From 6a55f060171825b5bbf838183b1df91e31695065 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 9 Jun 2025 22:25:26 +0100 Subject: [PATCH 1/5] \link{} issue --- R/checkClass.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/checkClass.R b/R/checkClass.R index 5cf86eac..db3316c4 100644 --- a/R/checkClass.R +++ b/R/checkClass.R @@ -3,7 +3,7 @@ #' @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 +#' @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{datashield.connections_default}. #' @param obj a string character, the name of the object to check for. #' @keywords internal From 22992942d7e710965f2bfa64c43549dc0a436990 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 10 Jun 2025 12:16:54 +0100 Subject: [PATCH 2/5] Link issues --- R/checkClass.R | 2 +- R/ds.abs.R | 2 +- R/ds.asCharacter.R | 2 +- R/ds.asDataMatrix.R | 2 +- R/ds.asFactor.R | 2 +- R/ds.asFactorSimple.R | 4 ++-- R/ds.asInteger.R | 2 +- R/ds.asList.R | 2 +- R/ds.asLogical.R | 2 +- R/ds.asMatrix.R | 2 +- R/ds.asNumeric.R | 2 +- R/ds.assign.R | 2 +- R/ds.auc.R | 4 ++-- R/ds.boxPlot.R | 2 +- R/ds.boxPlotGG.R | 4 ++-- R/ds.boxPlotGG_data_Treatment.R | 4 ++-- R/ds.boxPlotGG_data_Treatment_numeric.R | 2 +- R/ds.boxPlotGG_numeric.R | 2 +- R/ds.boxPlotGG_table.R | 2 +- R/ds.bp_standards.R | 4 ++-- R/ds.c.R | 2 +- R/ds.cbind.R | 2 +- R/ds.changeRefGroup.R | 2 +- R/ds.class.R | 2 +- R/ds.colnames.R | 2 +- R/ds.completeCases.R | 2 +- R/ds.cor.R | 2 +- R/ds.corTest.R | 2 +- R/ds.cov.R | 2 +- R/ds.dataFrame.R | 2 +- R/ds.dataFrameFill.R | 2 +- R/ds.dataFrameSort.R | 4 ++-- R/ds.dataFrameSubset.R | 2 +- R/ds.densityGrid.R | 2 +- R/ds.dim.R | 2 +- R/ds.elspline.R | 4 ++-- R/ds.exists.R | 2 +- R/ds.exp.R | 2 +- R/ds.hetcor.R | 4 ++-- R/ds.igb_standards.R | 4 ++-- R/ds.isNA.R | 2 +- R/ds.isValid.R | 2 +- R/ds.kurtosis.R | 2 +- R/ds.length.R | 2 +- R/ds.levels.R | 2 +- R/ds.list.R | 2 +- R/ds.listServersideFunctions.R | 2 +- R/ds.log.R | 2 +- R/ds.look.R | 2 +- R/ds.ls.R | 2 +- R/ds.lspline.R | 4 ++-- R/ds.matrixDet.R | 2 +- R/ds.matrixDet.report.R | 2 +- R/ds.matrixDimnames.R | 2 +- R/ds.matrixInvert.R | 2 +- R/ds.matrixMult.R | 2 +- R/ds.matrixTranspose.R | 2 +- R/ds.mean.R | 2 +- R/ds.meanByClass.R | 2 +- R/ds.message.R | 2 +- R/ds.metadata.R | 2 +- R/ds.names.R | 2 +- R/ds.ns.R | 4 ++-- R/ds.numNA.R | 2 +- R/ds.qlspline.R | 4 ++-- R/ds.quantileMean.R | 2 +- R/ds.rBinom.R | 2 +- R/ds.rPois.R | 2 +- R/ds.rbind.R | 2 +- R/ds.reShape.R | 2 +- R/ds.recodeLevels.R | 2 +- R/ds.recodeValues.R | 2 +- R/ds.rep.R | 2 +- R/ds.replaceNA.R | 2 +- R/ds.rm.R | 4 ++-- R/ds.rowColCalc.R | 2 +- R/ds.skewness.R | 2 +- R/ds.sqrt.R | 2 +- R/ds.subset.R | 2 +- R/ds.subsetByClass.R | 2 +- R/ds.summary.R | 2 +- R/ds.table1D.R | 2 +- R/ds.table2D.R | 2 +- R/ds.testObjExists.R | 2 +- R/ds.unList.R | 2 +- R/ds.unique.R | 2 +- R/ds.var.R | 2 +- R/ds.vectorCalc.R | 2 +- R/getPooledMean.R | 2 +- R/getPooledVar.R | 2 +- R/glmChecks.R | 2 +- R/isAssigned.R | 2 +- R/isDefined.R | 2 +- R/meanByClassHelper0a.R | 2 +- R/meanByClassHelper0b.R | 2 +- R/meanByClassHelper1.R | 2 +- R/meanByClassHelper2.R | 2 +- R/meanByClassHelper3.R | 2 +- R/meanByClassHelper4.R | 2 +- R/subsetHelper.R | 2 +- man/checkClass.Rd | 2 +- man/ds.abs.Rd | 2 +- man/ds.asCharacter.Rd | 2 +- man/ds.asDataMatrix.Rd | 2 +- man/ds.asFactor.Rd | 2 +- man/ds.asFactorSimple.Rd | 2 +- man/ds.asInteger.Rd | 2 +- man/ds.asList.Rd | 2 +- man/ds.asLogical.Rd | 2 +- man/ds.asMatrix.Rd | 2 +- man/ds.asNumeric.Rd | 2 +- man/ds.assign.Rd | 2 +- man/ds.auc.Rd | 2 +- man/ds.boxPlot.Rd | 2 +- man/ds.boxPlotGG.Rd | 2 +- man/ds.boxPlotGG_data_Treatment.Rd | 2 +- man/ds.boxPlotGG_data_Treatment_numeric.Rd | 2 +- man/ds.boxPlotGG_numeric.Rd | 2 +- man/ds.boxPlotGG_table.Rd | 2 +- man/ds.bp_standards.Rd | 2 +- man/ds.c.Rd | 2 +- man/ds.cbind.Rd | 2 +- man/ds.changeRefGroup.Rd | 2 +- man/ds.class.Rd | 2 +- man/ds.colnames.Rd | 2 +- man/ds.completeCases.Rd | 2 +- man/ds.cor.Rd | 2 +- man/ds.corTest.Rd | 2 +- man/ds.cov.Rd | 2 +- man/ds.dataFrame.Rd | 2 +- man/ds.dataFrameFill.Rd | 2 +- man/ds.dataFrameSort.Rd | 2 +- man/ds.dataFrameSubset.Rd | 2 +- man/ds.densityGrid.Rd | 2 +- man/ds.dim.Rd | 2 +- man/ds.elspline.Rd | 2 +- man/ds.exists.Rd | 2 +- man/ds.exp.Rd | 2 +- man/ds.hetcor.Rd | 2 +- man/ds.igb_standards.Rd | 2 +- man/ds.isNA.Rd | 2 +- man/ds.isValid.Rd | 2 +- man/ds.kurtosis.Rd | 2 +- man/ds.length.Rd | 2 +- man/ds.levels.Rd | 2 +- man/ds.list.Rd | 2 +- man/ds.listServersideFunctions.Rd | 2 +- man/ds.log.Rd | 2 +- man/ds.look.Rd | 2 +- man/ds.ls.Rd | 2 +- man/ds.lspline.Rd | 2 +- man/ds.matrixDet.Rd | 2 +- man/ds.matrixDet.report.Rd | 2 +- man/ds.matrixDimnames.Rd | 2 +- man/ds.matrixInvert.Rd | 2 +- man/ds.matrixMult.Rd | 2 +- man/ds.matrixTranspose.Rd | 2 +- man/ds.mean.Rd | 2 +- man/ds.meanByClass.Rd | 2 +- man/ds.message.Rd | 2 +- man/ds.metadata.Rd | 2 +- man/ds.names.Rd | 2 +- man/ds.ns.Rd | 2 +- man/ds.numNA.Rd | 2 +- man/ds.qlspline.Rd | 2 +- man/ds.quantileMean.Rd | 2 +- man/ds.rBinom.Rd | 2 +- man/ds.rPois.Rd | 2 +- man/ds.rbind.Rd | 2 +- man/ds.reShape.Rd | 2 +- man/ds.recodeLevels.Rd | 2 +- man/ds.recodeValues.Rd | 2 +- man/ds.rep.Rd | 2 +- man/ds.replaceNA.Rd | 2 +- man/ds.rm.Rd | 2 +- man/ds.rowColCalc.Rd | 2 +- man/ds.skewness.Rd | 2 +- man/ds.sqrt.Rd | 2 +- man/ds.subset.Rd | 2 +- man/ds.subsetByClass.Rd | 2 +- man/ds.summary.Rd | 2 +- man/ds.table1D.Rd | 2 +- man/ds.table2D.Rd | 2 +- man/ds.testObjExists.Rd | 2 +- man/ds.unList.Rd | 2 +- man/ds.unique.Rd | 2 +- man/ds.var.Rd | 2 +- man/ds.vectorCalc.Rd | 2 +- man/getPooledMean.Rd | 2 +- man/getPooledVar.Rd | 2 +- man/glmChecks.Rd | 2 +- man/isAssigned.Rd | 2 +- man/isDefined.Rd | 2 +- man/meanByClassHelper0a.Rd | 2 +- man/meanByClassHelper0b.Rd | 2 +- man/meanByClassHelper1.Rd | 2 +- man/meanByClassHelper2.Rd | 2 +- man/meanByClassHelper3.Rd | 2 +- man/meanByClassHelper4.Rd | 2 +- man/subsetHelper.Rd | 2 +- 200 files changed, 213 insertions(+), 213 deletions(-) diff --git a/R/checkClass.R b/R/checkClass.R index 5cf86eac..db3316c4 100644 --- a/R/checkClass.R +++ b/R/checkClass.R @@ -3,7 +3,7 @@ #' @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 +#' @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{datashield.connections_default}. #' @param obj a string character, the name of the object to check for. #' @keywords internal diff --git a/R/ds.abs.R b/R/ds.abs.R index 5b57b0ed..81db6c42 100644 --- a/R/ds.abs.R +++ b/R/ds.abs.R @@ -10,7 +10,7 @@ #' @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}}. #' @return \code{ds.abs} assigns a vector for each study that includes the absolute values of diff --git a/R/ds.asCharacter.R b/R/ds.asCharacter.R index 72acbd45..63e93931 100644 --- a/R/ds.asCharacter.R +++ b/R/ds.asCharacter.R @@ -9,7 +9,7 @@ #' 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}}. #' @return \code{ds.asCharacter} returns the object converted into a class character diff --git a/R/ds.asDataMatrix.R b/R/ds.asDataMatrix.R index 83b1037f..2541665d 100644 --- a/R/ds.asDataMatrix.R +++ b/R/ds.asDataMatrix.R @@ -8,7 +8,7 @@ #' 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}}. #' @return \code{ds.asDataMatrix} returns the object converted into a matrix diff --git a/R/ds.asFactor.R b/R/ds.asFactor.R index 7d6246d5..f72fa21d 100644 --- a/R/ds.asFactor.R +++ b/R/ds.asFactor.R @@ -130,7 +130,7 @@ #' 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}}. #' @return \code{ds.asFactor} returns the unique levels of the converted diff --git a/R/ds.asFactorSimple.R b/R/ds.asFactorSimple.R index dce56a8a..5a614579 100644 --- a/R/ds.asFactorSimple.R +++ b/R/ds.asFactorSimple.R @@ -14,7 +14,7 @@ #' 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}}. #' @return an output vector of class factor to the serverside. In addition, returns a validity @@ -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..0a959c8e 100644 --- a/R/ds.asInteger.R +++ b/R/ds.asInteger.R @@ -22,7 +22,7 @@ #' 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}}. #' @return \code{ds.asInteger} returns the R object converted into an integer diff --git a/R/ds.asList.R b/R/ds.asList.R index 5383c506..164c035c 100644 --- a/R/ds.asList.R +++ b/R/ds.asList.R @@ -9,7 +9,7 @@ #' 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}}. #' @return \code{ds.asList} returns the R object converted into a list diff --git a/R/ds.asLogical.R b/R/ds.asLogical.R index de2920bf..e3623037 100644 --- a/R/ds.asLogical.R +++ b/R/ds.asLogical.R @@ -8,7 +8,7 @@ #' 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}}. #' @return \code{ds.asLogical} returns the R object converted into a logical diff --git a/R/ds.asMatrix.R b/R/ds.asMatrix.R index 04186109..52e1c6c0 100644 --- a/R/ds.asMatrix.R +++ b/R/ds.asMatrix.R @@ -11,7 +11,7 @@ #' 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}}. #' @return \code{ds.asMatrix} returns the object converted into a matrix diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R index 0c4e9a03..540b9993 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -22,7 +22,7 @@ #' 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}}. #' @return \code{ds.asNumeric} returns the R object converted into a numeric class diff --git a/R/ds.assign.R b/R/ds.assign.R index 7c701726..2d91fa02 100644 --- a/R/ds.assign.R +++ b/R/ds.assign.R @@ -10,7 +10,7 @@ #' @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}}. #' @return \code{ds.assign} returns the R object assigned to a name diff --git a/R/ds.auc.R b/R/ds.auc.R index b971651a..3bb7eb6e 100644 --- a/R/ds.auc.R +++ b/R/ds.auc.R @@ -6,7 +6,7 @@ #' @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}}. #' @return returns the AUC and its standard error @@ -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..0d17e581 100644 --- a/R/ds.bp_standards.R +++ b/R/ds.bp_standards.R @@ -16,7 +16,7 @@ #' 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}}. #' @return assigns a new object on the server-side. The assigned object is a list @@ -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..1c5e8443 100644 --- a/R/ds.c.R +++ b/R/ds.c.R @@ -10,7 +10,7 @@ #' @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}}. #' @return \code{ds.c} returns the vector of concatenating R diff --git a/R/ds.cbind.R b/R/ds.cbind.R index fdd1b34b..8b64b70e 100644 --- a/R/ds.cbind.R +++ b/R/ds.cbind.R @@ -32,7 +32,7 @@ #' 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}}. #' @param notify.of.progress specifies if console output should be produced to indicate diff --git a/R/ds.changeRefGroup.R b/R/ds.changeRefGroup.R index 1b8ad556..f9ec7455 100644 --- a/R/ds.changeRefGroup.R +++ b/R/ds.changeRefGroup.R @@ -22,7 +22,7 @@ #' @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}}. #' @return \code{ds.changeRefGroup} returns a new vector with the specified level as a reference diff --git a/R/ds.class.R b/R/ds.class.R index 285b4045..841ddfcf 100644 --- a/R/ds.class.R +++ b/R/ds.class.R @@ -6,7 +6,7 @@ #' #' 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}}. #' @return \code{ds.class} returns the type of the R object. diff --git a/R/ds.colnames.R b/R/ds.colnames.R index 5950d99b..e8360601 100644 --- a/R/ds.colnames.R +++ b/R/ds.colnames.R @@ -6,7 +6,7 @@ #' #' 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}}. #' @return \code{ds.colnames} returns the column names of diff --git a/R/ds.completeCases.R b/R/ds.completeCases.R index fed43208..747d52ae 100644 --- a/R/ds.completeCases.R +++ b/R/ds.completeCases.R @@ -14,7 +14,7 @@ #' 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}}. #' @return \code{ds.completeCases} generates a modified data frame, matrix or vector from which diff --git a/R/ds.cor.R b/R/ds.cor.R index 1a5c86d6..2fcd7185 100644 --- a/R/ds.cor.R +++ b/R/ds.cor.R @@ -27,7 +27,7 @@ #' 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}}. #' @return \code{ds.cor} returns a list containing the number of missing values in each variable, diff --git a/R/ds.corTest.R b/R/ds.corTest.R index 7be1f992..ddd66b32 100644 --- a/R/ds.corTest.R +++ b/R/ds.corTest.R @@ -19,7 +19,7 @@ #' 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}}. #' @return \code{ds.corTest} returns to the client-side the results of the correlation test. diff --git a/R/ds.cov.R b/R/ds.cov.R index 58aedc94..79471788 100644 --- a/R/ds.cov.R +++ b/R/ds.cov.R @@ -35,7 +35,7 @@ #' \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}}. #' @return \code{ds.cov} returns a list containing the number of missing values in each variable, the number of missing values diff --git a/R/ds.dataFrame.R b/R/ds.dataFrame.R index e71c1daf..fa86a558 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -32,7 +32,7 @@ #' 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}}. #' @param notify.of.progress specifies if console output should be produced to indicate diff --git a/R/ds.dataFrameFill.R b/R/ds.dataFrameFill.R index eef95117..ccea6af8 100644 --- a/R/ds.dataFrameFill.R +++ b/R/ds.dataFrameFill.R @@ -13,7 +13,7 @@ #' 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}}. #' @return \code{ds.dataFrameFill} returns the object specified by the \code{newobj} argument which diff --git a/R/ds.dataFrameSort.R b/R/ds.dataFrameSort.R index d170dd87..76f9bf1f 100644 --- a/R/ds.dataFrameSort.R +++ b/R/ds.dataFrameSort.R @@ -33,7 +33,7 @@ #' @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}}. #' @return \code{ds.dataFrameSort} returns the sorted data frame is written to the server-side. @@ -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..1b531b96 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -28,7 +28,7 @@ #' 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}}. #' @param notify.of.progress specifies if console output should be produced to indicate diff --git a/R/ds.densityGrid.R b/R/ds.densityGrid.R index 33e1bb6d..123c6650 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -23,7 +23,7 @@ #' \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}}. #' @return \code{ds.densityGrid} returns a grid density matrix. diff --git a/R/ds.dim.R b/R/ds.dim.R index 613bd984..3755a2e4 100644 --- a/R/ds.dim.R +++ b/R/ds.dim.R @@ -22,7 +22,7 @@ #' 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}}. #' @return \code{ds.dim} retrieves to the client-side the dimension of the object diff --git a/R/ds.elspline.R b/R/ds.elspline.R index 1fc4cffe..30c56647 100644 --- a/R/ds.elspline.R +++ b/R/ds.elspline.R @@ -17,7 +17,7 @@ #' @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}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the @@ -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..2a04a355 100644 --- a/R/ds.exists.R +++ b/R/ds.exists.R @@ -10,7 +10,7 @@ #' #' 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}}. #' @return \code{ds.exists} returns a logical object. diff --git a/R/ds.exp.R b/R/ds.exp.R index 2fd9da3b..a9409e43 100644 --- a/R/ds.exp.R +++ b/R/ds.exp.R @@ -9,7 +9,7 @@ #' @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}}. #' @return \code{ds.exp} returns a vector for each study of the exponential values for the numeric vector diff --git a/R/ds.hetcor.R b/R/ds.hetcor.R index 1b0e77f6..71a98363 100644 --- a/R/ds.hetcor.R +++ b/R/ds.hetcor.R @@ -17,7 +17,7 @@ #' 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}}. #' @return Returns an object of class "hetcor" from each study, with the following components: the @@ -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.igb_standards.R b/R/ds.igb_standards.R index c3d74f40..a46f267d 100644 --- a/R/ds.igb_standards.R +++ b/R/ds.igb_standards.R @@ -15,7 +15,7 @@ #' "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}}. #' @note For gestational ages between 24 and 33 weeks, the INTERGROWTH very early preterm @@ -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..d34ad054 100644 --- a/R/ds.isNA.R +++ b/R/ds.isNA.R @@ -8,7 +8,7 @@ #' #' 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}}. #' @return \code{ds.isNA} returns a boolean. If it is TRUE the vector is empty diff --git a/R/ds.isValid.R b/R/ds.isValid.R index 34a94223..5d0424ba 100644 --- a/R/ds.isValid.R +++ b/R/ds.isValid.R @@ -10,7 +10,7 @@ #' #' 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}}. #' @return \code{ds.isValid} returns a boolean. If it is TRUE input object is valid, FALSE otherwise. diff --git a/R/ds.kurtosis.R b/R/ds.kurtosis.R index c262201b..bb8cf299 100644 --- a/R/ds.kurtosis.R +++ b/R/ds.kurtosis.R @@ -17,7 +17,7 @@ #' 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}}. #' @return a matrix showing the kurtosis of the input numeric variable, the number of valid observations and diff --git a/R/ds.length.R b/R/ds.length.R index a288de72..d5064795 100644 --- a/R/ds.length.R +++ b/R/ds.length.R @@ -17,7 +17,7 @@ #' @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}}. #' @return \code{ds.length} returns to the client-side the pooled length of a vector or a list, diff --git a/R/ds.levels.R b/R/ds.levels.R index 1943ea0c..4755522a 100644 --- a/R/ds.levels.R +++ b/R/ds.levels.R @@ -6,7 +6,7 @@ #' @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}}. #' @return \code{ds.levels} returns to the client-side the levels of a factor diff --git a/R/ds.list.R b/R/ds.list.R index 239399db..fa5ebf62 100644 --- a/R/ds.list.R +++ b/R/ds.list.R @@ -8,7 +8,7 @@ #' @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}}. #' @return \code{ds.list} returns a list of objects for each study that is stored on the server-side. diff --git a/R/ds.listServersideFunctions.R b/R/ds.listServersideFunctions.R index fb5128a2..f4b54595 100644 --- a/R/ds.listServersideFunctions.R +++ b/R/ds.listServersideFunctions.R @@ -8,7 +8,7 @@ #' 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}}. #' @return \code{ds.listServersideFunctions} returns to the client-side diff --git a/R/ds.log.R b/R/ds.log.R index faed3f10..07328b9a 100644 --- a/R/ds.log.R +++ b/R/ds.log.R @@ -8,7 +8,7 @@ #' 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}}. #' @return \code{ds.log} returns a vector for each study of the transformed values for the numeric vector diff --git a/R/ds.look.R b/R/ds.look.R index d45e5047..f864309e 100644 --- a/R/ds.look.R +++ b/R/ds.look.R @@ -20,7 +20,7 @@ #' 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}}. #' @return the output from the specified server-side aggregate function to the client-side. diff --git a/R/ds.ls.R b/R/ds.ls.R index 8cfbf3ca..fbc3d914 100644 --- a/R/ds.ls.R +++ b/R/ds.ls.R @@ -51,7 +51,7 @@ #' 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}}. #' @return \code{ds.ls} returns to the client-side a list containing: \cr diff --git a/R/ds.lspline.R b/R/ds.lspline.R index 5c5cee79..cf59090d 100644 --- a/R/ds.lspline.R +++ b/R/ds.lspline.R @@ -14,7 +14,7 @@ #' @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}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the @@ -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.matrixDet.R b/R/ds.matrixDet.R index 90ac58cf..fc825600 100644 --- a/R/ds.matrixDet.R +++ b/R/ds.matrixDet.R @@ -13,7 +13,7 @@ #' 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}}. #' @return \code{ds.matrixDet} returns the determinant of an existing matrix on the server-side. diff --git a/R/ds.matrixDet.report.R b/R/ds.matrixDet.report.R index 126e48a7..7965b399 100644 --- a/R/ds.matrixDet.report.R +++ b/R/ds.matrixDet.report.R @@ -12,7 +12,7 @@ #' @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}}. #' @return \code{ds.matrixDet.report} returns to the client-side diff --git a/R/ds.matrixDimnames.R b/R/ds.matrixDimnames.R index d8376210..1dd08162 100644 --- a/R/ds.matrixDimnames.R +++ b/R/ds.matrixDimnames.R @@ -11,7 +11,7 @@ #' 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}}. #' @return \code{ds.matrixDimnames} returns to the server-side diff --git a/R/ds.matrixInvert.R b/R/ds.matrixInvert.R index f7745ebb..d3f43b9f 100644 --- a/R/ds.matrixInvert.R +++ b/R/ds.matrixInvert.R @@ -9,7 +9,7 @@ #' @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}}. #' @return \code{ds.matrixInvert} returns to the server-side the inverts square matrix. diff --git a/R/ds.matrixMult.R b/R/ds.matrixMult.R index 89ce42ab..2198abbb 100644 --- a/R/ds.matrixMult.R +++ b/R/ds.matrixMult.R @@ -12,7 +12,7 @@ #' @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}}. #' @return \code{ds.matrixMult} returns to the server-side diff --git a/R/ds.matrixTranspose.R b/R/ds.matrixTranspose.R index 46556d46..51375a28 100644 --- a/R/ds.matrixTranspose.R +++ b/R/ds.matrixTranspose.R @@ -12,7 +12,7 @@ #' @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}}. #' @return \code{ds.matrixTranspose} returns to the server-side the transpose matrix. diff --git a/R/ds.mean.R b/R/ds.mean.R index e26ef636..d52fe4c2 100644 --- a/R/ds.mean.R +++ b/R/ds.mean.R @@ -38,7 +38,7 @@ #' 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}}. #' @return \code{ds.mean} returns to the client-side a list including: \cr diff --git a/R/ds.meanByClass.R b/R/ds.meanByClass.R index 279bf891..8e35db6b 100644 --- a/R/ds.meanByClass.R +++ b/R/ds.meanByClass.R @@ -22,7 +22,7 @@ #' \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}}. #' @return \code{ds.meanByClass} returns to the client-side a table or a list of tables that diff --git a/R/ds.message.R b/R/ds.message.R index 289c365b..7dd3a922 100644 --- a/R/ds.message.R +++ b/R/ds.message.R @@ -19,7 +19,7 @@ #' 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}}. #' @return \code{ds.message} returns a list object from each study, diff --git a/R/ds.metadata.R b/R/ds.metadata.R index 214bde6a..0a62b1eb 100644 --- a/R/ds.metadata.R +++ b/R/ds.metadata.R @@ -6,7 +6,7 @@ #' 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}}. #' @return \code{ds.metadata} returns to the client-side the metadata of associated to an object diff --git a/R/ds.names.R b/R/ds.names.R index 59af0990..d1b0448b 100644 --- a/R/ds.names.R +++ b/R/ds.names.R @@ -11,7 +11,7 @@ #' 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: diff --git a/R/ds.ns.R b/R/ds.ns.R index cc11be6a..2f25a000 100644 --- a/R/ds.ns.R +++ b/R/ds.ns.R @@ -22,7 +22,7 @@ #' 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}}. #' @return A matrix of dimension length(x) * df where either df was supplied or if knots were @@ -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..f109f550 100644 --- a/R/ds.numNA.R +++ b/R/ds.numNA.R @@ -7,7 +7,7 @@ #' #' 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}}. #' @return \code{ds.numNA} returns to the client-side the number of missing values diff --git a/R/ds.qlspline.R b/R/ds.qlspline.R index 0302ccc4..5a09bcce 100644 --- a/R/ds.qlspline.R +++ b/R/ds.qlspline.R @@ -22,7 +22,7 @@ #' @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}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the @@ -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..4818a6e0 100644 --- a/R/ds.quantileMean.R +++ b/R/ds.quantileMean.R @@ -15,7 +15,7 @@ #' @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}}. #' @return \code{ds.quantileMean} returns to the client-side the quantiles and statistical mean diff --git a/R/ds.rBinom.R b/R/ds.rBinom.R index be5d9220..787cf8b2 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -41,7 +41,7 @@ #' @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}}. #' @return \code{ds.rBinom} returns random number vectors diff --git a/R/ds.rPois.R b/R/ds.rPois.R index 5fc262ff..0903ad51 100644 --- a/R/ds.rPois.R +++ b/R/ds.rPois.R @@ -38,7 +38,7 @@ #' 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}}. #' @return \code{ds.rPois} returns random number vectors with a Poisson distribution for each study, diff --git a/R/ds.rbind.R b/R/ds.rbind.R index 85bca1d5..873cb4f8 100644 --- a/R/ds.rbind.R +++ b/R/ds.rbind.R @@ -22,7 +22,7 @@ #' 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}}. #' @param notify.of.progress specifies if console output should be produced to indicate diff --git a/R/ds.reShape.R b/R/ds.reShape.R index 2a4840e9..41f73f20 100644 --- a/R/ds.reShape.R +++ b/R/ds.reShape.R @@ -29,7 +29,7 @@ #' @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}}. #' @return \code{ds.reShape} returns to the server-side a reshaped data frame diff --git a/R/ds.recodeLevels.R b/R/ds.recodeLevels.R index 671401e4..9ba1c38f 100644 --- a/R/ds.recodeLevels.R +++ b/R/ds.recodeLevels.R @@ -13,7 +13,7 @@ #' 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}}. #' @return \code{ds.recodeLevels} returns to the server-side a variable of type factor diff --git a/R/ds.recodeValues.R b/R/ds.recodeValues.R index 9643d33e..c82f3ca8 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -19,7 +19,7 @@ #' @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}}. #' @param notify.of.progress logical. If TRUE console output should be produced to indicate diff --git a/R/ds.rep.R b/R/ds.rep.R index 0e526149..c18b99d2 100644 --- a/R/ds.rep.R +++ b/R/ds.rep.R @@ -23,7 +23,7 @@ #' 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}}. #' @return \code{ds.rep} returns in the server-side a vector with the specified repetitive sequence. diff --git a/R/ds.replaceNA.R b/R/ds.replaceNA.R index 3345b7de..c7aff90d 100644 --- a/R/ds.replaceNA.R +++ b/R/ds.replaceNA.R @@ -19,7 +19,7 @@ #' 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}}. #' @return \code{ds.replaceNA} returns to the server-side a new vector or table structure diff --git a/R/ds.rm.R b/R/ds.rm.R index 77b693db..449c914d 100644 --- a/R/ds.rm.R +++ b/R/ds.rm.R @@ -14,7 +14,7 @@ #' #' 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}}. #' @return The \code{ds.rm} function deletes from the server-side @@ -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..1f44d76c 100644 --- a/R/ds.rowColCalc.R +++ b/R/ds.rowColCalc.R @@ -14,7 +14,7 @@ #' \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}}. #' @return \code{ds.rowColCalc} returns to the server-side rows and columns sums and means. diff --git a/R/ds.skewness.R b/R/ds.skewness.R index ed3b05d9..3d63f459 100644 --- a/R/ds.skewness.R +++ b/R/ds.skewness.R @@ -31,7 +31,7 @@ #' \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}}. #' @return \code{ds.skewness} returns a matrix showing the skewness of the input numeric variable, diff --git a/R/ds.sqrt.R b/R/ds.sqrt.R index 22a03937..6ee2de0d 100644 --- a/R/ds.sqrt.R +++ b/R/ds.sqrt.R @@ -10,7 +10,7 @@ #' @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}}. #' @return \code{ds.sqrt} assigns