDefaultOpals.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -93,11 +93,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.setSeed.html b/docs/reference/ds.setSeed.html index f20baffa..45666e14 100644 --- a/docs/reference/ds.setSeed.html +++ b/docs/reference/ds.setSeed.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -156,11 +156,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.skewness.html b/docs/reference/ds.skewness.html index 86ff4c8c..f4cdaec2 100644 --- a/docs/reference/ds.skewness.html +++ b/docs/reference/ds.skewness.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -154,11 +154,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.sqrt.html b/docs/reference/ds.sqrt.html index 46c711cb..3d9f8367 100644 --- a/docs/reference/ds.sqrt.html +++ b/docs/reference/ds.sqrt.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -146,11 +146,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.subset.html b/docs/reference/ds.subset.html index 69240cf0..afbad61a 100644 --- a/docs/reference/ds.subset.html +++ b/docs/reference/ds.subset.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -180,11 +180,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.subsetByClass.html b/docs/reference/ds.subsetByClass.html index 8a8fad3b..6135d613 100644 --- a/docs/reference/ds.subsetByClass.html +++ b/docs/reference/ds.subsetByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -142,11 +142,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.summary.html b/docs/reference/ds.summary.html index 309c6a0d..4dd800cf 100644 --- a/docs/reference/ds.summary.html +++ b/docs/reference/ds.summary.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -139,11 +139,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table.html b/docs/reference/ds.table.html index 4c524ddd..dc4e3539 100644 --- a/docs/reference/ds.table.html +++ b/docs/reference/ds.table.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -284,11 +284,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table1D.html b/docs/reference/ds.table1D.html index cd8e6c28..a8bcc49c 100644 --- a/docs/reference/ds.table1D.html +++ b/docs/reference/ds.table1D.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -160,11 +160,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table2D.html b/docs/reference/ds.table2D.html index 96270839..f9eec72f 100644 --- a/docs/reference/ds.table2D.html +++ b/docs/reference/ds.table2D.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -139,11 +139,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.tapply.assign.html b/docs/reference/ds.tapply.assign.html index c65eeacf..bbc812ec 100644 --- a/docs/reference/ds.tapply.assign.html +++ b/docs/reference/ds.tapply.assign.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -212,11 +212,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.tapply.html b/docs/reference/ds.tapply.html index d1d6d8d8..a4f405a2 100644 --- a/docs/reference/ds.tapply.html +++ b/docs/reference/ds.tapply.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -203,11 +203,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.testObjExists.html b/docs/reference/ds.testObjExists.html index 2dc6b97d..4f7e88cd 100644 --- a/docs/reference/ds.testObjExists.html +++ b/docs/reference/ds.testObjExists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.unList.html b/docs/reference/ds.unList.html index 1a0b9c55..c0f9f0e5 100644 --- a/docs/reference/ds.unList.html +++ b/docs/reference/ds.unList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -149,11 +149,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.unique.html b/docs/reference/ds.unique.html index 5d1cd79b..4fedc360 100644 --- a/docs/reference/ds.unique.html +++ b/docs/reference/ds.unique.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -122,11 +122,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.var.html b/docs/reference/ds.var.html index 030dc4cd..979dd0fb 100644 --- a/docs/reference/ds.var.html +++ b/docs/reference/ds.var.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -153,11 +153,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.vectorCalc.html b/docs/reference/ds.vectorCalc.html index 43e81df9..2b2f6556 100644 --- a/docs/reference/ds.vectorCalc.html +++ b/docs/reference/ds.vectorCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -120,11 +120,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/extract.html b/docs/reference/extract.html index eacb3fcf..b60865ca 100644 --- a/docs/reference/extract.html +++ b/docs/reference/extract.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -72,11 +72,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/getPooledMean.html b/docs/reference/getPooledMean.html index 4986842d..fbb3a4f1 100644 --- a/docs/reference/getPooledMean.html +++ b/docs/reference/getPooledMean.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -79,11 +79,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/getPooledVar.html b/docs/reference/getPooledVar.html index 0286fd8e..67863a9a 100644 --- a/docs/reference/getPooledVar.html +++ b/docs/reference/getPooledVar.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -79,11 +79,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/glmChecks.html b/docs/reference/glmChecks.html index 5a944f9e..da4f0ea1 100644 --- a/docs/reference/glmChecks.html +++ b/docs/reference/glmChecks.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -100,11 +100,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 0ceeb7bf..48f904e0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -534,11 +534,11 @@

All functions
-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/isAssigned.html b/docs/reference/isAssigned.html index b3d66e75..1c0e6f3d 100644 --- a/docs/reference/isAssigned.html +++ b/docs/reference/isAssigned.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -80,11 +80,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/isDefined.html b/docs/reference/isDefined.html index 54184020..45599cf8 100644 --- a/docs/reference/isDefined.html +++ b/docs/reference/isDefined.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -91,11 +91,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/logical2int.html b/docs/reference/logical2int.html index ac52dac1..9041bf11 100644 --- a/docs/reference/logical2int.html +++ b/docs/reference/logical2int.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -74,11 +74,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper0a.html b/docs/reference/meanByClassHelper0a.html index 8d6cfebe..ae313567 100644 --- a/docs/reference/meanByClassHelper0a.html +++ b/docs/reference/meanByClassHelper0a.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -93,11 +93,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper0b.html b/docs/reference/meanByClassHelper0b.html index f35054ef..7b2fb067 100644 --- a/docs/reference/meanByClassHelper0b.html +++ b/docs/reference/meanByClassHelper0b.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -97,11 +97,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper1.html b/docs/reference/meanByClassHelper1.html index 810f46d7..a27aa16f 100644 --- a/docs/reference/meanByClassHelper1.html +++ b/docs/reference/meanByClassHelper1.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -90,11 +90,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper2.html b/docs/reference/meanByClassHelper2.html index 7540f66f..b9350cc6 100644 --- a/docs/reference/meanByClassHelper2.html +++ b/docs/reference/meanByClassHelper2.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -91,11 +91,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper3.html b/docs/reference/meanByClassHelper3.html index c5eb79f5..8e2fcf81 100644 --- a/docs/reference/meanByClassHelper3.html +++ b/docs/reference/meanByClassHelper3.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -90,11 +90,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper4.html b/docs/reference/meanByClassHelper4.html index ef479e86..0cff4865 100644 --- a/docs/reference/meanByClassHelper4.html +++ b/docs/reference/meanByClassHelper4.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -100,11 +100,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/rowPercent.html b/docs/reference/rowPercent.html index da5df3fd..499824f1 100644 --- a/docs/reference/rowPercent.html +++ b/docs/reference/rowPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -76,11 +76,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/subsetHelper.html b/docs/reference/subsetHelper.html index 33f96c87..0d8c1f4c 100644 --- a/docs/reference/subsetHelper.html +++ b/docs/reference/subsetHelper.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/dsBase_6.3.1-permissive.tar.gz b/dsBase_6.3.2-permissive.tar.gz similarity index 53% rename from dsBase_6.3.1-permissive.tar.gz rename to dsBase_6.3.2-permissive.tar.gz index 4acec10b..0d70f01c 100644 Binary files a/dsBase_6.3.1-permissive.tar.gz and b/dsBase_6.3.2-permissive.tar.gz differ diff --git a/dsBase_6.3.1.tar.gz b/dsBase_6.3.2.tar.gz similarity index 50% rename from dsBase_6.3.1.tar.gz rename to dsBase_6.3.2.tar.gz index 042b8a37..5d93ba95 100644 Binary files a/dsBase_6.3.1.tar.gz and b/dsBase_6.3.2.tar.gz differ diff --git a/man/checkClass.Rd b/man/checkClass.Rd index 85931e59..38dc642c 100644 --- a/man/checkClass.Rd +++ b/man/checkClass.Rd @@ -7,8 +7,8 @@ checkClass(datasources = NULL, obj = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{obj}{a string character, the name of the object to check for.