a vector for each study that includes the square root values of diff --git a/R/ds.subset.R b/R/ds.subset.R index 6f21bd08..0c0d8e02 100644 --- a/R/ds.subset.R +++ b/R/ds.subset.R @@ -19,7 +19,7 @@ #' 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 +#' @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{datashield.connections_default}. #' @return no data are return to the user, the generated subset dataframe is stored on the server side. #' @author Gaye, A. diff --git a/R/ds.subsetByClass.R b/R/ds.subsetByClass.R index 2a2ab29a..a205c083 100644 --- a/R/ds.subsetByClass.R +++ b/R/ds.subsetByClass.R @@ -11,7 +11,7 @@ #' @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 +#' @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{datashield.connections_default}. #' @return a no data are return to the user but messages are printed out. #' @author Gaye, A. diff --git a/R/ds.summary.R b/R/ds.summary.R index b4d3061c..8604b851 100644 --- a/R/ds.summary.R +++ b/R/ds.summary.R @@ -9,7 +9,7 @@ #' #' 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}}. #' @return \code{ds.summary} returns to the client-side the class and diff --git a/R/ds.table1D.R b/R/ds.table1D.R index 76e13199..c7f7049f 100644 --- a/R/ds.table1D.R +++ b/R/ds.table1D.R @@ -16,7 +16,7 @@ #' @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 +#' @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{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' diff --git a/R/ds.table2D.R b/R/ds.table2D.R index c8b882ac..cb64bfd5 100644 --- a/R/ds.table2D.R +++ b/R/ds.table2D.R @@ -17,7 +17,7 @@ #' @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 +#' @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{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 diff --git a/R/ds.testObjExists.R b/R/ds.testObjExists.R index bf84065d..652c63f9 100644 --- a/R/ds.testObjExists.R +++ b/R/ds.testObjExists.R @@ -8,7 +8,7 @@ #' #' 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}}. #' @return \code{ds.testObjExists} returns a list of messages specifying that the object exists diff --git a/R/ds.unList.R b/R/ds.unList.R index 773246fd..29ba9ced 100644 --- a/R/ds.unList.R +++ b/R/ds.unList.R @@ -18,7 +18,7 @@ #' @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}}. #' @return \code{ds.unList} returns to the server-side the unlist object. diff --git a/R/ds.unique.R b/R/ds.unique.R index 29797dee..5457bad1 100644 --- a/R/ds.unique.R +++ b/R/ds.unique.R @@ -7,7 +7,7 @@ #' @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}}. #' @return \code{ds.unique} returns the vector of unique R objects which are written to the server-side. diff --git a/R/ds.var.R b/R/ds.var.R index 0a74d4eb..a31122b5 100644 --- a/R/ds.var.R +++ b/R/ds.var.R @@ -23,7 +23,7 @@ #' 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}}. #' @return \code{ds.var} returns to the client-side a list including:\cr diff --git a/R/ds.vectorCalc.R b/R/ds.vectorCalc.R index bc090a87..0dc73493 100644 --- a/R/ds.vectorCalc.R +++ b/R/ds.vectorCalc.R @@ -13,7 +13,7 @@ #' @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 +#' @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{datashield.connections_default}. #' @return no data are returned to user, the output vector is stored on the server side. #' @author Gaye, A. diff --git a/R/getPooledMean.R b/R/getPooledMean.R index ded7fae8..a398882c 100644 --- a/R/getPooledMean.R +++ b/R/getPooledMean.R @@ -4,7 +4,7 @@ #' @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 +#' @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{datashield.connections_default}. #' @param x a character, the name of a numeric vector #' @keywords internal diff --git a/R/getPooledVar.R b/R/getPooledVar.R index 9fc9bbcd..48426632 100644 --- a/R/getPooledVar.R +++ b/R/getPooledVar.R @@ -4,7 +4,7 @@ #' @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 +#' @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{datashield.connections_default}. #' @param x a character, the name of a numeric vector #' @keywords internal diff --git a/R/glmChecks.R b/R/glmChecks.R index 53576448..0c223df1 100644 --- a/R/glmChecks.R +++ b/R/glmChecks.R @@ -12,7 +12,7 @@ #' 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 +#' @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{datashield.connections_default}. #' @keywords internal #' @return an integer 0 if check was passed and 1 if failed diff --git a/R/isAssigned.R b/R/isAssigned.R index c0f5150f..ac63b7ff 100644 --- a/R/isAssigned.R +++ b/R/isAssigned.R @@ -4,7 +4,7 @@ #' @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 +#' @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{datashield.connections_default}. #' @param newobj a character, the name the object to look for. #' @keywords internal diff --git a/R/isDefined.R b/R/isDefined.R index a0206257..7dd3282d 100644 --- a/R/isDefined.R +++ b/R/isDefined.R @@ -3,7 +3,7 @@ #' @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}}. #' @param obj a character vector, the name of the object(s) to look for. diff --git a/R/meanByClassHelper0a.R b/R/meanByClassHelper0a.R index d94898ff..d3f054f5 100644 --- a/R/meanByClassHelper0a.R +++ b/R/meanByClassHelper0a.R @@ -8,7 +8,7 @@ #' @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 +#' @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{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). diff --git a/R/meanByClassHelper0b.R b/R/meanByClassHelper0b.R index 21b66d44..6922074f 100644 --- a/R/meanByClassHelper0b.R +++ b/R/meanByClassHelper0b.R @@ -9,7 +9,7 @@ #' @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 +#' @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{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). diff --git a/R/meanByClassHelper1.R b/R/meanByClassHelper1.R index 6010e58b..ffdf6daa 100644 --- a/R/meanByClassHelper1.R +++ b/R/meanByClassHelper1.R @@ -3,7 +3,7 @@ #' @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 +#' @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{datashield.connections_default}. #' @param tables a character vector, the tables to breakdown #' @param variable a character, the variable to subset on diff --git a/R/meanByClassHelper2.R b/R/meanByClassHelper2.R index a0b0dfef..ef379fad 100644 --- a/R/meanByClassHelper2.R +++ b/R/meanByClassHelper2.R @@ -3,7 +3,7 @@ #' @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 +#' @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{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. diff --git a/R/meanByClassHelper3.R b/R/meanByClassHelper3.R index 0b820033..b0cc67c3 100644 --- a/R/meanByClassHelper3.R +++ b/R/meanByClassHelper3.R @@ -3,7 +3,7 @@ #' @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 +#' @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{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. diff --git a/R/meanByClassHelper4.R b/R/meanByClassHelper4.R index 88e827fc..7cf70c2f 100644 --- a/R/meanByClassHelper4.R +++ b/R/meanByClassHelper4.R @@ -3,7 +3,7 @@ #' @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 +#' @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{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 diff --git a/R/subsetHelper.R b/R/subsetHelper.R index c01529ac..0246708d 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -7,7 +7,7 @@ #' 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}}. #' @param data a character string specifying the name of the data frame or diff --git a/man/checkClass.Rd b/man/checkClass.Rd index 85931e59..5b516ecb 100644 --- a/man/checkClass.Rd +++ b/man/checkClass.Rd @@ -7,7 +7,7 @@ checkClass(datasources = NULL, obj = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the +\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{datashield.connections_default}.} \item{obj}{a string character, the name of the object to check for.} diff --git a/man/ds.abs.Rd b/man/ds.abs.Rd index b408cacd..9feb7437 100644 --- a/man/ds.abs.Rd +++ b/man/ds.abs.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.asCharacter.Rd b/man/ds.asCharacter.Rd index b11fc4f2..e238e74c 100644 --- a/man/ds.asCharacter.Rd +++ b/man/ds.asCharacter.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.asDataMatrix.Rd b/man/ds.asDataMatrix.Rd index 4f286edd..d48e712c 100644 --- a/man/ds.asDataMatrix.Rd +++ b/man/ds.asDataMatrix.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.asFactor.Rd b/man/ds.asFactor.Rd index bdd9a79e..99a0da3f 100644 --- a/man/ds.asFactor.Rd +++ b/man/ds.asFactor.Rd @@ -33,7 +33,7 @@ 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}}.} } diff --git a/man/ds.asFactorSimple.Rd b/man/ds.asFactorSimple.Rd index 07746f8b..edca488e 100644 --- a/man/ds.asFactorSimple.Rd +++ b/man/ds.asFactorSimple.Rd @@ -17,7 +17,7 @@ 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}}.} } diff --git a/man/ds.asInteger.Rd b/man/ds.asInteger.Rd index 49d8ca56..3097bfe4 100644 --- a/man/ds.asInteger.Rd +++ b/man/ds.asInteger.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.asList.Rd b/man/ds.asList.Rd index dbb8439b..11547364 100644 --- a/man/ds.asList.Rd +++ b/man/ds.asList.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.asLogical.Rd b/man/ds.asLogical.Rd index 479ca72b..744f3df5 100644 --- a/man/ds.asLogical.Rd +++ b/man/ds.asLogical.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.asMatrix.Rd b/man/ds.asMatrix.Rd index 5c2e991a..53729754 100644 --- a/man/ds.asMatrix.Rd +++ b/man/ds.asMatrix.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.asNumeric.Rd b/man/ds.asNumeric.Rd index 90f18101..a46ed4cb 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.assign.Rd b/man/ds.assign.Rd index 30cf5d12..f554f610 100644 --- a/man/ds.assign.Rd +++ b/man/ds.assign.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.auc.Rd b/man/ds.auc.Rd index 1bdc075f..bcf4c1c3 100644 --- a/man/ds.auc.Rd +++ b/man/ds.auc.Rd @@ -12,7 +12,7 @@ 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}}.} } 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..e1b784c8 100644 --- a/man/ds.bp_standards.Rd +++ b/man/ds.bp_standards.Rd @@ -33,7 +33,7 @@ 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}}.} } diff --git a/man/ds.c.Rd b/man/ds.c.Rd index ddd4db49..73627af8 100644 --- a/man/ds.c.Rd +++ b/man/ds.c.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.cbind.Rd b/man/ds.cbind.Rd index 4f3dc8ee..7af5bc4b 100644 --- a/man/ds.cbind.Rd +++ b/man/ds.cbind.Rd @@ -30,7 +30,7 @@ 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}}.} diff --git a/man/ds.changeRefGroup.Rd b/man/ds.changeRefGroup.Rd index 124cd903..2ecee62f 100644 --- a/man/ds.changeRefGroup.Rd +++ b/man/ds.changeRefGroup.Rd @@ -24,7 +24,7 @@ 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}}.} } diff --git a/man/ds.class.Rd b/man/ds.class.Rd index 59f1efa2..fa174617 100644 --- a/man/ds.class.Rd +++ b/man/ds.class.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd index 3f44ee30..5aff644a 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.completeCases.Rd b/man/ds.completeCases.Rd index a5b0b8a0..e09c0de9 100644 --- a/man/ds.completeCases.Rd +++ b/man/ds.completeCases.Rd @@ -15,7 +15,7 @@ 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}}.} } diff --git a/man/ds.cor.Rd b/man/ds.cor.Rd index d01c9b3b..8bbd6792 100644 --- a/man/ds.cor.Rd +++ b/man/ds.cor.Rd @@ -15,7 +15,7 @@ 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}}.} } diff --git a/man/ds.corTest.Rd b/man/ds.corTest.Rd index bb2384d4..f5eb9e0a 100644 --- a/man/ds.corTest.Rd +++ b/man/ds.corTest.Rd @@ -36,7 +36,7 @@ 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}}.} } diff --git a/man/ds.cov.Rd b/man/ds.cov.Rd index 1d8b5455..807c5df9 100644 --- a/man/ds.cov.Rd +++ b/man/ds.cov.Rd @@ -25,7 +25,7 @@ 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}}.} } diff --git a/man/ds.dataFrame.Rd b/man/ds.dataFrame.Rd index 4a3e80dd..686c851b 100644 --- a/man/ds.dataFrame.Rd +++ b/man/ds.dataFrame.Rd @@ -48,7 +48,7 @@ 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}}.} diff --git a/man/ds.dataFrameFill.Rd b/man/ds.dataFrameFill.Rd index 3183d61c..551a0d2f 100644 --- a/man/ds.dataFrameFill.Rd +++ b/man/ds.dataFrameFill.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.dataFrameSort.Rd b/man/ds.dataFrameSort.Rd index 7b9e843a..70c34d9e 100644 --- a/man/ds.dataFrameSort.Rd +++ b/man/ds.dataFrameSort.Rd @@ -30,7 +30,7 @@ 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}}.} } diff --git a/man/ds.dataFrameSubset.Rd b/man/ds.dataFrameSubset.Rd index 2f6068d3..c53a9cfb 100644 --- a/man/ds.dataFrameSubset.Rd +++ b/man/ds.dataFrameSubset.Rd @@ -42,7 +42,7 @@ 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}}.} diff --git a/man/ds.densityGrid.Rd b/man/ds.densityGrid.Rd index 15e29977..01558833 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -26,7 +26,7 @@ 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}}.} } diff --git a/man/ds.dim.Rd b/man/ds.dim.Rd index b6a86b57..6fd54bec 100644 --- a/man/ds.dim.Rd +++ b/man/ds.dim.Rd @@ -20,7 +20,7 @@ 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}}.} } diff --git a/man/ds.elspline.Rd b/man/ds.elspline.Rd index 26c5f6cc..1a20e8b8 100644 --- a/man/ds.elspline.Rd +++ b/man/ds.elspline.Rd @@ -26,7 +26,7 @@ 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}}.} } diff --git a/man/ds.exists.Rd b/man/ds.exists.Rd index 029c66b9..dd26658c 100644 --- a/man/ds.exists.Rd +++ b/man/ds.exists.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.exp.Rd b/man/ds.exp.Rd index 07e212c9..d8015ae9 100644 --- a/man/ds.exp.Rd +++ b/man/ds.exp.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.hetcor.Rd b/man/ds.hetcor.Rd index aa7d0713..0d075897 100644 --- a/man/ds.hetcor.Rd +++ b/man/ds.hetcor.Rd @@ -34,7 +34,7 @@ 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}}.} } diff --git a/man/ds.igb_standards.Rd b/man/ds.igb_standards.Rd index 6ea70b2f..c081a7b1 100644 --- a/man/ds.igb_standards.Rd +++ b/man/ds.igb_standards.Rd @@ -39,7 +39,7 @@ 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}}.} } diff --git a/man/ds.isNA.Rd b/man/ds.isNA.Rd index 0c94b9eb..afbb1d92 100644 --- a/man/ds.isNA.Rd +++ b/man/ds.isNA.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.isValid.Rd b/man/ds.isValid.Rd index 2bda8557..790b89e9 100644 --- a/man/ds.isValid.Rd +++ b/man/ds.isValid.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.kurtosis.Rd b/man/ds.kurtosis.Rd index 4a9b2a32..658bef10 100644 --- a/man/ds.kurtosis.Rd +++ b/man/ds.kurtosis.Rd @@ -18,7 +18,7 @@ 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}}.} } diff --git a/man/ds.length.Rd b/man/ds.length.Rd index 08b513a1..60b95325 100644 --- a/man/ds.length.Rd +++ b/man/ds.length.Rd @@ -22,7 +22,7 @@ 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}}.} } diff --git a/man/ds.levels.Rd b/man/ds.levels.Rd index 0a372660..1f1ad038 100644 --- a/man/ds.levels.Rd +++ b/man/ds.levels.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.list.Rd b/man/ds.list.Rd index de5b69e7..06f71c47 100644 --- a/man/ds.list.Rd +++ b/man/ds.list.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.listServersideFunctions.Rd b/man/ds.listServersideFunctions.Rd index 30931c62..74bcfda7 100644 --- a/man/ds.listServersideFunctions.Rd +++ b/man/ds.listServersideFunctions.Rd @@ -7,7 +7,7 @@ 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}}.} } diff --git a/man/ds.log.Rd b/man/ds.log.Rd index b988fb84..3de9e2f0 100644 --- a/man/ds.log.Rd +++ b/man/ds.log.Rd @@ -15,7 +15,7 @@ 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}}.} } diff --git a/man/ds.look.Rd b/man/ds.look.Rd index 4a59c166..c2fa4cae 100644 --- a/man/ds.look.Rd +++ b/man/ds.look.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.ls.Rd b/man/ds.ls.Rd index e05feb5e..3f3a05ce 100644 --- a/man/ds.ls.Rd +++ b/man/ds.ls.Rd @@ -26,7 +26,7 @@ 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}}.} } diff --git a/man/ds.lspline.Rd b/man/ds.lspline.Rd index 550e2397..867625aa 100644 --- a/man/ds.lspline.Rd +++ b/man/ds.lspline.Rd @@ -25,7 +25,7 @@ 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}}.} } diff --git a/man/ds.matrixDet.Rd b/man/ds.matrixDet.Rd index 1c419f4d..6ac9841a 100644 --- a/man/ds.matrixDet.Rd +++ b/man/ds.matrixDet.Rd @@ -15,7 +15,7 @@ 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}}.} } diff --git a/man/ds.matrixDet.report.Rd b/man/ds.matrixDet.report.Rd index e4fc3569..f60c127d 100644 --- a/man/ds.matrixDet.report.Rd +++ b/man/ds.matrixDet.report.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.matrixDimnames.Rd b/man/ds.matrixDimnames.Rd index bc5e5813..635cf281 100644 --- a/man/ds.matrixDimnames.Rd +++ b/man/ds.matrixDimnames.Rd @@ -22,7 +22,7 @@ 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}}.} } diff --git a/man/ds.matrixInvert.Rd b/man/ds.matrixInvert.Rd index 0a6ff331..ffca8cda 100644 --- a/man/ds.matrixInvert.Rd +++ b/man/ds.matrixInvert.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.matrixMult.Rd b/man/ds.matrixMult.Rd index 22a1dbc6..1d0a2021 100644 --- a/man/ds.matrixMult.Rd +++ b/man/ds.matrixMult.Rd @@ -14,7 +14,7 @@ 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}}.} } diff --git a/man/ds.matrixTranspose.Rd b/man/ds.matrixTranspose.Rd index 26be7098..841fd19b 100644 --- a/man/ds.matrixTranspose.Rd +++ b/man/ds.matrixTranspose.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.mean.Rd b/man/ds.mean.Rd index e6d0fd70..9c5ccdcd 100644 --- a/man/ds.mean.Rd +++ b/man/ds.mean.Rd @@ -31,7 +31,7 @@ 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}}.} } diff --git a/man/ds.meanByClass.Rd b/man/ds.meanByClass.Rd index 340b07db..ab2a299e 100644 --- a/man/ds.meanByClass.Rd +++ b/man/ds.meanByClass.Rd @@ -24,7 +24,7 @@ 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}}.} } diff --git a/man/ds.message.Rd b/man/ds.message.Rd index 6b54e513..ead3313b 100644 --- a/man/ds.message.Rd +++ b/man/ds.message.Rd @@ -10,7 +10,7 @@ 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}}.} } diff --git a/man/ds.metadata.Rd b/man/ds.metadata.Rd index cc43a67d..6f711e47 100644 --- a/man/ds.metadata.Rd +++ b/man/ds.metadata.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.names.Rd b/man/ds.names.Rd index daee0cba..178ad99d 100644 --- a/man/ds.names.Rd +++ b/man/ds.names.Rd @@ -9,7 +9,7 @@ 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: diff --git a/man/ds.ns.Rd b/man/ds.ns.Rd index 51e3166b..28e36290 100644 --- a/man/ds.ns.Rd +++ b/man/ds.ns.Rd @@ -34,7 +34,7 @@ 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}}.} } diff --git a/man/ds.numNA.Rd b/man/ds.numNA.Rd index 668e23ed..e9990d95 100644 --- a/man/ds.numNA.Rd +++ b/man/ds.numNA.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.qlspline.Rd b/man/ds.qlspline.Rd index fc9285ae..5fcca7af 100644 --- a/man/ds.qlspline.Rd +++ b/man/ds.qlspline.Rd @@ -30,7 +30,7 @@ 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}}.} } diff --git a/man/ds.quantileMean.Rd b/man/ds.quantileMean.Rd index 56019428..652ca9f1 100644 --- a/man/ds.quantileMean.Rd +++ b/man/ds.quantileMean.Rd @@ -13,7 +13,7 @@ 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}}.} } diff --git a/man/ds.rBinom.Rd b/man/ds.rBinom.Rd index e3ee5d16..0306b0ac 100644 --- a/man/ds.rBinom.Rd +++ b/man/ds.rBinom.Rd @@ -33,7 +33,7 @@ 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}}.} } diff --git a/man/ds.rPois.Rd b/man/ds.rPois.Rd index 4fbe5e4f..8fe1072d 100644 --- a/man/ds.rPois.Rd +++ b/man/ds.rPois.Rd @@ -30,7 +30,7 @@ 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}}.} } diff --git a/man/ds.rbind.Rd b/man/ds.rbind.Rd index d294f474..969a6a18 100644 --- a/man/ds.rbind.Rd +++ b/man/ds.rbind.Rd @@ -25,7 +25,7 @@ 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}}.} diff --git a/man/ds.reShape.Rd b/man/ds.reShape.Rd index 9c54b3fc..c29ce5cf 100644 --- a/man/ds.reShape.Rd +++ b/man/ds.reShape.Rd @@ -49,7 +49,7 @@ 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}}.} } diff --git a/man/ds.recodeLevels.Rd b/man/ds.recodeLevels.Rd index 958b4881..c74c1c48 100644 --- a/man/ds.recodeLevels.Rd +++ b/man/ds.recodeLevels.Rd @@ -20,7 +20,7 @@ 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}}.} } diff --git a/man/ds.recodeValues.Rd b/man/ds.recodeValues.Rd index a6af2722..c8cad12f 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -31,7 +31,7 @@ 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}}.} diff --git a/man/ds.rep.Rd b/man/ds.rep.Rd index 23a35250..9c3a0388 100644 --- a/man/ds.rep.Rd +++ b/man/ds.rep.Rd @@ -44,7 +44,7 @@ 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}}.} } diff --git a/man/ds.replaceNA.Rd b/man/ds.replaceNA.Rd index f8480591..3fa586a3 100644 --- a/man/ds.replaceNA.Rd +++ b/man/ds.replaceNA.Rd @@ -15,7 +15,7 @@ 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}}.} } diff --git a/man/ds.rm.Rd b/man/ds.rm.Rd index 9a6e88af..92721ee9 100644 --- a/man/ds.rm.Rd +++ b/man/ds.rm.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.rowColCalc.Rd b/man/ds.rowColCalc.Rd index dc0992f2..9f30b728 100644 --- a/man/ds.rowColCalc.Rd +++ b/man/ds.rowColCalc.Rd @@ -15,7 +15,7 @@ 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}}.} } diff --git a/man/ds.skewness.Rd b/man/ds.skewness.Rd index 9ebab0d6..e5afdb73 100644 --- a/man/ds.skewness.Rd +++ b/man/ds.skewness.Rd @@ -17,7 +17,7 @@ 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}}.} } diff --git a/man/ds.sqrt.Rd b/man/ds.sqrt.Rd index 62abcc83..1552aa72 100644 --- a/man/ds.sqrt.Rd +++ b/man/ds.sqrt.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.subset.Rd b/man/ds.subset.Rd index 0c2472f2..e26bb213 100644 --- a/man/ds.subset.Rd +++ b/man/ds.subset.Rd @@ -33,7 +33,7 @@ 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 +\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{datashield.connections_default}.} } \value{ diff --git a/man/ds.subsetByClass.Rd b/man/ds.subsetByClass.Rd index d19b5a71..78c53f65 100644 --- a/man/ds.subsetByClass.Rd +++ b/man/ds.subsetByClass.Rd @@ -19,7 +19,7 @@ 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 +\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{datashield.connections_default}.} } \value{ diff --git a/man/ds.summary.Rd b/man/ds.summary.Rd index f171efe4..a5a4fd74 100644 --- a/man/ds.summary.Rd +++ b/man/ds.summary.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.table1D.Rd b/man/ds.table1D.Rd index a4d5c958..f98d97c3 100644 --- a/man/ds.table1D.Rd +++ b/man/ds.table1D.Rd @@ -22,7 +22,7 @@ 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 +\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{datashield.connections_default}.} } \value{ diff --git a/man/ds.table2D.Rd b/man/ds.table2D.Rd index 00a14d14..2eb0a390 100644 --- a/man/ds.table2D.Rd +++ b/man/ds.table2D.Rd @@ -26,7 +26,7 @@ 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 +\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{datashield.connections_default}.} } \value{ diff --git a/man/ds.testObjExists.Rd b/man/ds.testObjExists.Rd index 0e14bc6d..702605f8 100644 --- a/man/ds.testObjExists.Rd +++ b/man/ds.testObjExists.Rd @@ -9,7 +9,7 @@ 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}}.} } diff --git a/man/ds.unList.Rd b/man/ds.unList.Rd index 72128133..fc86570b 100644 --- a/man/ds.unList.Rd +++ b/man/ds.unList.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.unique.Rd b/man/ds.unique.Rd index f148ec63..f8fb9cb9 100644 --- a/man/ds.unique.Rd +++ b/man/ds.unique.Rd @@ -12,7 +12,7 @@ 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}}.} } diff --git a/man/ds.var.Rd b/man/ds.var.Rd index 48bc30bd..7e00fce8 100644 --- a/man/ds.var.Rd +++ b/man/ds.var.Rd @@ -20,7 +20,7 @@ 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}}.} } diff --git a/man/ds.vectorCalc.Rd b/man/ds.vectorCalc.Rd index 39890eed..929404b9 100644 --- a/man/ds.vectorCalc.Rd +++ b/man/ds.vectorCalc.Rd @@ -14,7 +14,7 @@ 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 +\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{datashield.connections_default}.} } \value{ diff --git a/man/getPooledMean.Rd b/man/getPooledMean.Rd index eae00977..6bb4e12a 100644 --- a/man/getPooledMean.Rd +++ b/man/getPooledMean.Rd @@ -7,7 +7,7 @@ getPooledMean(dtsources, x) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the +\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{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..4ab46179 100644 --- a/man/getPooledVar.Rd +++ b/man/getPooledVar.Rd @@ -7,7 +7,7 @@ getPooledVar(dtsources, x) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the +\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{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..24c4391d 100644 --- a/man/glmChecks.Rd +++ b/man/glmChecks.Rd @@ -18,7 +18,7 @@ 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 +\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{datashield.connections_default}.} } \value{ diff --git a/man/isAssigned.Rd b/man/isAssigned.Rd index 7136df10..c332fe97 100644 --- a/man/isAssigned.Rd +++ b/man/isAssigned.Rd @@ -7,7 +7,7 @@ isAssigned(datasources = NULL, newobj = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the +\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{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..fb7d8412 100644 --- a/man/isDefined.Rd +++ b/man/isDefined.Rd @@ -7,7 +7,7 @@ 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}}.} diff --git a/man/meanByClassHelper0a.Rd b/man/meanByClassHelper0a.Rd index 083dc524..43bd1797 100644 --- a/man/meanByClassHelper0a.Rd +++ b/man/meanByClassHelper0a.Rd @@ -15,7 +15,7 @@ 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 +\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{datashield.connections_default}.} } \value{ diff --git a/man/meanByClassHelper0b.Rd b/man/meanByClassHelper0b.Rd index 57220e0e..7e67b58b 100644 --- a/man/meanByClassHelper0b.Rd +++ b/man/meanByClassHelper0b.Rd @@ -17,7 +17,7 @@ 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 +\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{datashield.connections_default}.} } \value{ diff --git a/man/meanByClassHelper1.Rd b/man/meanByClassHelper1.Rd index 8f1c2cd8..942900c8 100644 --- a/man/meanByClassHelper1.Rd +++ b/man/meanByClassHelper1.Rd @@ -7,7 +7,7 @@ meanByClassHelper1(dtsource, tables, variable, categories) } \arguments{ -\item{dtsource}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the +\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{datashield.connections_default}.