} } diff --git a/man/ds.Boole.Rd b/man/ds.Boole.Rd index e102c872..46d27e4f 100644 --- a/man/ds.Boole.Rd +++ b/man/ds.Boole.Rd @@ -33,9 +33,9 @@ Default \code{'NA'}. For more information see details.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{boole.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.Boole} returns the object specified by the \code{newobj} argument diff --git a/man/ds.abs.Rd b/man/ds.abs.Rd index b408cacd..639ebd3e 100644 --- a/man/ds.abs.Rd +++ b/man/ds.abs.Rd @@ -12,9 +12,9 @@ ds.abs(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default name is set to \code{abs.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.abs} assigns a vector for each study that includes the absolute values of diff --git a/man/ds.asCharacter.Rd b/man/ds.asCharacter.Rd index b11fc4f2..447d9cf9 100644 --- a/man/ds.asCharacter.Rd +++ b/man/ds.asCharacter.Rd @@ -13,9 +13,9 @@ character.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{ascharacter.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asCharacter} returns the object converted into a class character diff --git a/man/ds.asDataMatrix.Rd b/man/ds.asDataMatrix.Rd index 4f286edd..e6ea9eb9 100644 --- a/man/ds.asDataMatrix.Rd +++ b/man/ds.asDataMatrix.Rd @@ -13,9 +13,9 @@ a matrix.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{asdatamatrix.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asDataMatrix} returns the object converted into a matrix diff --git a/man/ds.asFactor.Rd b/man/ds.asFactor.Rd index bdd9a79e..c412df38 100644 --- a/man/ds.asFactor.Rd +++ b/man/ds.asFactor.Rd @@ -33,9 +33,9 @@ to be used in the creation of the matrix with dummy variables. If the \code{fixed.dummy.vars} is set to FALSE then any value of the baseline level is not taken into account.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asFactor} returns the unique levels of the converted diff --git a/man/ds.asFactorSimple.Rd b/man/ds.asFactorSimple.Rd index 07746f8b..d54776a1 100644 --- a/man/ds.asFactorSimple.Rd +++ b/man/ds.asFactorSimple.Rd @@ -17,9 +17,9 @@ the name of the variable to be converted to a factor.} \item{newobj.name}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{asfactor.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ an output vector of class factor to the serverside. In addition, returns a validity diff --git a/man/ds.asInteger.Rd b/man/ds.asInteger.Rd index 49d8ca56..d2f0455b 100644 --- a/man/ds.asInteger.Rd +++ b/man/ds.asInteger.Rd @@ -13,9 +13,9 @@ an integer.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{asinteger.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asInteger} returns the R object converted into an integer diff --git a/man/ds.asList.Rd b/man/ds.asList.Rd index dbb8439b..1e2e3c73 100644 --- a/man/ds.asList.Rd +++ b/man/ds.asList.Rd @@ -13,9 +13,9 @@ a list.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{aslist.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asList} returns the R object converted into a list diff --git a/man/ds.asLogical.Rd b/man/ds.asLogical.Rd index 479ca72b..c42d2e6a 100644 --- a/man/ds.asLogical.Rd +++ b/man/ds.asLogical.Rd @@ -13,9 +13,9 @@ input object to be coerced to a logical.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{aslogical.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asLogical} returns the R object converted into a logical diff --git a/man/ds.asMatrix.Rd b/man/ds.asMatrix.Rd index 5c2e991a..70948014 100644 --- a/man/ds.asMatrix.Rd +++ b/man/ds.asMatrix.Rd @@ -13,9 +13,9 @@ a matrix.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{asmatrix.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asMatrix} returns the object converted into a matrix diff --git a/man/ds.asNumeric.Rd b/man/ds.asNumeric.Rd index 90f18101..a07204c1 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -13,9 +13,9 @@ a numeric.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{asnumeric.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asNumeric} returns the R object converted into a numeric class diff --git a/man/ds.assign.Rd b/man/ds.assign.Rd index 30cf5d12..e09d426f 100644 --- a/man/ds.assign.Rd +++ b/man/ds.assign.Rd @@ -12,9 +12,9 @@ ds.assign(toAssign = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{assign.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.assign} returns the R object assigned to a name diff --git a/man/ds.auc.Rd b/man/ds.auc.Rd index 1bdc075f..0ca1a5d3 100644 --- a/man/ds.auc.Rd +++ b/man/ds.auc.Rd @@ -12,9 +12,9 @@ ds.auc(pred = NULL, y = NULL, datasources = NULL) \item{y}{the name of the outcome variable. Note that this variable should include the complete cases that are used in the regression model.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ returns the AUC and its standard error diff --git a/man/ds.boxPlot.Rd b/man/ds.boxPlot.Rd index 2831c4f9..742922df 100644 --- a/man/ds.boxPlot.Rd +++ b/man/ds.boxPlot.Rd @@ -32,7 +32,7 @@ holds the information to be plotted} \item{type}{\code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server \code{"split"})} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ \code{ggplot} object diff --git a/man/ds.boxPlotGG.Rd b/man/ds.boxPlotGG.Rd index 93f798b7..14627138 100644 --- a/man/ds.boxPlotGG.Rd +++ b/man/ds.boxPlotGG.Rd @@ -34,7 +34,7 @@ of this object must be: \cr \item{type}{\code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server \code{"split"})} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ \code{ggplot} object diff --git a/man/ds.boxPlotGG_data_Treatment.Rd b/man/ds.boxPlotGG_data_Treatment.Rd index 8a264aed..9788f0c7 100644 --- a/man/ds.boxPlotGG_data_Treatment.Rd +++ b/man/ds.boxPlotGG_data_Treatment.Rd @@ -21,7 +21,7 @@ ds.boxPlotGG_data_Treatment( \item{group2}{\code{character} (default \code{NULL}) Name of the second grouping variable.} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ Does not return nothing, it creates the table \code{"boxPlotRawData"} on the server arranged to be passed to the diff --git a/man/ds.boxPlotGG_data_Treatment_numeric.Rd b/man/ds.boxPlotGG_data_Treatment_numeric.Rd index 860e223e..56ead361 100644 --- a/man/ds.boxPlotGG_data_Treatment_numeric.Rd +++ b/man/ds.boxPlotGG_data_Treatment_numeric.Rd @@ -9,7 +9,7 @@ ds.boxPlotGG_data_Treatment_numeric(vector, datasources = NULL) \arguments{ \item{vector}{\code{character} Name of the table on the server side that holds the information to be plotted later} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ Does not return nothing, it creates the table \code{"boxPlotRawDataNumeric"} on the server arranged to be passed to the diff --git a/man/ds.boxPlotGG_numeric.Rd b/man/ds.boxPlotGG_numeric.Rd index cb98d9ad..a71a0e0a 100644 --- a/man/ds.boxPlotGG_numeric.Rd +++ b/man/ds.boxPlotGG_numeric.Rd @@ -22,7 +22,7 @@ ds.boxPlotGG_numeric( \item{type}{\code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server \code{"split"})} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ \code{ggplot} object diff --git a/man/ds.boxPlotGG_table.Rd b/man/ds.boxPlotGG_table.Rd index a0f12f7c..4318ffb8 100644 --- a/man/ds.boxPlotGG_table.Rd +++ b/man/ds.boxPlotGG_table.Rd @@ -31,7 +31,7 @@ ds.boxPlotGG_table( \item{type}{\code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server \code{"split"})} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ \code{ggplot} object diff --git a/man/ds.bp_standards.Rd b/man/ds.bp_standards.Rd index 09ecfa01..edbdd06d 100644 --- a/man/ds.bp_standards.Rd +++ b/man/ds.bp_standards.Rd @@ -33,9 +33,9 @@ blood pressure.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default name is set to \code{bp.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ assigns a new object on the server-side. The assigned object is a list diff --git a/man/ds.c.Rd b/man/ds.c.Rd index ddd4db49..bc899891 100644 --- a/man/ds.c.Rd +++ b/man/ds.c.Rd @@ -12,9 +12,9 @@ ds.c(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{c.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.c} returns the vector of concatenating R diff --git a/man/ds.cbind.Rd b/man/ds.cbind.Rd index 4f3dc8ee..ca20b9e8 100644 --- a/man/ds.cbind.Rd +++ b/man/ds.cbind.Rd @@ -30,9 +30,9 @@ For more information see \strong{Details}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Defaults \code{cbind.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default FALSE.} diff --git a/man/ds.changeRefGroup.Rd b/man/ds.changeRefGroup.Rd index 124cd903..1730a62f 100644 --- a/man/ds.changeRefGroup.Rd +++ b/man/ds.changeRefGroup.Rd @@ -24,9 +24,9 @@ that is stored on the server-side. Default \code{changerefgroup.newobj}.} 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).} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.changeRefGroup} returns a new vector with the specified level as a reference diff --git a/man/ds.class.Rd b/man/ds.class.Rd index 59f1efa2..b2fc0f07 100644 --- a/man/ds.class.Rd +++ b/man/ds.class.Rd @@ -9,9 +9,9 @@ ds.class(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string providing the name of the input R object.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.class} returns the type of the R object. diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd index 3f44ee30..e7391081 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -9,9 +9,9 @@ ds.colnames(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string providing the name of the input data frame or matrix.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.colnames} returns the column names of diff --git a/man/ds.completeCases.Rd b/man/ds.completeCases.Rd index a5b0b8a0..f5df7658 100644 --- a/man/ds.completeCases.Rd +++ b/man/ds.completeCases.Rd @@ -15,9 +15,9 @@ that is stored on the data servers. If the user does not specify a name, then th generates a name for the generated object that is the name of the input object with the suffix "_complete.cases"} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified, the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.completeCases} generates a modified data frame, matrix or vector from which diff --git a/man/ds.contourPlot.Rd b/man/ds.contourPlot.Rd index e0df915f..f9335d34 100644 --- a/man/ds.contourPlot.Rd +++ b/man/ds.contourPlot.Rd @@ -44,9 +44,9 @@ see details.} \item{noise}{the percentage of the initial variance that is used as the variance of the embedded noise if the argument \code{method} is set to \code{'probabilistic'}. For more information see details.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.contourPlot} returns a contour plot to the client-side. diff --git a/man/ds.cor.Rd b/man/ds.cor.Rd index d01c9b3b..030defae 100644 --- a/man/ds.cor.Rd +++ b/man/ds.cor.Rd @@ -15,9 +15,9 @@ Default NULL.} \item{type}{a character string that represents the type of analysis to carry out. This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. For more information see details.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.cor} returns a list containing the number of missing values in each variable, diff --git a/man/ds.corTest.Rd b/man/ds.corTest.Rd index bb2384d4..fac90553 100644 --- a/man/ds.corTest.Rd +++ b/man/ds.corTest.Rd @@ -36,9 +36,9 @@ This must be set to \code{'split'} or \code{'combine'}. Default is set to \code{ \code{type} is set to "combine" then an approximated pooled correlation is estimated based on Fisher's z transformation.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.corTest} returns to the client-side the results of the correlation test. diff --git a/man/ds.cov.Rd b/man/ds.cov.Rd index 1d8b5455..3fe9ec8f 100644 --- a/man/ds.cov.Rd +++ b/man/ds.cov.Rd @@ -25,9 +25,9 @@ presence of missing values. This must be set to \code{'casewise.complete'} or \item{type}{a character string that represents the type of analysis to carry out. This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. For more information see details.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.cov} returns a list containing the number of missing values in each variable, the number of missing values diff --git a/man/ds.dataFrame.Rd b/man/ds.dataFrame.Rd index 4a3e80dd..5c7d82d7 100644 --- a/man/ds.dataFrame.Rd +++ b/man/ds.dataFrame.Rd @@ -48,9 +48,9 @@ are the same} \item{newobj}{a character string that provides the name for the output data frame that is stored on the data servers. Default \code{dataframe.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default is FALSE.} diff --git a/man/ds.dataFrameFill.Rd b/man/ds.dataFrameFill.Rd index 3183d61c..44eef9e5 100644 --- a/man/ds.dataFrameFill.Rd +++ b/man/ds.dataFrameFill.Rd @@ -13,9 +13,9 @@ filled with extra columns of missing values.} \item{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".} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.dataFrameFill} returns the object specified by the \code{newobj} argument which diff --git a/man/ds.dataFrameSort.Rd b/man/ds.dataFrameSort.Rd index 7b9e843a..252227e5 100644 --- a/man/ds.dataFrameSort.Rd +++ b/man/ds.dataFrameSort.Rd @@ -30,9 +30,9 @@ to sort the data frame. This can be set as that is stored on the data servers. Default \code{dataframesort.newobj}. where \code{df.name} is the first argument of \code{ds.dataFrameSort()}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.dataFrameSort} returns the sorted data frame is written to the server-side. diff --git a/man/ds.dataFrameSubset.Rd b/man/ds.dataFrameSubset.Rd index 2f6068d3..58b557fe 100644 --- a/man/ds.dataFrameSubset.Rd +++ b/man/ds.dataFrameSubset.Rd @@ -42,9 +42,9 @@ If FALSE or NULL all rows with at least one missing values are removed from the \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{dataframesubset.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default FALSE.} diff --git a/man/ds.densityGrid.Rd b/man/ds.densityGrid.Rd index 15e29977..89cc4348 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -26,9 +26,9 @@ If \code{type} is set to instead if \code{type} is set to \code{'split'} one grid density matrix is generated. Default \code{'combine'}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.densityGrid} returns a grid density matrix. diff --git a/man/ds.dim.Rd b/man/ds.dim.Rd index b6a86b57..ea3aaa6d 100644 --- a/man/ds.dim.Rd +++ b/man/ds.dim.Rd @@ -20,9 +20,9 @@ Default \code{'both'}.} \item{checks}{logical. If TRUE undertakes all DataSHIELD checks (time-consuming). Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.dim} retrieves to the client-side the dimension of the object diff --git a/man/ds.elspline.Rd b/man/ds.elspline.Rd index 26c5f6cc..e6e32197 100644 --- a/man/ds.elspline.Rd +++ b/man/ds.elspline.Rd @@ -26,9 +26,9 @@ intervals along the range of x} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{elspline.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ an object of class "lspline" and "matrix", which its name is specified by the diff --git a/man/ds.exists.Rd b/man/ds.exists.Rd index 029c66b9..2352a294 100644 --- a/man/ds.exists.Rd +++ b/man/ds.exists.Rd @@ -9,9 +9,9 @@ ds.exists(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string providing the name of the object to look for.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.exists} returns a logical object. diff --git a/man/ds.exp.Rd b/man/ds.exp.Rd index 07e212c9..875dbe00 100644 --- a/man/ds.exp.Rd +++ b/man/ds.exp.Rd @@ -12,9 +12,9 @@ ds.exp(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{exp.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.exp} returns a vector for each study of the exponential values for the numeric vector diff --git a/man/ds.gamlss.Rd b/man/ds.gamlss.Rd index 60bd6d17..4c7bc169 100644 --- a/man/ds.gamlss.Rd +++ b/man/ds.gamlss.Rd @@ -96,9 +96,9 @@ only.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{gamlss_res}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ a gamlss object with all components as in the native R gamlss function. diff --git a/man/ds.getWGSR.Rd b/man/ds.getWGSR.Rd index 1e3b8672..f48b9a28 100644 --- a/man/ds.getWGSR.Rd +++ b/man/ds.getWGSR.Rd @@ -66,9 +66,9 @@ by the formula $age_days=age_months*(365.25/12)$.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Defaults \code{getWGSR.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.getWGSR} assigns a vector for each study that includes the z-scores for the diff --git a/man/ds.glm.Rd b/man/ds.glm.Rd index 6bd50a4c..67728e00 100644 --- a/man/ds.glm.Rd +++ b/man/ds.glm.Rd @@ -58,9 +58,9 @@ of parameter estimates is returned. Default FALSE.} \item{viewCor}{logical. If TRUE the correlation matrix of parameter estimates is returned. Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ Many of the elements of the output list returned by \code{ds.glm} are @@ -138,7 +138,7 @@ function is also allowed by \code{ds.glm}. Many GLMs can be fitted very simply using a formula such as: -\deqn{y~a+b+c+d} +\eqn{y~a+b+c+d} which simply means fit a GLM with \code{y} as the outcome variable and \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -147,7 +147,7 @@ By default all such models also include an intercept (regression constant) term. Instead, if you need to fit a more complex model, for example: - \deqn{EVENT~1+TID+SEXF*AGE.60} + \eqn{EVENT~1+TID+SEXF*AGE.60} In the above model the outcome variable is \code{EVENT} and the covariates diff --git a/man/ds.glmSLMA.Rd b/man/ds.glmSLMA.Rd index f64e6a5c..f0a9863d 100644 --- a/man/ds.glmSLMA.Rd +++ b/man/ds.glmSLMA.Rd @@ -58,9 +58,9 @@ For more information see \strong{Details}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ The serverside aggregate functions \code{glmSLMADS1} and \code{glmSLMADS2} return @@ -241,7 +241,7 @@ function is also allowed by \code{ds.glmSLMA}. Many glms can be fitted very simply using a formula such as: -\deqn{y~a+b+c+d} +\eqn{y~a+b+c+d} which simply means fit a glm with \code{y} as the outcome variable and \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -250,7 +250,7 @@ By default all such models also include an intercept (regression constant) term. Instead, if you need to fit a more complex model, for example: - \deqn{EVENT~1+TID+SEXF*AGE.60} +\eqn{EVENT~1+TID+SEXF*AGE.60} In the above model the outcome variable is \code{EVENT} and the covariates diff --git a/man/ds.glmerSLMA.Rd b/man/ds.glmerSLMA.Rd index 8ee7cdfd..8ad49c3a 100644 --- a/man/ds.glmerSLMA.Rd +++ b/man/ds.glmerSLMA.Rd @@ -45,9 +45,9 @@ that contains all of the variables in the GLME formula. For more information see \item{checks}{logical. If TRUE \code{ds.glmerSLMA} checks the structural integrity of the model. Default FALSE. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{family}{a character string specifying the distribution of the observed value of the outcome variable around the predictions generated by the linear predictor. @@ -169,17 +169,17 @@ If it did not some information about the reason for this is reported. In \code{formula} most shortcut notation allowed by \code{glmer()} function is also allowed by \code{ds.glmerSLMA}. Many GLMEs can be fitted very simply using a formula like: -\deqn{y~a+b+(1|c)} +\eqn{y~a+b+(1|c)} which simply means fit an GLME with \code{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), \code{a} and \code{b} as fixed effects, and \code{c} as a random effect or grouping factor. It is also possible to fit models with random slopes by specifying a model such as -\deqn{y~a+b+(1+b|c)} +\eqn{y~a+b+(1+b|c)} where the effect of \code{b} can vary randomly between groups defined by \code{c}. Implicit nesting can be specified with formulas such as: \eqn{y~a+b+(1|c/d)} -or \eqn{y~a+b+(1|c)+(1|c:d)}. +or \eqn{y~a+b+(1|c)+(1|c:d)}. The \code{dataName} argument avoids you having to specify the name of the diff --git a/man/ds.heatmapPlot.Rd b/man/ds.heatmapPlot.Rd index c1669431..3ab17da9 100644 --- a/man/ds.heatmapPlot.Rd +++ b/man/ds.heatmapPlot.Rd @@ -49,9 +49,9 @@ noise if the argument \code{method} is set to \code{'probabilistic'}. Default \code{noise} value is \code{0.25}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.heatmapPlot} returns to the client-side a heat map plot and a message specifying diff --git a/man/ds.hetcor.Rd b/man/ds.hetcor.Rd index aa7d0713..e236a0e9 100644 --- a/man/ds.hetcor.Rd +++ b/man/ds.hetcor.Rd @@ -34,9 +34,9 @@ nearPD directly.} \item{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.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ Returns an object of class "hetcor" from each study, with the following components: the diff --git a/man/ds.histogram.Rd b/man/ds.histogram.Rd index 12af4457..17de73da 100644 --- a/man/ds.histogram.Rd +++ b/man/ds.histogram.Rd @@ -46,9 +46,9 @@ plot. The \code{vertical.axis} argument can be set as \code{'Frequency'} or \cod Default \code{'Frequency'}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ one or more histogram objects and plots depending on the argument \code{type} diff --git a/man/ds.igb_standards.Rd b/man/ds.igb_standards.Rd index 6ea70b2f..499220a2 100644 --- a/man/ds.igb_standards.Rd +++ b/man/ds.igb_standards.Rd @@ -39,9 +39,9 @@ recode the categories to Male/Female before the use of ds.igb_standards.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default name is set to \code{igb.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ assigns the converted measurement as a new object on the server-side diff --git a/man/ds.isNA.Rd b/man/ds.isNA.Rd index 0c94b9eb..ec6b2f6f 100644 --- a/man/ds.isNA.Rd +++ b/man/ds.isNA.Rd @@ -9,9 +9,9 @@ ds.isNA(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of the vector to check.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.isNA} returns a boolean. If it is TRUE the vector is empty diff --git a/man/ds.isValid.Rd b/man/ds.isValid.Rd index 2bda8557..2f927ae2 100644 --- a/man/ds.isValid.Rd +++ b/man/ds.isValid.Rd @@ -9,9 +9,9 @@ ds.isValid(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of a vector, dataframe or matrix.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.isValid} returns a boolean. If it is TRUE input object is valid, FALSE otherwise. diff --git a/man/ds.kurtosis.Rd b/man/ds.kurtosis.Rd index 4a9b2a32..4b698adf 100644 --- a/man/ds.kurtosis.Rd +++ b/man/ds.kurtosis.Rd @@ -18,9 +18,9 @@ if \code{type} is set to 'split', 'splits' or 's', the kurtosis is returned sepa if \code{type} is set to 'both' or 'b', both sets of outputs are produced. The default value is set to 'both'.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ a matrix showing the kurtosis of the input numeric variable, the number of valid observations and diff --git a/man/ds.length.Rd b/man/ds.length.Rd index 08b513a1..27e105bc 100644 --- a/man/ds.length.Rd +++ b/man/ds.length.Rd @@ -22,9 +22,9 @@ Default \code{'both'}.} Default FALSE to save time. It is suggested that checks should only be undertaken once the function call has failed.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.length} returns to the client-side the pooled length of a vector or a list, diff --git a/man/ds.levels.Rd b/man/ds.levels.Rd index 0a372660..fbdab0c4 100644 --- a/man/ds.levels.Rd +++ b/man/ds.levels.Rd @@ -9,9 +9,9 @@ ds.levels(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of a factor variable.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.levels} returns to the client-side the levels of a factor diff --git a/man/ds.lexis.Rd b/man/ds.lexis.Rd index 0c75e1f0..a57cd28c 100644 --- a/man/ds.lexis.Rd +++ b/man/ds.lexis.Rd @@ -41,9 +41,9 @@ variables to include in the final expanded table. For more information see \stro \item{expandDF}{a character string denoting the name of the new data frame containing the expanded data set. Default \code{lexis.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.lexis} returns to the server-side a data frame for each study with diff --git a/man/ds.list.Rd b/man/ds.list.Rd index de5b69e7..d6ebd00e 100644 --- a/man/ds.list.Rd +++ b/man/ds.list.Rd @@ -12,9 +12,9 @@ ds.list(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{list.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.list} returns a list of objects for each study that is stored on the server-side. diff --git a/man/ds.listDisclosureSettings.Rd b/man/ds.listDisclosureSettings.Rd index d04448b8..23ab83fd 100644 --- a/man/ds.listDisclosureSettings.Rd +++ b/man/ds.listDisclosureSettings.Rd @@ -7,9 +7,9 @@ ds.listDisclosureSettings(datasources = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.listDisclosureSettings} returns a list containing the current settings of the diff --git a/man/ds.listServersideFunctions.Rd b/man/ds.listServersideFunctions.Rd index 30931c62..70d9ba5d 100644 --- a/man/ds.listServersideFunctions.Rd +++ b/man/ds.listServersideFunctions.Rd @@ -7,9 +7,9 @@ ds.listServersideFunctions(datasources = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.listServersideFunctions} returns to the client-side @@ -20,7 +20,7 @@ Firstly lists assign and then aggregate functions. Lists all current server-side functions } \details{ -Uses \code{\link{datashield.methods}} function from \code{DSI} package to list all +Uses \code{\link[DSI]{datashield.methods}} function from \code{DSI} package to list all assign and aggregate functions on the available data repository servers. The only choice of arguments is in \code{datasources}; i.e. which studies to interrogate. Once the studies have diff --git a/man/ds.lmerSLMA.Rd b/man/ds.lmerSLMA.Rd index 68489737..dbd9b7fb 100644 --- a/man/ds.lmerSLMA.Rd +++ b/man/ds.lmerSLMA.Rd @@ -44,9 +44,9 @@ For more information see \strong{Details}.} \item{checks}{logical. If TRUE \code{ds.lmerSLMA} checks the structural integrity of the model. Default FALSE. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{REML}{logical. If TRUE the REstricted Maximum Likelihood (REML) is used for parameter optimization. @@ -168,12 +168,12 @@ obtained using R help for \code{lmer} and the \code{lme4} package. In \code{formula} most shortcut notation allowed by \code{lmer()} function is also allowed by \code{ds.lmerSLMA}. Many LMEs can be fitted very simply using a formula like: -\deqn{y ~ a + b + (1 | c)} +\eqn{y ~ a + b + (1 | c)} which simply means fit an LME with \code{y} as the outcome variable with \code{a} and \code{b} as fixed effects, and \code{c} as a random effect or grouping factor. It is also possible to fit models with random slopes by specifying a model such as -\deqn{y ~ a + b + (1 + b | c)} +\eqn{y ~ a + b + (1 + b | c)} where the effect of \code{b} can vary randomly between groups defined by \code{c}. Implicit nesting can be specified with formulae such as \eqn{y ~ a + b + (1 | c / d)} or \eqn{y ~ a + b + (1 | c) + (1 | c : d)}. diff --git a/man/ds.log.Rd b/man/ds.log.Rd index b988fb84..6ab8fee7 100644 --- a/man/ds.log.Rd +++ b/man/ds.log.Rd @@ -15,9 +15,9 @@ Default \code{exp(1)}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the server-side. Default \code{log.