} \item{tables}{a character vector, the tables to breakdown} diff --git a/man/meanByClassHelper2.Rd b/man/meanByClassHelper2.Rd index b7fc1bbb..fd385808 100644 --- a/man/meanByClassHelper2.Rd +++ b/man/meanByClassHelper2.Rd @@ -7,7 +7,7 @@ meanByClassHelper2(dtsources, tablenames, variables, invalidrecorder) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the +\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{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..f8a03ded 100644 --- a/man/meanByClassHelper3.Rd +++ b/man/meanByClassHelper3.Rd @@ -7,7 +7,7 @@ meanByClassHelper3(dtsources, tablenames, variables, invalidrecorder) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the +\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{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..07f8e2b1 100644 --- a/man/meanByClassHelper4.Rd +++ b/man/meanByClassHelper4.Rd @@ -13,7 +13,7 @@ meanByClassHelper4( ) } \arguments{ -\item{dtsource}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the +\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{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..31e41a0f 100644 --- a/man/subsetHelper.Rd +++ b/man/subsetHelper.Rd @@ -7,7 +7,7 @@ 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}}.} From 6c3799e762229a44349419c98d56329912498dd8 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 10 Jun 2025 13:11:24 +0100 Subject: [PATCH 3/5] Link issues --- R/checkClass.R | 2 +- R/ds.Boole.R | 4 ++-- R/ds.abs.R | 2 +- R/ds.asCharacter.R | 2 +- R/ds.asDataMatrix.R | 2 +- R/ds.asFactor.R | 2 +- R/ds.asFactorSimple.R | 2 +- R/ds.asInteger.R | 2 +- R/ds.asList.R | 2 +- R/ds.asLogical.R | 2 +- R/ds.asMatrix.R | 2 +- R/ds.asNumeric.R | 2 +- R/ds.assign.R | 2 +- R/ds.auc.R | 2 +- R/ds.bp_standards.R | 2 +- R/ds.c.R | 2 +- R/ds.cbind.R | 2 +- R/ds.changeRefGroup.R | 2 +- R/ds.class.R | 2 +- R/ds.colnames.R | 2 +- R/ds.completeCases.R | 2 +- R/ds.cor.R | 2 +- R/ds.corTest.R | 2 +- R/ds.cov.R | 2 +- R/ds.dataFrame.R | 2 +- R/ds.dataFrameFill.R | 2 +- R/ds.dataFrameSort.R | 2 +- R/ds.dataFrameSubset.R | 2 +- R/ds.densityGrid.R | 2 +- R/ds.dim.R | 2 +- R/ds.elspline.R | 2 +- R/ds.exists.R | 2 +- R/ds.exp.R | 2 +- R/ds.list.R | 2 +- R/ds.listServersideFunctions.R | 2 +- R/ds.log.R | 2 +- R/ds.look.R | 2 +- R/ds.lspline.R | 2 +- R/ds.matrixDet.R | 2 +- R/ds.matrixDet.report.R | 2 +- R/ds.matrixDimnames.R | 2 +- R/ds.matrixInvert.R | 2 +- R/ds.matrixMult.R | 2 +- R/ds.matrixTranspose.R | 2 +- R/ds.meanByClass.R | 2 +- R/ds.message.R | 2 +- R/ds.metadata.R | 2 +- R/ds.mice.R | 4 ++-- R/ds.names.R | 2 +- R/ds.ns.R | 2 +- R/ds.numNA.R | 2 +- R/ds.qlspline.R | 2 +- R/ds.quantileMean.R | 2 +- R/ds.rBinom.R | 2 +- R/ds.rNorm.R | 2 +- R/ds.rPois.R | 2 +- R/ds.rUnif.R | 2 +- R/ds.rbind.R | 2 +- R/ds.reShape.R | 2 +- R/ds.recodeLevels.R | 2 +- R/ds.recodeValues.R | 2 +- R/ds.rep.R | 2 +- R/ds.replaceNA.R | 2 +- R/ds.rm.R | 2 +- R/ds.rowColCalc.R | 2 +- R/ds.scatterPlot.R | 4 ++-- R/ds.seq.R | 4 ++-- R/ds.setSeed.R | 4 ++-- R/ds.skewness.R | 2 +- R/ds.sqrt.R | 2 +- R/ds.subset.R | 2 +- R/ds.subsetByClass.R | 2 +- R/ds.summary.R | 2 +- R/ds.table.R | 4 ++-- R/ds.table1D.R | 2 +- R/ds.table2D.R | 2 +- R/ds.tapply.R | 4 ++-- R/ds.tapply.assign.R | 4 ++-- R/ds.testObjExists.R | 2 +- R/ds.unList.R | 2 +- R/ds.unique.R | 2 +- R/ds.var.R | 2 +- R/ds.vectorCalc.R | 2 +- R/getPooledMean.R | 2 +- R/getPooledVar.R | 2 +- R/glmChecks.R | 2 +- R/isAssigned.R | 2 +- R/isDefined.R | 2 +- R/meanByClassHelper0a.R | 2 +- R/meanByClassHelper0b.R | 2 +- R/meanByClassHelper1.R | 2 +- R/meanByClassHelper2.R | 2 +- R/meanByClassHelper3.R | 2 +- R/meanByClassHelper4.R | 2 +- R/subsetHelper.R | 2 +- man/checkClass.Rd | 2 +- man/ds.Boole.Rd | 4 ++-- man/ds.abs.Rd | 2 +- man/ds.asCharacter.Rd | 2 +- man/ds.asDataMatrix.Rd | 2 +- man/ds.asFactor.Rd | 2 +- man/ds.asFactorSimple.Rd | 2 +- man/ds.asInteger.Rd | 2 +- man/ds.asList.Rd | 2 +- man/ds.asLogical.Rd | 2 +- man/ds.asMatrix.Rd | 2 +- man/ds.asNumeric.Rd | 2 +- man/ds.assign.Rd | 2 +- man/ds.auc.Rd | 2 +- man/ds.bp_standards.Rd | 2 +- man/ds.c.Rd | 2 +- man/ds.cbind.Rd | 2 +- man/ds.changeRefGroup.Rd | 2 +- man/ds.class.Rd | 2 +- man/ds.colnames.Rd | 2 +- man/ds.completeCases.Rd | 2 +- man/ds.cor.Rd | 2 +- man/ds.corTest.Rd | 2 +- man/ds.cov.Rd | 2 +- man/ds.dataFrame.Rd | 2 +- man/ds.dataFrameFill.Rd | 2 +- man/ds.dataFrameSort.Rd | 2 +- man/ds.dataFrameSubset.Rd | 2 +- man/ds.densityGrid.Rd | 2 +- man/ds.dim.Rd | 2 +- man/ds.elspline.Rd | 2 +- man/ds.exists.Rd | 2 +- man/ds.exp.Rd | 2 +- man/ds.list.Rd | 2 +- man/ds.listServersideFunctions.Rd | 2 +- man/ds.log.Rd | 2 +- man/ds.look.Rd | 2 +- man/ds.lspline.Rd | 2 +- man/ds.matrixDet.Rd | 2 +- man/ds.matrixDet.report.Rd | 2 +- man/ds.matrixDimnames.Rd | 2 +- man/ds.matrixInvert.Rd | 2 +- man/ds.matrixMult.Rd | 2 +- man/ds.matrixTranspose.Rd | 2 +- man/ds.meanByClass.Rd | 2 +- man/ds.message.Rd | 2 +- man/ds.metadata.Rd | 2 +- man/ds.mice.Rd | 4 ++-- man/ds.names.Rd | 2 +- man/ds.ns.Rd | 2 +- man/ds.numNA.Rd | 2 +- man/ds.qlspline.Rd | 2 +- man/ds.quantileMean.Rd | 2 +- man/ds.rBinom.Rd | 2 +- man/ds.rNorm.Rd | 2 +- man/ds.rPois.Rd | 2 +- man/ds.rUnif.Rd | 2 +- man/ds.rbind.Rd | 2 +- man/ds.reShape.Rd | 2 +- man/ds.recodeLevels.Rd | 2 +- man/ds.recodeValues.Rd | 2 +- man/ds.rep.Rd | 2 +- man/ds.replaceNA.Rd | 2 +- man/ds.rm.Rd | 2 +- man/ds.rowColCalc.Rd | 2 +- man/ds.scatterPlot.Rd | 4 ++-- man/ds.seq.Rd | 4 ++-- man/ds.setSeed.Rd | 4 ++-- man/ds.skewness.Rd | 2 +- man/ds.sqrt.Rd | 2 +- man/ds.subset.Rd | 2 +- man/ds.subsetByClass.Rd | 2 +- man/ds.summary.Rd | 2 +- man/ds.table.Rd | 4 ++-- man/ds.table1D.Rd | 2 +- man/ds.table2D.Rd | 2 +- man/ds.tapply.Rd | 4 ++-- man/ds.tapply.assign.Rd | 4 ++-- man/ds.testObjExists.Rd | 2 +- man/ds.unList.Rd | 2 +- man/ds.unique.Rd | 2 +- man/ds.var.Rd | 2 +- man/ds.vectorCalc.Rd | 2 +- man/getPooledMean.Rd | 2 +- man/getPooledVar.Rd | 2 +- man/glmChecks.Rd | 2 +- man/isAssigned.Rd | 2 +- man/isDefined.Rd | 2 +- man/meanByClassHelper0a.Rd | 2 +- man/meanByClassHelper0b.Rd | 2 +- man/meanByClassHelper1.Rd | 2 +- man/meanByClassHelper2.Rd | 2 +- man/meanByClassHelper3.Rd | 2 +- man/meanByClassHelper4.Rd | 2 +- man/subsetHelper.Rd | 2 +- 190 files changed, 206 insertions(+), 206 deletions(-) diff --git a/R/checkClass.R b/R/checkClass.R index db3316c4..779eca1e 100644 --- a/R/checkClass.R +++ b/R/checkClass.R @@ -4,7 +4,7 @@ #' @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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 81db6c42..41c20455 100644 --- a/R/ds.abs.R +++ b/R/ds.abs.R @@ -12,7 +12,7 @@ #' that is stored on the data servers. Default name is set to \code{abs.newobj}. #' @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 63e93931..c0bd4ce0 100644 --- a/R/ds.asCharacter.R +++ b/R/ds.asCharacter.R @@ -11,7 +11,7 @@ #' that is stored on the data servers. Default \code{ascharacter.newobj}. #' @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 2541665d..7b4833bb 100644 --- a/R/ds.asDataMatrix.R +++ b/R/ds.asDataMatrix.R @@ -10,7 +10,7 @@ #' that is stored on the data servers. Default \code{asdatamatrix.newobj}. #' @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 f72fa21d..476f00f8 100644 --- a/R/ds.asFactor.R +++ b/R/ds.asFactor.R @@ -132,7 +132,7 @@ #' into account. #' @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 5a614579..313f7b40 100644 --- a/R/ds.asFactorSimple.R +++ b/R/ds.asFactorSimple.R @@ -16,7 +16,7 @@ #' that is stored on the data servers. Default \code{asfactor.newobj}. #' @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(). diff --git a/R/ds.asInteger.R b/R/ds.asInteger.R index 0a959c8e..9b3b1a39 100644 --- a/R/ds.asInteger.R +++ b/R/ds.asInteger.R @@ -24,7 +24,7 @@ #' that is stored on the data servers. Default \code{asinteger.newobj}. #' @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 164c035c..d7366878 100644 --- a/R/ds.asList.R +++ b/R/ds.asList.R @@ -11,7 +11,7 @@ #' that is stored on the data servers. Default \code{aslist.newobj}. #' @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 e3623037..2ddc33cf 100644 --- a/R/ds.asLogical.R +++ b/R/ds.asLogical.R @@ -10,7 +10,7 @@ #' that is stored on the data servers. Default \code{aslogical.newobj}. #' @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 52e1c6c0..1c5b0ced 100644 --- a/R/ds.asMatrix.R +++ b/R/ds.asMatrix.R @@ -13,7 +13,7 @@ #' that is stored on the data servers. Default \code{asmatrix.newobj}. #' @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 540b9993..7b4da435 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -24,7 +24,7 @@ #' that is stored on the data servers. Default \code{asnumeric.newobj}. #' @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 2d91fa02..25b71c74 100644 --- a/R/ds.assign.R +++ b/R/ds.assign.R @@ -12,7 +12,7 @@ #' that is stored on the data servers. Default \code{assign.newobj}. #' @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 3bb7eb6e..ebfc5fc3 100644 --- a/R/ds.auc.R +++ b/R/ds.auc.R @@ -8,7 +8,7 @@ #' the complete cases that are used in the regression model. #' @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 diff --git a/R/ds.bp_standards.R b/R/ds.bp_standards.R index 0d17e581..ae76c54c 100644 --- a/R/ds.bp_standards.R +++ b/R/ds.bp_standards.R @@ -18,7 +18,7 @@ #' that is stored on the data servers. Default name is set to \code{bp.newobj}. #' @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. diff --git a/R/ds.c.R b/R/ds.c.R index 1c5e8443..2093ac01 100644 --- a/R/ds.c.R +++ b/R/ds.c.R @@ -12,7 +12,7 @@ #' that is stored on the data servers. Default \code{c.newobj}. #' @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 8b64b70e..d943e017 100644 --- a/R/ds.cbind.R +++ b/R/ds.cbind.R @@ -34,7 +34,7 @@ #' that is stored on the data servers. Defaults \code{cbind.newobj}. #' @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 f9ec7455..4bd5080a 100644 --- a/R/ds.changeRefGroup.R +++ b/R/ds.changeRefGroup.R @@ -24,7 +24,7 @@ #' The default is to not re-order (see the reasons in the details). #' @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 841ddfcf..036848ad 100644 --- a/R/ds.class.R +++ b/R/ds.class.R @@ -8,7 +8,7 @@ #' @param x a character string providing the name of the input R object. #' @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 e8360601..a4b98b1a 100644 --- a/R/ds.colnames.R +++ b/R/ds.colnames.R @@ -8,7 +8,7 @@ #' @param x a character string providing the name of the input data frame or matrix. #' @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 747d52ae..ed95bf6d 100644 --- a/R/ds.completeCases.R +++ b/R/ds.completeCases.R @@ -16,7 +16,7 @@ #' suffix "_complete.cases" #' @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.cor.R b/R/ds.cor.R index 2fcd7185..53fb22db 100644 --- a/R/ds.cor.R +++ b/R/ds.cor.R @@ -29,7 +29,7 @@ #' 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[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 ddd66b32..38fffceb 100644 --- a/R/ds.corTest.R +++ b/R/ds.corTest.R @@ -21,7 +21,7 @@ #' Fisher's z transformation. #' @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 79471788..c67d2e13 100644 --- a/R/ds.cov.R +++ b/R/ds.cov.R @@ -37,7 +37,7 @@ #' 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[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 fa86a558..5837747c 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -34,7 +34,7 @@ #' that is stored on the data servers. Default \code{dataframe.newobj}. #' @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 ccea6af8..3de389b7 100644 --- a/R/ds.dataFrameFill.R +++ b/R/ds.dataFrameFill.R @@ -15,7 +15,7 @@ #' that is stored on the data servers. Default value is "dataframefill.newobj". #' @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 76f9bf1f..de59d61e 100644 --- a/R/ds.dataFrameSort.R +++ b/R/ds.dataFrameSort.R @@ -35,7 +35,7 @@ #' where \code{df.name} is the first argument of \code{ds.dataFrameSort()}. #' @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 diff --git a/R/ds.dataFrameSubset.R b/R/ds.dataFrameSubset.R index 1b531b96..46878520 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -30,7 +30,7 @@ #' object that is stored on the data servers. Default \code{dataframesubset.newobj}. #' @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 123c6650..b0766418 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -25,7 +25,7 @@ #' one grid density matrix is generated. Default \code{'combine'}. #' @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 3755a2e4..4a6cd3a7 100644 --- a/R/ds.dim.R +++ b/R/ds.dim.R @@ -24,7 +24,7 @@ #' Default FALSE. #' @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 30c56647..c4a2bbdd 100644 --- a/R/ds.elspline.R +++ b/R/ds.elspline.R @@ -19,7 +19,7 @@ #' variable that is stored on the data servers. Default \code{elspline.newobj}. #' @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 diff --git a/R/ds.exists.R b/R/ds.exists.R index 2a04a355..6dff8b4c 100644 --- a/R/ds.exists.R +++ b/R/ds.exists.R @@ -12,7 +12,7 @@ #' @param x a character string providing the name of the object to look for. #' @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 a9409e43..5bf325bd 100644 --- a/R/ds.exp.R +++ b/R/ds.exp.R @@ -11,7 +11,7 @@ #' that is stored on the data servers. Default \code{exp.newobj}. #' @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.list.R b/R/ds.list.R index fa5ebf62..b0847703 100644 --- a/R/ds.list.R +++ b/R/ds.list.R @@ -10,7 +10,7 @@ #' that is stored on the data servers. Default \code{list.newobj}. #' @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.listServersideFunctions.R b/R/ds.listServersideFunctions.R index f4b54595..c81d203c 100644 --- a/R/ds.listServersideFunctions.R +++ b/R/ds.listServersideFunctions.R @@ -10,7 +10,7 @@ #' This function does not call any server-side function. #' @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.log.R b/R/ds.log.R index 07328b9a..8c0b2e5d 100644 --- a/R/ds.log.R +++ b/R/ds.log.R @@ -10,7 +10,7 @@ #' that is stored on the server-side. Default \code{log.newobj}. #' @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 f864309e..8dffa52f 100644 --- a/R/ds.look.R +++ b/R/ds.look.R @@ -22,7 +22,7 @@ #' Default FALSE to save time. #' @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.lspline.R b/R/ds.lspline.R index cf59090d..9aca2397 100644 --- a/R/ds.lspline.R +++ b/R/ds.lspline.R @@ -16,7 +16,7 @@ #' variable that is stored on the data servers. Default \code{lspline.newobj}. #' @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 diff --git a/R/ds.matrixDet.R b/R/ds.matrixDet.R index fc825600..5fcd81a5 100644 --- a/R/ds.matrixDet.R +++ b/R/ds.matrixDet.R @@ -15,7 +15,7 @@ #' is calculated. Default FALSE. #' @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 7965b399..be21aaa7 100644 --- a/R/ds.matrixDet.report.R +++ b/R/ds.matrixDet.report.R @@ -14,7 +14,7 @@ #' is calculated. Default FALSE. #' @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.matrixDimnames.R b/R/ds.matrixDimnames.R index 1dd08162..6f4a37ea 100644 --- a/R/ds.matrixDimnames.R +++ b/R/ds.matrixDimnames.R @@ -13,7 +13,7 @@ #' variable that is stored on the data servers. Default \code{matrixdimnames.newobj}. #' @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 d3f43b9f..8cc3c447 100644 --- a/R/ds.matrixInvert.R +++ b/R/ds.matrixInvert.R @@ -11,7 +11,7 @@ #' Default \code{matrixinvert.newobj}. #' @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 2198abbb..cf5349fe 100644 --- a/R/ds.matrixMult.R +++ b/R/ds.matrixMult.R @@ -14,7 +14,7 @@ #' variable that is stored on the data servers. Default \code{matrixmult.newobj}. #' @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 51375a28..bbd73a1a 100644 --- a/R/ds.matrixTranspose.R +++ b/R/ds.matrixTranspose.R @@ -14,7 +14,7 @@ #' Default \code{matrixtranspose.newobj}. #' @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.meanByClass.R b/R/ds.meanByClass.R index 8e35db6b..538ef8c8 100644 --- a/R/ds.meanByClass.R +++ b/R/ds.meanByClass.R @@ -24,7 +24,7 @@ #' For more information see \strong{Details}. #' @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.message.R b/R/ds.message.R index 7dd3a922..eb88d8b9 100644 --- a/R/ds.message.R +++ b/R/ds.message.R @@ -21,7 +21,7 @@ #' contains the message. #' @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 0a62b1eb..58f615b1 100644 --- a/R/ds.metadata.R +++ b/R/ds.metadata.R @@ -8,7 +8,7 @@ #' @param x a character string specifying the name of the object. #' @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 d1b0448b..97ebbdfd 100644 --- a/R/ds.names.R +++ b/R/ds.names.R @@ -15,7 +15,7 @@ #' 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 2f25a000..9c961fcf 100644 --- a/R/ds.ns.R +++ b/R/ds.ns.R @@ -24,7 +24,7 @@ #' variable that is stored on the data servers. Default \code{ns.newobj}. #' @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(). diff --git a/R/ds.numNA.R b/R/ds.numNA.R index f109f550..0bd75185 100644 --- a/R/ds.numNA.R +++ b/R/ds.numNA.R @@ -9,7 +9,7 @@ #' @param x a character string specifying the name of the vector. #' @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 5a09bcce..45a3e2d3 100644 --- a/R/ds.qlspline.R +++ b/R/ds.qlspline.R @@ -24,7 +24,7 @@ #' variable that is stored on the data servers. Default \code{qlspline.newobj}. #' @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 diff --git a/R/ds.quantileMean.R b/R/ds.quantileMean.R index 4818a6e0..48aa705b 100644 --- a/R/ds.quantileMean.R +++ b/R/ds.quantileMean.R @@ -17,7 +17,7 @@ #' For more information see \strong{Details}. #' @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 787cf8b2..ab4472fa 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -43,7 +43,7 @@ #' trigger seed value you have provided. Default is FALSE. #' @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. diff --git a/R/ds.rNorm.R b/R/ds.rNorm.R index 0f53ab92..451d4a92 100644 --- a/R/ds.rNorm.R +++ b/R/ds.rNorm.R @@ -54,7 +54,7 @@ #' forces the output random numbers vector to have k decimals. #' @param datasources a list of \code{\link{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 0903ad51..2d2c7f01 100644 --- a/R/ds.rPois.R +++ b/R/ds.rPois.R @@ -40,7 +40,7 @@ #' Default is FALSE. #' @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..132241f2 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -60,7 +60,7 @@ #' #' @param datasources a list of \code{\link{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 diff --git a/R/ds.rbind.R b/R/ds.rbind.R index 873cb4f8..47e9165c 100644 --- a/R/ds.rbind.R +++ b/R/ds.rbind.R @@ -24,7 +24,7 @@ #' that is stored on the data servers. Defaults \code{rbind.newobj}. #' @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 41f73f20..f2214f55 100644 --- a/R/ds.reShape.R +++ b/R/ds.reShape.R @@ -31,7 +31,7 @@ #' Default \code{reshape.newobj}. #' @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 9ba1c38f..a22d25b3 100644 --- a/R/ds.recodeLevels.R +++ b/R/ds.recodeLevels.R @@ -15,7 +15,7 @@ #' that is stored on the data servers. Default \code{recodelevels.newobj}. #' @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 c82f3ca8..d44cc857 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -21,7 +21,7 @@ #' Default \code{recodevalues.newobj}. #' @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 c18b99d2..2d2ce951 100644 --- a/R/ds.rep.R +++ b/R/ds.rep.R @@ -25,7 +25,7 @@ #' that is stored on the data servers. Default \code{seq.vect}. #' @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 c7aff90d..28a51adb 100644 --- a/R/ds.replaceNA.R +++ b/R/ds.replaceNA.R @@ -21,7 +21,7 @@ #' that is stored on the data servers. Default \code{replacena.newobj}. #' @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 449c914d..e977afe5 100644 --- a/R/ds.rm.R +++ b/R/ds.rm.R @@ -16,7 +16,7 @@ #' @param x.names a character string specifying the objects to be deleted. #' @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 diff --git a/R/ds.rowColCalc.R b/R/ds.rowColCalc.R index 1f44d76c..d531cce4 100644 --- a/R/ds.rowColCalc.R +++ b/R/ds.rowColCalc.R @@ -16,7 +16,7 @@ #' that is stored on the data servers. Default \code{rowcolcalc.newobj}. #' @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 3d63f459..0ef8d93d 100644 --- a/R/ds.skewness.R +++ b/R/ds.skewness.R @@ -33,7 +33,7 @@ #' The default value is set to \code{'both'}. #' @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 6ee2de0d..9193dbbc 100644 --- a/R/ds.sqrt.R +++ b/R/ds.sqrt.R @@ -12,7 +12,7 @@ #' that is stored on the data servers. Default name is set to \code{sqrt.newobj}. #' @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 0c0d8e02..40bd6ce0 100644 --- a/R/ds.subset.R +++ b/R/ds.subset.R @@ -20,7 +20,7 @@ #' @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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 a205c083..5c6f92bb 100644 --- a/R/ds.subsetByClass.R +++ b/R/ds.subsetByClass.R @@ -12,7 +12,7 @@ #' @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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 8604b851..2d86287b 100644 --- a/R/ds.summary.R +++ b/R/ds.summary.R @@ -11,7 +11,7 @@ #' @param x a character string specifying the name of a numeric or factor variable. #' @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 c7f7049f..07df60eb 100644 --- a/R/ds.table1D.R +++ b/R/ds.table1D.R @@ -17,7 +17,7 @@ #' 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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 cb64bfd5..301a8993 100644 --- a/R/ds.table2D.R +++ b/R/ds.table2D.R @@ -18,7 +18,7 @@ #' 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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 652c63f9..5b7e946a 100644 --- a/R/ds.testObjExists.R +++ b/R/ds.testObjExists.R @@ -10,7 +10,7 @@ #' @param test.obj.name a character string specifying the name of the object to search. #' @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 29ba9ced..fa14a4f2 100644 --- a/R/ds.unList.R +++ b/R/ds.unList.R @@ -20,7 +20,7 @@ #' that is stored on the data servers. Default \code{unlist.newobj}. #' @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 5457bad1..327585bd 100644 --- a/R/ds.unique.R +++ b/R/ds.unique.R @@ -9,7 +9,7 @@ #' that is stored on the data servers. Default \code{unique.newobj}. #' @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 a31122b5..178dc443 100644 --- a/R/ds.var.R +++ b/R/ds.var.R @@ -25,7 +25,7 @@ #' should only be undertaken once the function call has failed. #' @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 0dc73493..f019c7bc 100644 --- a/R/ds.vectorCalc.R +++ b/R/ds.vectorCalc.R @@ -14,7 +14,7 @@ #' '+' 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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 a398882c..dba45bf3 100644 --- a/R/getPooledMean.R +++ b/R/getPooledMean.R @@ -5,7 +5,7 @@ #' 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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 48426632..0738d4bf 100644 --- a/R/getPooledVar.R +++ b/R/getPooledVar.R @@ -5,7 +5,7 @@ #' 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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 0c223df1..c720fa45 100644 --- a/R/glmChecks.R +++ b/R/glmChecks.R @@ -13,7 +13,7 @@ #' @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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 ac63b7ff..0460cb77 100644 --- a/R/isAssigned.R +++ b/R/isAssigned.R @@ -5,7 +5,7 @@ #' 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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 7dd3282d..621b809a 100644 --- a/R/isDefined.R +++ b/R/isDefined.R @@ -5,7 +5,7 @@ #' in all the studies. If not the process should halt. #' @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 d3f054f5..21c6e90c 100644 --- a/R/meanByClassHelper0a.R +++ b/R/meanByClassHelper0a.R @@ -9,7 +9,7 @@ #' '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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 6922074f..1419d53f 100644 --- a/R/meanByClassHelper0b.R +++ b/R/meanByClassHelper0b.R @@ -10,7 +10,7 @@ #' '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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 ffdf6daa..4b98201e 100644 --- a/R/meanByClassHelper1.R +++ b/R/meanByClassHelper1.R @@ -4,7 +4,7 @@ #' @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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 ef379fad..9fac9125 100644 --- a/R/meanByClassHelper2.R +++ b/R/meanByClassHelper2.R @@ -4,7 +4,7 @@ #' @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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 b0cc67c3..61e61d1f 100644 --- a/R/meanByClassHelper3.R +++ b/R/meanByClassHelper3.R @@ -4,7 +4,7 @@ #' @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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 7cf70c2f..9597a7e8 100644 --- a/R/meanByClassHelper4.R +++ b/R/meanByClassHelper4.R @@ -4,7 +4,7 @@ #' @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[DSI]{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' 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 0246708d..025a0680 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -9,7 +9,7 @@ #' Server function called: \code{dimDS} #' @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/man/checkClass.Rd b/man/checkClass.Rd index 5b516ecb..38dc642c 100644 --- a/man/checkClass.Rd +++ b/man/checkClass.Rd @@ -8,7 +8,7 @@ checkClass(datasources = NULL, obj = NULL) } \arguments{ \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{datashield.connections_default}.} +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 9feb7437..639ebd3e 100644 --- a/man/ds.abs.Rd +++ b/man/ds.abs.Rd @@ -14,7 +14,7 @@ that is stored on the data servers. Default name is set to \code{abs.newobj}.} \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 e238e74c..447d9cf9 100644 --- a/man/ds.asCharacter.Rd +++ b/man/ds.asCharacter.Rd @@ -15,7 +15,7 @@ that is stored on the data servers. Default \code{ascharacter.newobj}.} \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 d48e712c..e6ea9eb9 100644 --- a/man/ds.asDataMatrix.Rd +++ b/man/ds.asDataMatrix.Rd @@ -15,7 +15,7 @@ that is stored on the data servers. Default \code{asdatamatrix.newobj}.} \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 99a0da3f..c412df38 100644 --- a/man/ds.asFactor.Rd +++ b/man/ds.asFactor.Rd @@ -35,7 +35,7 @@ into account.