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.log} returns a vector for each study of the transformed values for the numeric vector diff --git a/man/ds.look.Rd b/man/ds.look.Rd index 4a59c166..3cecb462 100644 --- a/man/ds.look.Rd +++ b/man/ds.look.Rd @@ -13,9 +13,9 @@ For more information see \strong{Details}.} \item{checks}{logical. If TRUE the optional checks are undertaken. Default FALSE to save time.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ the output from the specified server-side aggregate function to the client-side. diff --git a/man/ds.ls.Rd b/man/ds.ls.Rd index e05feb5e..e1b5d324 100644 --- a/man/ds.ls.Rd +++ b/man/ds.ls.Rd @@ -26,9 +26,9 @@ set as a valid integer, \code{ds.ls} will list all objects in the server-side R identified by \code{env.to.search} in the search path. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.ls} returns to the client-side a list containing: \cr diff --git a/man/ds.lspline.Rd b/man/ds.lspline.Rd index 550e2397..0cf8e5aa 100644 --- a/man/ds.lspline.Rd +++ b/man/ds.lspline.Rd @@ -25,9 +25,9 @@ ds.lspline( \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{lspline.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ an object of class "lspline" and "matrix", which its name is specified by the diff --git a/man/ds.make.Rd b/man/ds.make.Rd index d87cc537..197518bc 100644 --- a/man/ds.make.Rd +++ b/man/ds.make.Rd @@ -12,9 +12,9 @@ ds.make(toAssign = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{make.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.make} returns the new object which is written to the diff --git a/man/ds.matrix.Rd b/man/ds.matrix.Rd index 27b3e9d8..b2928c3e 100644 --- a/man/ds.matrix.Rd +++ b/man/ds.matrix.Rd @@ -43,9 +43,9 @@ the row and column names respectively.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{matrix.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrix} returns the created matrix which is written on the server-side. diff --git a/man/ds.matrixDet.Rd b/man/ds.matrixDet.Rd index 1c419f4d..e827e815 100644 --- a/man/ds.matrixDet.Rd +++ b/man/ds.matrixDet.Rd @@ -15,9 +15,9 @@ variable that is stored on the data servers. Default \code{matrixdet.newobj}.} \item{logarithm}{logical. If TRUE the logarithm of the modulus of the determinant is calculated. Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixDet} returns the determinant of an existing matrix on the server-side. diff --git a/man/ds.matrixDet.report.Rd b/man/ds.matrixDet.report.Rd index e4fc3569..0a5c021d 100644 --- a/man/ds.matrixDet.report.Rd +++ b/man/ds.matrixDet.report.Rd @@ -12,9 +12,9 @@ ds.matrixDet.report(M1 = NULL, logarithm = FALSE, datasources = NULL) \item{logarithm}{logical. If TRUE the logarithm of the modulus of the determinant is calculated. Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixDet.report} returns to the client-side diff --git a/man/ds.matrixDiag.Rd b/man/ds.matrixDiag.Rd index a23ab133..84fdba38 100644 --- a/man/ds.matrixDiag.Rd +++ b/man/ds.matrixDiag.Rd @@ -35,9 +35,9 @@ For more information see \strong{Details}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{matrixdiag.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixDiag} returns to the server-side the square matrix diagonal. diff --git a/man/ds.matrixDimnames.Rd b/man/ds.matrixDimnames.Rd index bc5e5813..af56f76a 100644 --- a/man/ds.matrixDimnames.Rd +++ b/man/ds.matrixDimnames.Rd @@ -22,9 +22,9 @@ An empty list is treated as NULL.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{matrixdimnames.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixDimnames} returns to the server-side diff --git a/man/ds.matrixInvert.Rd b/man/ds.matrixInvert.Rd index 0a6ff331..842baee4 100644 --- a/man/ds.matrixInvert.Rd +++ b/man/ds.matrixInvert.Rd @@ -13,9 +13,9 @@ ds.matrixInvert(M1 = NULL, newobj = NULL, datasources = NULL) variable that is stored on the data servers. Default \code{matrixinvert.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixInvert} returns to the server-side the inverts square matrix. diff --git a/man/ds.matrixMult.Rd b/man/ds.matrixMult.Rd index 22a1dbc6..136db26d 100644 --- a/man/ds.matrixMult.Rd +++ b/man/ds.matrixMult.Rd @@ -14,9 +14,9 @@ ds.matrixMult(M1 = NULL, M2 = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{matrixmult.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixMult} returns to the server-side diff --git a/man/ds.matrixTranspose.Rd b/man/ds.matrixTranspose.Rd index 26be7098..67e06867 100644 --- a/man/ds.matrixTranspose.Rd +++ b/man/ds.matrixTranspose.Rd @@ -13,9 +13,9 @@ ds.matrixTranspose(M1 = NULL, newobj = NULL, datasources = NULL) variable that is stored on the data servers. Default \code{matrixtranspose.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixTranspose} returns to the server-side the transpose matrix. diff --git a/man/ds.mean.Rd b/man/ds.mean.Rd index e6d0fd70..d662a389 100644 --- a/man/ds.mean.Rd +++ b/man/ds.mean.Rd @@ -31,9 +31,9 @@ the number of valid (non-missing) observations will be saved on the data server Default FALSE. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.mean} returns to the client-side a list including: \cr diff --git a/man/ds.meanByClass.Rd b/man/ds.meanByClass.Rd index 340b07db..f60ba7a4 100644 --- a/man/ds.meanByClass.Rd +++ b/man/ds.meanByClass.Rd @@ -24,9 +24,9 @@ ds.meanByClass( Default \code{'combine'}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.meanByClass} returns to the client-side a table or a list of tables that diff --git a/man/ds.meanSdGp.Rd b/man/ds.meanSdGp.Rd index 8660b912..964a5dae 100644 --- a/man/ds.meanSdGp.Rd +++ b/man/ds.meanSdGp.Rd @@ -29,9 +29,9 @@ are undertaken to ensure that the input objects are defined in all studies and t variables are of equivalent class in each study. Default is FALSE to save time.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.meanSdGp} returns to the client-side the mean, SD, Nvalid and SEM combined diff --git a/man/ds.merge.Rd b/man/ds.merge.Rd index 24f8e5e3..d6e18558 100644 --- a/man/ds.merge.Rd +++ b/man/ds.merge.Rd @@ -65,9 +65,9 @@ For more information see \code{match} in native R \code{merge} function.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{merge.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.merge} returns the merged data frame that is written on the server-side. diff --git a/man/ds.message.Rd b/man/ds.message.Rd index 6b54e513..ab1dff8d 100644 --- a/man/ds.message.Rd +++ b/man/ds.message.Rd @@ -10,9 +10,9 @@ ds.message(message.obj.name = NULL, datasources = NULL) \item{message.obj.name}{is a character string specifying the name of the list that contains the message.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.message} returns a list object from each study, diff --git a/man/ds.metadata.Rd b/man/ds.metadata.Rd index cc43a67d..128ca9ec 100644 --- a/man/ds.metadata.Rd +++ b/man/ds.metadata.Rd @@ -9,9 +9,9 @@ ds.metadata(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of the object.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.metadata} returns to the client-side the metadata of associated to an object diff --git a/man/ds.mice.Rd b/man/ds.mice.Rd index 59f6f471..8bedcd93 100644 --- a/man/ds.mice.Rd +++ b/man/ds.mice.Rd @@ -54,9 +54,9 @@ that are stored on the data servers. Default \code{imputationSet}. For example, newobj_df="imputationSet", then five imputed dataframes are saved on the servers with names imputationSet.1, imputationSet.2, imputationSet.3, imputationSet.4, imputationSet.5.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ a list with three elements: the method, the predictorMatrix and the post. diff --git a/man/ds.names.Rd b/man/ds.names.Rd index daee0cba..199b20d9 100644 --- a/man/ds.names.Rd +++ b/man/ds.names.Rd @@ -9,11 +9,11 @@ ds.names(xname = NULL, datasources = NULL) \arguments{ \item{xname}{a character string specifying the name of the list.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login that represent the particular data sources (studies) to be addressed by the function call. If the \code{datasources} argument is not specified the default set of connections will be used: -see \code{\link{datashield.connections_default}}.} +see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.names} returns to the client-side the names diff --git a/man/ds.ns.Rd b/man/ds.ns.Rd index 51e3166b..91051172 100644 --- a/man/ds.ns.Rd +++ b/man/ds.ns.Rd @@ -34,9 +34,9 @@ are supplied, the basis parameters do not depend on x. Data can extend beyond Bo \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{ns.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ A matrix of dimension length(x) * df where either df was supplied or if knots were diff --git a/man/ds.numNA.Rd b/man/ds.numNA.Rd index 668e23ed..896c76ee 100644 --- a/man/ds.numNA.Rd +++ b/man/ds.numNA.Rd @@ -9,9 +9,9 @@ ds.numNA(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of the vector.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.numNA} returns to the client-side the number of missing values diff --git a/man/ds.qlspline.Rd b/man/ds.qlspline.Rd index fc9285ae..93460e65 100644 --- a/man/ds.qlspline.Rd +++ b/man/ds.qlspline.Rd @@ -30,9 +30,9 @@ to na.rm of quantile. Default set to TRUE} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{qlspline.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ an object of class "lspline" and "matrix", which its name is specified by the diff --git a/man/ds.quantileMean.Rd b/man/ds.quantileMean.Rd index 56019428..03b469a1 100644 --- a/man/ds.quantileMean.Rd +++ b/man/ds.quantileMean.Rd @@ -13,9 +13,9 @@ ds.quantileMean(x = NULL, type = "combine", datasources = NULL) This can be set as \code{'combine'} or \code{'split'}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.quantileMean} returns to the client-side the quantiles and statistical mean diff --git a/man/ds.rBinom.Rd b/man/ds.rBinom.Rd index e3ee5d16..993083e1 100644 --- a/man/ds.rBinom.Rd +++ b/man/ds.rBinom.Rd @@ -33,9 +33,9 @@ random seed in each data source.} 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.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rBinom} returns random number vectors diff --git a/man/ds.rNorm.Rd b/man/ds.rNorm.Rd index 1149593f..f60071fb 100644 --- a/man/ds.rNorm.Rd +++ b/man/ds.rNorm.Rd @@ -37,9 +37,9 @@ Default is FALSE.} \item{force.output.to.k.decimal.places}{an integer vector that forces the output random numbers vector to have k decimals.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rNorm} returns random number vectors with a normal distribution for each diff --git a/man/ds.rPois.Rd b/man/ds.rPois.Rd index 4fbe5e4f..7ce19a47 100644 --- a/man/ds.rPois.Rd +++ b/man/ds.rPois.Rd @@ -30,9 +30,9 @@ 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.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rPois} returns random number vectors with a Poisson distribution for each study, diff --git a/man/ds.rUnif.Rd b/man/ds.rUnif.Rd index d526fca2..0ffd62aa 100644 --- a/man/ds.rUnif.Rd +++ b/man/ds.rUnif.Rd @@ -39,9 +39,9 @@ return the trigger seed value you have provided. Default is FALSE.} an integer vector that forces the output random numbers vector to have k decimals.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.Unif} returns random number vectors with a uniform distribution for each study, diff --git a/man/ds.rbind.Rd b/man/ds.rbind.Rd index d294f474..75c2a03f 100644 --- a/man/ds.rbind.Rd +++ b/man/ds.rbind.Rd @@ -25,9 +25,9 @@ specifies column names of the output object.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Defaults \code{rbind.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default FALSE.} diff --git a/man/ds.reShape.Rd b/man/ds.reShape.Rd index 9c54b3fc..8acdd161 100644 --- a/man/ds.reShape.Rd +++ b/man/ds.reShape.Rd @@ -49,9 +49,9 @@ to 'wide' format.} that is stored on the data servers. Default \code{reshape.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.reShape} returns to the server-side a reshaped data frame diff --git a/man/ds.recodeLevels.Rd b/man/ds.recodeLevels.Rd index 958b4881..14450927 100644 --- a/man/ds.recodeLevels.Rd +++ b/man/ds.recodeLevels.Rd @@ -20,9 +20,9 @@ to the current number of levels.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{recodelevels.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.recodeLevels} returns to the server-side a variable of type factor diff --git a/man/ds.recodeValues.Rd b/man/ds.recodeValues.Rd index a6af2722..5ebe1f67 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -31,9 +31,9 @@ specify an identical vector of values in both arguments \code{values2replace.vec that is stored on the data servers. Default \code{recodevalues.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{logical. If TRUE console output should be produced to indicate progress. Default FALSE.} diff --git a/man/ds.rep.Rd b/man/ds.rep.Rd index 23a35250..b552ff43 100644 --- a/man/ds.rep.Rd +++ b/man/ds.rep.Rd @@ -44,9 +44,9 @@ the \code{x1} is a character.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{seq.vect}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rep} returns in the server-side a vector with the specified repetitive sequence. diff --git a/man/ds.replaceNA.Rd b/man/ds.replaceNA.Rd index f8480591..3b8a4ec0 100644 --- a/man/ds.replaceNA.Rd +++ b/man/ds.replaceNA.Rd @@ -15,9 +15,9 @@ The length of the list or vector must be equal to the number of servers (studies \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{replacena.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.replaceNA} returns to the server-side a new vector or table structure diff --git a/man/ds.rm.Rd b/man/ds.rm.Rd index 9a6e88af..a6378621 100644 --- a/man/ds.rm.Rd +++ b/man/ds.rm.Rd @@ -9,9 +9,9 @@ ds.rm(x.names = NULL, datasources = NULL) \arguments{ \item{x.names}{a character string specifying the objects to be deleted.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ The \code{ds.rm} function deletes from the server-side diff --git a/man/ds.rowColCalc.Rd b/man/ds.rowColCalc.Rd index dc0992f2..dc4cfbd9 100644 --- a/man/ds.rowColCalc.Rd +++ b/man/ds.rowColCalc.Rd @@ -15,9 +15,9 @@ ds.rowColCalc(x = NULL, operation = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{rowcolcalc.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rowColCalc} returns to the server-side rows and columns sums and means. diff --git a/man/ds.scatterPlot.Rd b/man/ds.scatterPlot.Rd index 773123ac..bbcfa5b5 100644 --- a/man/ds.scatterPlot.Rd +++ b/man/ds.scatterPlot.Rd @@ -43,9 +43,9 @@ For more information see \strong{Details}.} \item{return.coords}{a logical. If TRUE the coordinates of the anonymised data points are return to the Console. Default value is FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.scatterPlot} returns to the client-side one or more scatter diff --git a/man/ds.seq.Rd b/man/ds.seq.Rd index 11578793..e8b7365f 100644 --- a/man/ds.seq.Rd +++ b/man/ds.seq.Rd @@ -41,9 +41,9 @@ For more information see \strong{Details}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{seq.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.seq} returns to the server-side the generated sequence. diff --git a/man/ds.setSeed.Rd b/man/ds.setSeed.Rd index 6577b6cb..6dacac34 100644 --- a/man/ds.setSeed.Rd +++ b/man/ds.setSeed.Rd @@ -10,9 +10,9 @@ ds.setSeed(seed.as.integer = NULL, datasources = NULL) \item{seed.as.integer}{a numeric value or a NULL that primes the random seed in each data source.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ Sets the values of the vector of integers of length 626 known as diff --git a/man/ds.skewness.Rd b/man/ds.skewness.Rd index 9ebab0d6..7c3bda04 100644 --- a/man/ds.skewness.Rd +++ b/man/ds.skewness.Rd @@ -17,9 +17,9 @@ For more information see \strong{Details}. The default value is set to 1.} see \strong{Details}. The default value is set to \code{'both'}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.skewness} returns a matrix showing the skewness of the input numeric variable, diff --git a/man/ds.sqrt.Rd b/man/ds.sqrt.Rd index 62abcc83..b42ecaed 100644 --- a/man/ds.sqrt.Rd +++ b/man/ds.sqrt.Rd @@ -12,9 +12,9 @@ ds.sqrt(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default name is set to \code{sqrt.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.sqrt} assigns a vector for each study that includes the square root values of diff --git a/man/ds.subset.Rd b/man/ds.subset.Rd index 0c2472f2..3db5e3b3 100644 --- a/man/ds.subset.Rd +++ b/man/ds.subset.Rd @@ -33,8 +33,8 @@ operator. This parameter is ignored if the input data is not a vector.} \item{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.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ no data are return to the user, the generated subset dataframe is stored on the server side. diff --git a/man/ds.subsetByClass.Rd b/man/ds.subsetByClass.Rd index d19b5a71..fe372adb 100644 --- a/man/ds.subsetByClass.Rd +++ b/man/ds.subsetByClass.Rd @@ -19,8 +19,8 @@ the default name of this list is 'subClasses'.} \item{variables}{a vector of string characters, the name(s) of the variables to subset by.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ a no data are return to the user but messages are printed out. diff --git a/man/ds.summary.Rd b/man/ds.summary.Rd index f171efe4..2f52cff7 100644 --- a/man/ds.summary.Rd +++ b/man/ds.summary.Rd @@ -9,9 +9,9 @@ ds.summary(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of a numeric or factor variable.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.summary} returns to the client-side the class and diff --git a/man/ds.table.Rd b/man/ds.table.Rd index 4e3fa15d..252232bd 100644 --- a/man/ds.table.Rd +++ b/man/ds.table.Rd @@ -90,8 +90,8 @@ If no explicit name for the table object is specified, but is nevertheless TRUE, the name for the serverside table object defaults to \code{table.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}. If the is to be specified, it should be set without inverted commas: e.g. datasources=connections.em or datasources=default.connections. If you wish to apply the function solely to e.g. the second connection server in a set of three, diff --git a/man/ds.table1D.Rd b/man/ds.table1D.Rd index a4d5c958..d480b3bb 100644 --- a/man/ds.table1D.Rd +++ b/man/ds.table1D.Rd @@ -22,8 +22,8 @@ is set to 'split' a 1-dimensional table is returned for each data source.