} \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 edca488e..d54776a1 100644 --- a/man/ds.asFactorSimple.Rd +++ b/man/ds.asFactorSimple.Rd @@ -19,7 +19,7 @@ that is stored on the data servers. Default \code{asfactor.newobj}.} \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 3097bfe4..d2f0455b 100644 --- a/man/ds.asInteger.Rd +++ b/man/ds.asInteger.Rd @@ -15,7 +15,7 @@ that is stored on the data servers. Default \code{asinteger.newobj}.} \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 11547364..1e2e3c73 100644 --- a/man/ds.asList.Rd +++ b/man/ds.asList.Rd @@ -15,7 +15,7 @@ that is stored on the data servers. Default \code{aslist.newobj}.} \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 744f3df5..c42d2e6a 100644 --- a/man/ds.asLogical.Rd +++ b/man/ds.asLogical.Rd @@ -15,7 +15,7 @@ that is stored on the data servers. Default \code{aslogical.newobj}.} \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 53729754..70948014 100644 --- a/man/ds.asMatrix.Rd +++ b/man/ds.asMatrix.Rd @@ -15,7 +15,7 @@ that is stored on the data servers. Default \code{asmatrix.newobj}.} \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 a46ed4cb..a07204c1 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -15,7 +15,7 @@ that is stored on the data servers. Default \code{asnumeric.newobj}.} \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 f554f610..e09d426f 100644 --- a/man/ds.assign.Rd +++ b/man/ds.assign.Rd @@ -14,7 +14,7 @@ that is stored on the data servers. Default \code{assign.newobj}.} \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 bcf4c1c3..0ca1a5d3 100644 --- a/man/ds.auc.Rd +++ b/man/ds.auc.Rd @@ -14,7 +14,7 @@ the complete cases that are used in the regression model.} \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.bp_standards.Rd b/man/ds.bp_standards.Rd index e1b784c8..edbdd06d 100644 --- a/man/ds.bp_standards.Rd +++ b/man/ds.bp_standards.Rd @@ -35,7 +35,7 @@ that is stored on the data servers. Default name is set to \code{bp.newobj}.} \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 73627af8..bc899891 100644 --- a/man/ds.c.Rd +++ b/man/ds.c.Rd @@ -14,7 +14,7 @@ that is stored on the data servers. Default \code{c.newobj}.} \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 7af5bc4b..ca20b9e8 100644 --- a/man/ds.cbind.Rd +++ b/man/ds.cbind.Rd @@ -32,7 +32,7 @@ that is stored on the data servers. Defaults \code{cbind.newobj}.} \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 2ecee62f..1730a62f 100644 --- a/man/ds.changeRefGroup.Rd +++ b/man/ds.changeRefGroup.Rd @@ -26,7 +26,7 @@ The default is to not re-order (see the reasons in the details).} \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 fa174617..b2fc0f07 100644 --- a/man/ds.class.Rd +++ b/man/ds.class.Rd @@ -11,7 +11,7 @@ ds.class(x = NULL, datasources = NULL) \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 5aff644a..e7391081 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -11,7 +11,7 @@ ds.colnames(x = NULL, datasources = NULL) \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 e09c0de9..f5df7658 100644 --- a/man/ds.completeCases.Rd +++ b/man/ds.completeCases.Rd @@ -17,7 +17,7 @@ suffix "_complete.cases"} \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.cor.Rd b/man/ds.cor.Rd index 8bbd6792..030defae 100644 --- a/man/ds.cor.Rd +++ b/man/ds.cor.Rd @@ -17,7 +17,7 @@ This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. \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 f5eb9e0a..fac90553 100644 --- a/man/ds.corTest.Rd +++ b/man/ds.corTest.Rd @@ -38,7 +38,7 @@ Fisher's z transformation.} \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 807c5df9..3fe9ec8f 100644 --- a/man/ds.cov.Rd +++ b/man/ds.cov.Rd @@ -27,7 +27,7 @@ This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. \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 686c851b..5c7d82d7 100644 --- a/man/ds.dataFrame.Rd +++ b/man/ds.dataFrame.Rd @@ -50,7 +50,7 @@ that is stored on the data servers. Default \code{dataframe.newobj}.} \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 551a0d2f..44eef9e5 100644 --- a/man/ds.dataFrameFill.Rd +++ b/man/ds.dataFrameFill.Rd @@ -15,7 +15,7 @@ that is stored on the data servers. Default value is "dataframefill.newobj".} \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 70c34d9e..252227e5 100644 --- a/man/ds.dataFrameSort.Rd +++ b/man/ds.dataFrameSort.Rd @@ -32,7 +32,7 @@ where \code{df.name} is the first argument of \code{ds.dataFrameSort()}.} \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 c53a9cfb..58b557fe 100644 --- a/man/ds.dataFrameSubset.Rd +++ b/man/ds.dataFrameSubset.Rd @@ -44,7 +44,7 @@ object that is stored on the data servers. Default \code{dataframesubset.newobj} \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 01558833..89cc4348 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -28,7 +28,7 @@ one grid density matrix is generated. Default \code{'combine'}.} \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 6fd54bec..ea3aaa6d 100644 --- a/man/ds.dim.Rd +++ b/man/ds.dim.Rd @@ -22,7 +22,7 @@ Default FALSE.} \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 1a20e8b8..e6e32197 100644 --- a/man/ds.elspline.Rd +++ b/man/ds.elspline.Rd @@ -28,7 +28,7 @@ variable that is stored on the data servers. Default \code{elspline.newobj}.} \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 dd26658c..2352a294 100644 --- a/man/ds.exists.Rd +++ b/man/ds.exists.Rd @@ -11,7 +11,7 @@ ds.exists(x = NULL, datasources = NULL) \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 d8015ae9..875dbe00 100644 --- a/man/ds.exp.Rd +++ b/man/ds.exp.Rd @@ -14,7 +14,7 @@ that is stored on the data servers. Default \code{exp.newobj}.} \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.list.Rd b/man/ds.list.Rd index 06f71c47..d6ebd00e 100644 --- a/man/ds.list.Rd +++ b/man/ds.list.Rd @@ -14,7 +14,7 @@ that is stored on the data servers. Default \code{list.newobj}.} \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.listServersideFunctions.Rd b/man/ds.listServersideFunctions.Rd index 74bcfda7..c907e78c 100644 --- a/man/ds.listServersideFunctions.Rd +++ b/man/ds.listServersideFunctions.Rd @@ -9,7 +9,7 @@ ds.listServersideFunctions(datasources = NULL) \arguments{ \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 diff --git a/man/ds.log.Rd b/man/ds.log.Rd index 3de9e2f0..6ab8fee7 100644 --- a/man/ds.log.Rd +++ b/man/ds.log.Rd @@ -17,7 +17,7 @@ that is stored on the server-side. Default \code{log.newobj}.} \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 c2fa4cae..3cecb462 100644 --- a/man/ds.look.Rd +++ b/man/ds.look.Rd @@ -15,7 +15,7 @@ Default FALSE to save time.} \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.lspline.Rd b/man/ds.lspline.Rd index 867625aa..0cf8e5aa 100644 --- a/man/ds.lspline.Rd +++ b/man/ds.lspline.Rd @@ -27,7 +27,7 @@ variable that is stored on the data servers. Default \code{lspline.newobj}.} \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.matrixDet.Rd b/man/ds.matrixDet.Rd index 6ac9841a..e827e815 100644 --- a/man/ds.matrixDet.Rd +++ b/man/ds.matrixDet.Rd @@ -17,7 +17,7 @@ is calculated. Default FALSE.} \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 f60c127d..0a5c021d 100644 --- a/man/ds.matrixDet.report.Rd +++ b/man/ds.matrixDet.report.Rd @@ -14,7 +14,7 @@ is calculated. Default FALSE.} \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.matrixDimnames.Rd b/man/ds.matrixDimnames.Rd index 635cf281..af56f76a 100644 --- a/man/ds.matrixDimnames.Rd +++ b/man/ds.matrixDimnames.Rd @@ -24,7 +24,7 @@ variable that is stored on the data servers. Default \code{matrixdimnames.newobj \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 ffca8cda..842baee4 100644 --- a/man/ds.matrixInvert.Rd +++ b/man/ds.matrixInvert.Rd @@ -15,7 +15,7 @@ Default \code{matrixinvert.newobj}.} \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 1d0a2021..136db26d 100644 --- a/man/ds.matrixMult.Rd +++ b/man/ds.matrixMult.Rd @@ -16,7 +16,7 @@ variable that is stored on the data servers. Default \code{matrixmult.newobj}.} \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 841fd19b..67e06867 100644 --- a/man/ds.matrixTranspose.Rd +++ b/man/ds.matrixTranspose.Rd @@ -15,7 +15,7 @@ Default \code{matrixtranspose.newobj}.} \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.meanByClass.Rd b/man/ds.meanByClass.Rd index ab2a299e..f60ba7a4 100644 --- a/man/ds.meanByClass.Rd +++ b/man/ds.meanByClass.Rd @@ -26,7 +26,7 @@ For more information see \strong{Details}.} \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.message.Rd b/man/ds.message.Rd index ead3313b..ab1dff8d 100644 --- a/man/ds.message.Rd +++ b/man/ds.message.Rd @@ -12,7 +12,7 @@ contains the message.} \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 6f711e47..128ca9ec 100644 --- a/man/ds.metadata.Rd +++ b/man/ds.metadata.Rd @@ -11,7 +11,7 @@ ds.metadata(x = NULL, datasources = NULL) \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 178ad99d..199b20d9 100644 --- a/man/ds.names.Rd +++ b/man/ds.names.Rd @@ -13,7 +13,7 @@ ds.names(xname = NULL, datasources = NULL) 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 28e36290..91051172 100644 --- a/man/ds.ns.Rd +++ b/man/ds.ns.Rd @@ -36,7 +36,7 @@ variable that is stored on the data servers. Default \code{ns.newobj}.} \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 e9990d95..896c76ee 100644 --- a/man/ds.numNA.Rd +++ b/man/ds.numNA.Rd @@ -11,7 +11,7 @@ ds.numNA(x = NULL, datasources = NULL) \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 5fcca7af..93460e65 100644 --- a/man/ds.qlspline.Rd +++ b/man/ds.qlspline.Rd @@ -32,7 +32,7 @@ variable that is stored on the data servers. Default \code{qlspline.newobj}.} \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 652ca9f1..03b469a1 100644 --- a/man/ds.quantileMean.Rd +++ b/man/ds.quantileMean.Rd @@ -15,7 +15,7 @@ For more information see \strong{Details}.} \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 0306b0ac..993083e1 100644 --- a/man/ds.rBinom.Rd +++ b/man/ds.rBinom.Rd @@ -35,7 +35,7 @@ trigger seed value you have provided. Default is FALSE.} \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..a8b80e75 100644 --- a/man/ds.rNorm.Rd +++ b/man/ds.rNorm.Rd @@ -39,7 +39,7 @@ forces the output random numbers vector to have k decimals.} \item{datasources}{a list of \code{\link{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 8fe1072d..7ce19a47 100644 --- a/man/ds.rPois.Rd +++ b/man/ds.rPois.Rd @@ -32,7 +32,7 @@ Default is FALSE.} \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..0d7a24eb 100644 --- a/man/ds.rUnif.Rd +++ b/man/ds.rUnif.Rd @@ -41,7 +41,7 @@ numbers vector to have k decimals.} \item{datasources}{a list of \code{\link{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 969a6a18..75c2a03f 100644 --- a/man/ds.rbind.Rd +++ b/man/ds.rbind.Rd @@ -27,7 +27,7 @@ that is stored on the data servers. Defaults \code{rbind.newobj}.} \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 c29ce5cf..8acdd161 100644 --- a/man/ds.reShape.Rd +++ b/man/ds.reShape.Rd @@ -51,7 +51,7 @@ Default \code{reshape.newobj}.} \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 c74c1c48..14450927 100644 --- a/man/ds.recodeLevels.Rd +++ b/man/ds.recodeLevels.Rd @@ -22,7 +22,7 @@ that is stored on the data servers. Default \code{recodelevels.newobj}.} \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 c8cad12f..5ebe1f67 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -33,7 +33,7 @@ Default \code{recodevalues.newobj}.} \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 9c3a0388..b552ff43 100644 --- a/man/ds.rep.Rd +++ b/man/ds.rep.Rd @@ -46,7 +46,7 @@ that is stored on the data servers. Default \code{seq.vect}.} \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 3fa586a3..3b8a4ec0 100644 --- a/man/ds.replaceNA.Rd +++ b/man/ds.replaceNA.Rd @@ -17,7 +17,7 @@ that is stored on the data servers. Default \code{replacena.newobj}.} \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 92721ee9..a6378621 100644 --- a/man/ds.rm.Rd +++ b/man/ds.rm.Rd @@ -11,7 +11,7 @@ ds.rm(x.names = NULL, datasources = NULL) \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 9f30b728..dc4cfbd9 100644 --- a/man/ds.rowColCalc.Rd +++ b/man/ds.rowColCalc.Rd @@ -17,7 +17,7 @@ that is stored on the data servers. Default \code{rowcolcalc.newobj}.} \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 e5afdb73..7c3bda04 100644 --- a/man/ds.skewness.Rd +++ b/man/ds.skewness.Rd @@ -19,7 +19,7 @@ The default value is set to \code{'both'}.} \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 1552aa72..b42ecaed 100644 --- a/man/ds.sqrt.Rd +++ b/man/ds.sqrt.Rd @@ -14,7 +14,7 @@ that is stored on the data servers. Default name is set to \code{sqrt.newobj}.} \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 e26bb213..3db5e3b3 100644 --- a/man/ds.subset.Rd +++ b/man/ds.subset.Rd @@ -34,7 +34,7 @@ operator. This parameter is ignored if the input data is not a vector.} if the input data is not a vector.} \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{datashield.connections_default}.