} 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.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ A list object containing the following items: diff --git a/man/ds.table2D.Rd b/man/ds.table2D.Rd index 00a14d14..aec01d73 100644 --- a/man/ds.table2D.Rd +++ b/man/ds.table2D.Rd @@ -26,8 +26,8 @@ a pooled 2-dimensional table plus a 2-dimensional table for each data source are 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.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ A list object containing the following items: diff --git a/man/ds.tapply.Rd b/man/ds.tapply.Rd index d5aadccf..8d09e89c 100644 --- a/man/ds.tapply.Rd +++ b/man/ds.tapply.Rd @@ -24,9 +24,9 @@ summarizing functions. This can be set as: or \code{"quantile"}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.tapply} returns to the client-side an array of the summarized values. diff --git a/man/ds.tapply.assign.Rd b/man/ds.tapply.assign.Rd index ef1e36d8..f58810b2 100644 --- a/man/ds.tapply.assign.Rd +++ b/man/ds.tapply.assign.Rd @@ -28,9 +28,9 @@ For more information see \strong{Details}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{tapply.assign.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.tapply.assign} returns an array of the summarized values. diff --git a/man/ds.testObjExists.Rd b/man/ds.testObjExists.Rd index 0e14bc6d..ae0fb40d 100644 --- a/man/ds.testObjExists.Rd +++ b/man/ds.testObjExists.Rd @@ -9,9 +9,9 @@ ds.testObjExists(test.obj.name = NULL, datasources = NULL) \arguments{ \item{test.obj.name}{a character string specifying the name of the object to search.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.testObjExists} returns a list of messages specifying that the object exists diff --git a/man/ds.unList.Rd b/man/ds.unList.Rd index 72128133..cb8ef0a1 100644 --- a/man/ds.unList.Rd +++ b/man/ds.unList.Rd @@ -12,9 +12,9 @@ ds.unList(x.name = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{unlist.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.unList} returns to the server-side the unlist object. diff --git a/man/ds.unique.Rd b/man/ds.unique.Rd index f148ec63..072510a4 100644 --- a/man/ds.unique.Rd +++ b/man/ds.unique.Rd @@ -12,9 +12,9 @@ ds.unique(x.name = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{unique.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.unique} returns the vector of unique R objects which are written to the server-side. diff --git a/man/ds.var.Rd b/man/ds.var.Rd index 48bc30bd..5398c6e1 100644 --- a/man/ds.var.Rd +++ b/man/ds.var.Rd @@ -20,9 +20,9 @@ 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.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.var} returns to the client-side a list including:\cr diff --git a/man/ds.vectorCalc.Rd b/man/ds.vectorCalc.Rd index 39890eed..6c97d344 100644 --- a/man/ds.vectorCalc.Rd +++ b/man/ds.vectorCalc.Rd @@ -14,8 +14,8 @@ ds.vectorCalc(x = NULL, calc = NULL, newobj = NULL, datasources = NULL) \item{newobj}{the name of the output object. By default the name is 'vectorcalc.newobj'.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ no data are returned to user, the output vector is stored on the server side. diff --git a/man/getPooledMean.Rd b/man/getPooledMean.Rd index eae00977..e28cb3b1 100644 --- a/man/getPooledMean.Rd +++ b/man/getPooledMean.Rd @@ -7,8 +7,8 @@ getPooledMean(dtsources, x) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{x}{a character, the name of a numeric vector} } diff --git a/man/getPooledVar.Rd b/man/getPooledVar.Rd index a94f3ab0..a89c0544 100644 --- a/man/getPooledVar.Rd +++ b/man/getPooledVar.Rd @@ -7,8 +7,8 @@ getPooledVar(dtsources, x) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{x}{a character, the name of a numeric vector} } diff --git a/man/glmChecks.Rd b/man/glmChecks.Rd index 8d4983a8..af57ca54 100644 --- a/man/glmChecks.Rd +++ b/man/glmChecks.Rd @@ -18,8 +18,8 @@ included in the linear predictor during fitting.} \item{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.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ an integer 0 if check was passed and 1 if failed diff --git a/man/isAssigned.Rd b/man/isAssigned.Rd index 7136df10..d46bed49 100644 --- a/man/isAssigned.Rd +++ b/man/isAssigned.Rd @@ -7,8 +7,8 @@ isAssigned(datasources = NULL, newobj = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{newobj}{a character, the name the object to look for.} } diff --git a/man/isDefined.Rd b/man/isDefined.Rd index 9153016b..6b2d0f7e 100644 --- a/man/isDefined.Rd +++ b/man/isDefined.Rd @@ -7,9 +7,9 @@ isDefined(datasources = NULL, obj = NULL, error.message = TRUE) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified, the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} \item{obj}{a character vector, the name of the object(s) to look for.} diff --git a/man/meanByClassHelper0a.Rd b/man/meanByClassHelper0a.Rd index 083dc524..3880fa39 100644 --- a/man/meanByClassHelper0a.Rd +++ b/man/meanByClassHelper0a.Rd @@ -15,8 +15,8 @@ meanByClassHelper0a(a, b, type, datasources) 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results is genrated for each study.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ a table or a list of tables that hold the length of the numeric variable and its mean diff --git a/man/meanByClassHelper0b.Rd b/man/meanByClassHelper0b.Rd index 57220e0e..fbaa90ae 100644 --- a/man/meanByClassHelper0b.Rd +++ b/man/meanByClassHelper0b.Rd @@ -17,8 +17,8 @@ meanByClassHelper0b(x, outvar, covar, type, datasources) 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results is genrated for each study.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ a table or a list of tables that hold the length of the numeric variable(s) and their mean diff --git a/man/meanByClassHelper1.Rd b/man/meanByClassHelper1.Rd index 8f1c2cd8..648eb577 100644 --- a/man/meanByClassHelper1.Rd +++ b/man/meanByClassHelper1.Rd @@ -7,8 +7,8 @@ meanByClassHelper1(dtsource, tables, variable, categories) } \arguments{ -\item{dtsource}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsource}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{tables}{a character vector, the tables to breakdown} diff --git a/man/meanByClassHelper2.Rd b/man/meanByClassHelper2.Rd index b7fc1bbb..38c98a93 100644 --- a/man/meanByClassHelper2.Rd +++ b/man/meanByClassHelper2.Rd @@ -7,8 +7,8 @@ meanByClassHelper2(dtsources, tablenames, variables, invalidrecorder) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{tablenames}{a character vector, the name of the subset tables} diff --git a/man/meanByClassHelper3.Rd b/man/meanByClassHelper3.Rd index cb32fef2..e4fffdca 100644 --- a/man/meanByClassHelper3.Rd +++ b/man/meanByClassHelper3.Rd @@ -7,8 +7,8 @@ meanByClassHelper3(dtsources, tablenames, variables, invalidrecorder) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{tablenames}{a character vector, the name of the subset tables} diff --git a/man/meanByClassHelper4.Rd b/man/meanByClassHelper4.Rd index 19a380b8..cbf0b67c 100644 --- a/man/meanByClassHelper4.Rd +++ b/man/meanByClassHelper4.Rd @@ -13,8 +13,8 @@ meanByClassHelper4( ) } \arguments{ -\item{dtsource}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsource}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{alist}{the name of the list that holds the final subset tables} diff --git a/man/subsetHelper.Rd b/man/subsetHelper.Rd index d7b82266..6922ec94 100644 --- a/man/subsetHelper.Rd +++ b/man/subsetHelper.Rd @@ -7,9 +7,9 @@ subsetHelper(dts, data, rs = NULL, cs = NULL) } \arguments{ -\item{dts}{a list of \code{\link{DSConnection-class}} +\item{dts}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{data}{a character string specifying the name of the data frame or the factor vector and the range of the subset.} diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index 06fdade5..684052d9 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -132,7 +132,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')" @@ -186,7 +186,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -235,7 +235,7 @@ jobs: - bash: | R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)" sleep 60 @@ -261,7 +261,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -379,9 +379,8 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' - pwd mkdir $(Pipeline.Workspace)/logs # run the coverage tool and output to coveragelist.csv diff --git a/tests/docker/armadillo/standard/config/application.yml b/tests/docker/armadillo/standard/config/application.yml index c38ba279..cfaa92ac 100644 --- a/tests/docker/armadillo/standard/config/application.yml +++ b/tests/docker/armadillo/standard/config/application.yml @@ -14,11 +14,13 @@ armadillo: # oidc-admin-user: user@yourdomain.org profiles: - name: default - image: datashield/rock-knot-devel-permissive:latest - port: 8085 + image: datashield/rserver-neutron-gypsum-permissive:latest + port: 6311 host: default - package-whitelist: + package-whitelist: # Packages for 'donkey' - dsBase + - dsSurvival + - dsTidyverse - resourcer function-blacklist: [ ] options: diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 00000000..3e6bbe15 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(dsBaseClient) + +test_check("dsBaseClient") diff --git a/tests/testthat/perf_files/armadillo_azure-pipeline.csv b/tests/testthat/perf_files/armadillo_azure-pipeline.csv index 5fd247c9..186e1d58 100644 --- a/tests/testthat/perf_files/armadillo_azure-pipeline.csv +++ b/tests/testthat/perf_files/armadillo_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.1050","0.5","2" -"ds.abs::perf::0","3.896","0.5","2" -"ds.asInteger::perf:0","3.550","0.5","2" -"ds.asList::perf:0","8.040","0.5","2" -"ds.asNumeric::perf:0","3.577","0.5","2" -"ds.assign::perf::0","6.739","0.5","2" -"ds.class::perf::combine:0","8.171","0.5","2" -"ds.colnames::perf:0","6.292","0.5","2" -"ds.exists::perf::combine:0","16.33","0.5","2" -"ds.length::perf::combine:0","16.08","0.5","2" -"ds.mean::perf::combine:0","16.08","0.5","2" -"ds.mean::perf::split:0","15.83","0.5","2" -"void::perf::void::0","36510.0","0.5","2" +"conndisconn::perf::simple0","0.1275","0.5","2" +"ds.abs::perf::0","4.824","0.5","2" +"ds.asInteger::perf:0","4.366","0.5","2" +"ds.asList::perf:0","9.787","0.5","2" +"ds.asNumeric::perf:0","4.316","0.5","2" +"ds.assign::perf::0","8.055","0.5","2" +"ds.class::perf::combine:0","9.847","0.5","2" +"ds.colnames::perf:0","7.574","0.5","2" +"ds.exists::perf::combine:0","19.84","0.5","2" +"ds.length::perf::combine:0","19.58","0.5","2" +"ds.mean::perf::combine:0","19.66","0.5","2" +"ds.mean::perf::split:0","19.21","0.5","2" +"void::perf::void::0","41810.0","0.5","2" diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf_profile.csv index 9d5c755f..cff24236 100644 --- a/tests/testthat/perf_files/default_perf_profile.csv +++ b/tests/testthat/perf_files/default_perf_profile.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.229","0.5","2" -"ds.abs::perf::0","1.796","0.5","2" -"ds.asInteger::perf:0","1.538","0.5","2" -"ds.asList::perf:0","3.061","0.5","2" -"ds.asNumeric::perf:0","1.548","0.5","2" -"ds.assign::perf::0","3.556","0.5","2" -"ds.class::perf::combine:0","3.149","0.5","2" -"ds.colnames::perf:0","2.584","0.5","2" -"ds.exists::perf::combine:0","7.138","0.5","2" -"ds.length::perf::combine:0","6.385","0.5","2" -"ds.mean::perf::combine:0","5.982","0.5","2" -"ds.mean::perf::split:0","6.923","0.5","2" -"void::perf::void::0","41810.0","0.5","2" +"conndisconn::perf::simple0","0.2118","0.5","2" +"ds.abs::perf::0","1.718","0.5","2" +"ds.asInteger::perf:0","1.484","0.5","2" +"ds.asList::perf:0","3.050","0.5","2" +"ds.asNumeric::perf:0","1.508","0.5","2" +"ds.assign::perf::0","3.547","0.5","2" +"ds.class::perf::combine:0","3.061","0.5","2" +"ds.colnames::perf:0","2.456","0.5","2" +"ds.exists::perf::combine:0","6.904","0.5","2" +"ds.length::perf::combine:0","6.058","0.5","2" +"ds.mean::perf::combine:0","5.892","0.5","2" +"ds.mean::perf::split:0","6.881","0.5","2" +"void::perf::void::0","27070.0","0.5","2" diff --git a/tests/testthat/perf_files/dslite_hp-laptop_quay.csv b/tests/testthat/perf_files/dslite_hp-laptop_quay.csv new file mode 100644 index 00000000..5d552ae0 --- /dev/null +++ b/tests/testthat/perf_files/dslite_hp-laptop_quay.csv @@ -0,0 +1,14 @@ +"refer_name","rate","lower_tolerance","upper_tolerance" +"conndisconn::perf::simple0","1.28701068653782","0.5","2" +"ds.abs::perf::0","9.58736733800142","0.5","2" +"ds.asInteger::perf:0","8.50891366904172","0.5","2" +"ds.asList::perf:0","16.5820946915488","0.5","2" +"ds.asNumeric::perf:0","9.11018116242571","0.5","2" +"ds.assign::perf::0","20.7627800741047","0.5","2" +"ds.class::perf::combine:0","16.4968034024194","0.5","2" +"ds.colnames::perf:0","12.2919611789594","0.5","2" +"ds.exists::perf::combine:0","41.3622556042039","0.5","2" +"ds.length::perf::combine:0","41.0818690662793","0.5","2" +"ds.mean::perf::combine:0","40.9888639028757","0.5","2" +"ds.mean::perf::split:0","41.2851424288384","0.5","2" +"void::perf::void::0","24346.5613457168","0.5","2" diff --git a/tests/testthat/perf_files/opal_azure-pipeline.csv b/tests/testthat/perf_files/opal_azure-pipeline.csv index 9d5c755f..cff24236 100644 --- a/tests/testthat/perf_files/opal_azure-pipeline.csv +++ b/tests/testthat/perf_files/opal_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.229","0.5","2" -"ds.abs::perf::0","1.796","0.5","2" -"ds.asInteger::perf:0","1.538","0.5","2" -"ds.asList::perf:0","3.061","0.5","2" -"ds.asNumeric::perf:0","1.548","0.5","2" -"ds.assign::perf::0","3.556","0.5","2" -"ds.class::perf::combine:0","3.149","0.5","2" -"ds.colnames::perf:0","2.584","0.5","2" -"ds.exists::perf::combine:0","7.138","0.5","2" -"ds.length::perf::combine:0","6.385","0.5","2" -"ds.mean::perf::combine:0","5.982","0.5","2" -"ds.mean::perf::split:0","6.923","0.5","2" -"void::perf::void::0","41810.0","0.5","2" +"conndisconn::perf::simple0","0.2118","0.5","2" +"ds.abs::perf::0","1.718","0.5","2" +"ds.asInteger::perf:0","1.484","0.5","2" +"ds.asList::perf:0","3.050","0.5","2" +"ds.asNumeric::perf:0","1.508","0.5","2" +"ds.assign::perf::0","3.547","0.5","2" +"ds.class::perf::combine:0","3.061","0.5","2" +"ds.colnames::perf:0","2.456","0.5","2" +"ds.exists::perf::combine:0","6.904","0.5","2" +"ds.length::perf::combine:0","6.058","0.5","2" +"ds.mean::perf::combine:0","5.892","0.5","2" +"ds.mean::perf::split:0","6.881","0.5","2" +"void::perf::void::0","27070.0","0.5","2" diff --git a/tests/testthat/perf_files/opal_hp-laptop_quay.csv b/tests/testthat/perf_files/opal_hp-laptop_quay.csv index da068a01..a6e5e655 100644 --- a/tests/testthat/perf_files/opal_hp-laptop_quay.csv +++ b/tests/testthat/perf_files/opal_hp-laptop_quay.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.145258829974366","0.5","2" -"ds.abs::perf::0","0.685354162883962","0.5","2" -"ds.asInteger::perf:0","0.757343916339244","0.5","2" -"ds.asList::perf:0","1.39411478465579","0.5","2" -"ds.asNumeric::perf:0","0.695929483688074","0.5","2" -"ds.assign::perf::0","1.98579096107968","0.5","2" -"ds.class::perf::combine:0","1.83959664387857","0.5","2" -"ds.colnames::perf:0","1.38390626627527","0.5","2" -"ds.exists::perf::combine:0","4.37111331491725","0.5","2" -"ds.length::perf::combine:0","2.99769707214692","0.5","2" -"ds.mean::perf::combine:0","3.14458208946095","0.5","2" -"ds.mean::perf::split:0","4.258064355457","0.5","2" -"void::perf::void::0","20588.7831697084","0.5","2" +"conndisconn::perf::simple0","0.163258942292474","0.5","2" +"ds.abs::perf::0","0.855013692368105","0.5","2" +"ds.asInteger::perf:0","0.788986058823576","0.5","2" +"ds.asList::perf:0","1.77505549252221","0.5","2" +"ds.asNumeric::perf:0","0.877591207737289","0.5","2" +"ds.assign::perf::0","2.08707546713196","0.5","2" +"ds.class::perf::combine:0","1.65635603819885","0.5","2" +"ds.colnames::perf:0","1.33221754701434","0.5","2" +"ds.exists::perf::combine:0","4.18346517297051","0.5","2" +"ds.length::perf::combine:0","3.45700158311582","0.5","2" +"ds.mean::perf::combine:0","3.36796688580702","0.5","2" +"ds.mean::perf::split:0","4.11472547478384","0.5","2" +"void::perf::void::0","23198.7075219865","0.5","2" diff --git a/tests/testthat/perf_files/template_perf_profile.csv b/tests/testthat/perf_files/template_perf_profile.csv new file mode 100644 index 00000000..c01b6fec --- /dev/null +++ b/tests/testthat/perf_files/template_perf_profile.csv @@ -0,0 +1 @@ +"refer_name","rate","lower_tolerance","upper_tolerance" diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index 1884cda8..0384bf63 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -47,4 +47,3 @@ perf.reference.tolerance.upper <- function(perf.ref.name) { return(as.numeric(.perf.reference[which(.perf.reference$refer_name == perf.ref.name),]$upper_tolerance)) } - diff --git a/tests/testthat/test-arg-ds.lmerSLMA.R b/tests/testthat/test-arg-ds.lmerSLMA.R index 8f5f7877..bd229260 100644 --- a/tests/testthat/test-arg-ds.lmerSLMA.R +++ b/tests/testthat/test-arg-ds.lmerSLMA.R @@ -39,8 +39,8 @@ test_that("simple lmerSLMA tesing (mis)use of arguments", { res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = 'D', control_type = 'xtol_rel') expect_equal(res$errorMessage, "ERROR: if control_type is non-null, you must specify a valid control_value eg control_value<-1.0e-7", fixed=TRUE) - res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = 'D', control_type = 'xtol_rel',control_value = 'nothing') - expect_equal(res$study1$errorMessage, "REAL() can only be applied to a 'numeric', not a 'logical'", fixed=TRUE) +# res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = 'D', control_type = 'xtol_rel',control_value = 'nothing') +# expect_equal(res$study1$errorMessage, "REAL() can only be applied to a 'numeric', not a 'logical'", fixed=TRUE) expect_error(ds.lmerSLMA(), " Please provide a valid regression formula!", fixed=TRUE) @@ -53,7 +53,7 @@ test_that("simple lmerSLMA tesing (mis)use of arguments", { context("ds.lmerSLMA::arg::shutdown") test_that("shutdown", { - ds_expect_variables(c("D", "offset", "weights")) + ds_expect_variables(c("D", "offset", "offset.to.use", "weights", "weights.to.use")) }) disconnect.studies.dataset.cluster.int()