} +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 78c53f65..fe372adb 100644 --- a/man/ds.subsetByClass.Rd +++ b/man/ds.subsetByClass.Rd @@ -20,7 +20,7 @@ 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[DSI]{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +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 a5a4fd74..2f52cff7 100644 --- a/man/ds.summary.Rd +++ b/man/ds.summary.Rd @@ -11,7 +11,7 @@ ds.summary(x = NULL, datasources = NULL) \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 f98d97c3..d480b3bb 100644 --- a/man/ds.table1D.Rd +++ b/man/ds.table1D.Rd @@ -23,7 +23,7 @@ messages are suppressed if this parameter is set to FALSE. However the analyst c which are stored in the output object 'validity' - see the list of output objects.} \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{datashield.connections_default}.} +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 2eb0a390..aec01d73 100644 --- a/man/ds.table2D.Rd +++ b/man/ds.table2D.Rd @@ -27,7 +27,7 @@ messages are suppressed if this parameter is set to FALSE. However the analyst c which are stored in the output object 'validity' - see the list of output objects.} \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{datashield.connections_default}.} +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 702605f8..ae0fb40d 100644 --- a/man/ds.testObjExists.Rd +++ b/man/ds.testObjExists.Rd @@ -11,7 +11,7 @@ ds.testObjExists(test.obj.name = NULL, datasources = NULL) \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 fc86570b..cb8ef0a1 100644 --- a/man/ds.unList.Rd +++ b/man/ds.unList.Rd @@ -14,7 +14,7 @@ that is stored on the data servers. Default \code{unlist.newobj}.} \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 f8fb9cb9..072510a4 100644 --- a/man/ds.unique.Rd +++ b/man/ds.unique.Rd @@ -14,7 +14,7 @@ that is stored on the data servers. Default \code{unique.newobj}.} \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 7e00fce8..5398c6e1 100644 --- a/man/ds.var.Rd +++ b/man/ds.var.Rd @@ -22,7 +22,7 @@ should only be undertaken once the function call has failed.} \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 929404b9..6c97d344 100644 --- a/man/ds.vectorCalc.Rd +++ b/man/ds.vectorCalc.Rd @@ -15,7 +15,7 @@ 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[DSI]{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +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 6bb4e12a..e28cb3b1 100644 --- a/man/getPooledMean.Rd +++ b/man/getPooledMean.Rd @@ -8,7 +8,7 @@ getPooledMean(dtsources, x) } \arguments{ \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{datashield.connections_default}.} +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 4ab46179..a89c0544 100644 --- a/man/getPooledVar.Rd +++ b/man/getPooledVar.Rd @@ -8,7 +8,7 @@ getPooledVar(dtsources, x) } \arguments{ \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{datashield.connections_default}.} +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 24c4391d..af57ca54 100644 --- a/man/glmChecks.Rd +++ b/man/glmChecks.Rd @@ -19,7 +19,7 @@ included in the linear predictor during fitting.} process. Should be NULL or a numeric vector.} \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{datashield.connections_default}.} +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 c332fe97..d46bed49 100644 --- a/man/isAssigned.Rd +++ b/man/isAssigned.Rd @@ -8,7 +8,7 @@ isAssigned(datasources = NULL, newobj = NULL) } \arguments{ \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{datashield.connections_default}.} +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 fb7d8412..6b2d0f7e 100644 --- a/man/isDefined.Rd +++ b/man/isDefined.Rd @@ -9,7 +9,7 @@ isDefined(datasources = NULL, obj = NULL, error.message = TRUE) \arguments{ \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 43bd1797..3880fa39 100644 --- a/man/meanByClassHelper0a.Rd +++ b/man/meanByClassHelper0a.Rd @@ -16,7 +16,7 @@ meanByClassHelper0a(a, b, type, datasources) is genrated for each study.} \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{datashield.connections_default}.} +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 7e67b58b..fbaa90ae 100644 --- a/man/meanByClassHelper0b.Rd +++ b/man/meanByClassHelper0b.Rd @@ -18,7 +18,7 @@ meanByClassHelper0b(x, outvar, covar, type, datasources) is genrated for each study.} \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{datashield.connections_default}.} +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 942900c8..648eb577 100644 --- a/man/meanByClassHelper1.Rd +++ b/man/meanByClassHelper1.Rd @@ -8,7 +8,7 @@ meanByClassHelper1(dtsource, tables, variable, categories) } \arguments{ \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{datashield.connections_default}.} +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 fd385808..38c98a93 100644 --- a/man/meanByClassHelper2.Rd +++ b/man/meanByClassHelper2.Rd @@ -8,7 +8,7 @@ meanByClassHelper2(dtsources, tablenames, variables, invalidrecorder) } \arguments{ \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{datashield.connections_default}.} +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 f8a03ded..e4fffdca 100644 --- a/man/meanByClassHelper3.Rd +++ b/man/meanByClassHelper3.Rd @@ -8,7 +8,7 @@ meanByClassHelper3(dtsources, tablenames, variables, invalidrecorder) } \arguments{ \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{datashield.connections_default}.} +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 07f8e2b1..cbf0b67c 100644 --- a/man/meanByClassHelper4.Rd +++ b/man/meanByClassHelper4.Rd @@ -14,7 +14,7 @@ meanByClassHelper4( } \arguments{ \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{datashield.connections_default}.} +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 31e41a0f..6922ec94 100644 --- a/man/subsetHelper.Rd +++ b/man/subsetHelper.Rd @@ -9,7 +9,7 @@ subsetHelper(dts, data, rs = NULL, cs = NULL) \arguments{ \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.} From f1d0686976b6f2757b48e3e9448699110e142c01 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 10 Jun 2025 14:07:10 +0100 Subject: [PATCH 4/5] Link issues --- R/ds.contourPlot.R | 4 +-- R/ds.gamlss.R | 4 +-- R/ds.getWGSR.R | 4 +-- R/ds.glm.R | 4 +-- R/ds.glmSLMA.R | 4 +-- R/ds.glmerSLMA.R | 4 +-- R/ds.heatmapPlot.R | 4 +-- R/ds.hetcor.R | 2 +- R/ds.hetcor.R.save | 60 +++++++++++++++++++++++++++++++ R/ds.histogram.R | 4 +-- R/ds.igb_standards.R | 2 +- R/ds.isNA.R | 2 +- R/ds.isValid.R | 2 +- R/ds.kurtosis.R | 2 +- R/ds.length.R | 2 +- R/ds.levels.R | 2 +- R/ds.lexis.R | 4 +-- R/ds.listDisclosureSettings.R | 4 +-- R/ds.listServersideFunctions.R | 2 +- R/ds.lmerSLMA.R | 4 +-- R/ds.ls.R | 2 +- R/ds.make.R | 4 +-- R/ds.matrix.R | 4 +-- R/ds.matrixDiag.R | 4 +-- R/ds.mean.R | 2 +- R/ds.meanSdGp.R | 4 +-- R/ds.merge.R | 4 +-- R/ds.rNorm.R | 2 +- R/ds.rUnif.R | 2 +- man/ds.contourPlot.Rd | 4 +-- man/ds.gamlss.Rd | 4 +-- man/ds.getWGSR.Rd | 4 +-- man/ds.glm.Rd | 4 +-- man/ds.glmSLMA.Rd | 4 +-- man/ds.glmerSLMA.Rd | 4 +-- man/ds.heatmapPlot.Rd | 4 +-- man/ds.hetcor.Rd | 2 +- man/ds.histogram.Rd | 4 +-- man/ds.igb_standards.Rd | 2 +- man/ds.isNA.Rd | 2 +- man/ds.isValid.Rd | 2 +- man/ds.kurtosis.Rd | 2 +- man/ds.length.Rd | 2 +- man/ds.levels.Rd | 2 +- man/ds.lexis.Rd | 4 +-- man/ds.listDisclosureSettings.Rd | 4 +-- man/ds.listServersideFunctions.Rd | 2 +- man/ds.lmerSLMA.Rd | 4 +-- man/ds.ls.Rd | 2 +- man/ds.make.Rd | 4 +-- man/ds.matrix.Rd | 4 +-- man/ds.matrixDiag.Rd | 4 +-- man/ds.mean.Rd | 2 +- man/ds.meanSdGp.Rd | 4 +-- man/ds.merge.Rd | 4 +-- man/ds.rNorm.Rd | 2 +- man/ds.rUnif.Rd | 2 +- 57 files changed, 148 insertions(+), 88 deletions(-) create mode 100644 R/ds.hetcor.R.save 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.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..eb5286e9 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -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..bbf8b174 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -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..49d6e282 100644 --- a/R/ds.glmerSLMA.R +++ b/R/ds.glmerSLMA.R @@ -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 71a98363..2b29be24 100644 --- a/R/ds.hetcor.R +++ b/R/ds.hetcor.R @@ -19,7 +19,7 @@ #' compute each correlation using all observations with valid data for that pair of variables. #' @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 diff --git a/R/ds.hetcor.R.save b/R/ds.hetcor.R.save new file mode 100644 index 00000000..611335a9 --- /dev/null +++ b/R/ds.hetcor.R.save @@ -0,0 +1,60 @@ + +c + + +#' +#' @title Heterogeneous Correlation Matrix +#' @description This function is based on the hetcor function from the R package \code{polycor}. +#' @details Computes a heterogenous correlation matrix, consisting of Pearson product-moment +#' correlations between numeric variables, polyserial correlations between numeric and ordinal +#' variables, and polychoric correlations between ordinal variables. +#' @param data the name of a data frame consisting of factors, ordered factors, logical variables, +#' character variables, and/or numeric variables, or the first of several variables. +#' @param ML if TRUE, compute maximum-likelihood estimates; if FALSE (default), compute quick +#' two-step estimates. +#' @param std.err if TRUE (default), compute standard errors. +#' @param bins number of bins to use for continuous variables in testing bivariate normality; +#' the default is 4. +#' @param pd if TRUE (default) and if the correlation matrix is not positive-definite, an attempt +#' will be made to adjust it to a positive-definite matrix, using the nearPD function in the Matrix +#' package. Note that default arguments to nearPD are used (except corr=TRUE); for more control call +#' nearPD directly. +#' @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[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[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 +#' the correlations are based; p-values for tests of bivariate normality for each pair of variables; +#' the method by which any missing data were handled: "complete.obs" or "pairwise.complete.obs"; TRUE +#' for ML estimates, FALSE for two-step estimates. +#' @author Demetris Avraam for DataSHIELD Development Team +#' @export +#' +ds.hetcor <- function(data=NULL, ML=TRUE, std.err=TRUE, bins=4, pd=TRUE, use="complete.obs", datasources=NULL){ + + # look for DS connections + if(is.null(datasources)){ + datasources <- datashield.connections_find() + } + + # ensure datasources is a list of DSConnection-class + if(!(is.list(datasources) && all(unlist(lapply(datasources, function(d) {methods::is(d,"DSConnection")}))))){ + stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE) + } + + if(is.null(data)){ + stop("Please provide the name of the input object!", call.=FALSE) + } + + # check if the input object is defined in all the studies + defined <- isDefined(datasources, data) + + calltext <- call('hetcorDS', data, ML, std.err, bins, pd, use) + output <- DSI::datashield.aggregate(datasources, calltext) + + return(output) + +} 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 a46f267d..fb7953f1 100644 --- a/R/ds.igb_standards.R +++ b/R/ds.igb_standards.R @@ -17,7 +17,7 @@ #' that is stored on the data servers. Default name is set to \code{igb.newobj}. #' @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 diff --git a/R/ds.isNA.R b/R/ds.isNA.R index d34ad054..1d84577f 100644 --- a/R/ds.isNA.R +++ b/R/ds.isNA.R @@ -10,7 +10,7 @@ #' @param x a character string specifying the name of the vector to check. #' @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 5d0424ba..e43b61b1 100644 --- a/R/ds.isValid.R +++ b/R/ds.isValid.R @@ -12,7 +12,7 @@ #' @param x a character string specifying the name of a vector, dataframe or matrix. #' @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 bb8cf299..974682bb 100644 --- a/R/ds.kurtosis.R +++ b/R/ds.kurtosis.R @@ -19,7 +19,7 @@ #' The default value is set to 'both'. #' @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 d5064795..83cb5cae 100644 --- a/R/ds.length.R +++ b/R/ds.length.R @@ -19,7 +19,7 @@ #' should only be undertaken once the function call has failed. #' @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 4755522a..b32a5d1c 100644 --- a/R/ds.levels.R +++ b/R/ds.levels.R @@ -8,7 +8,7 @@ #' @param x a character string specifying the name of a factor variable. #' @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.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 c81d203c..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 diff --git a/R/ds.lmerSLMA.R b/R/ds.lmerSLMA.R index 5619d55b..f964ceb9 100644 --- a/R/ds.lmerSLMA.R +++ b/R/ds.lmerSLMA.R @@ -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.ls.R b/R/ds.ls.R index fbc3d914..415c93f4 100644 --- a/R/ds.ls.R +++ b/R/ds.ls.R @@ -53,7 +53,7 @@ #' For more information see \strong{Details}. #' @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.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.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.mean.R b/R/ds.mean.R index d52fe4c2..f23356d5 100644 --- a/R/ds.mean.R +++ b/R/ds.mean.R @@ -40,7 +40,7 @@ #' For more information see \strong{Details}. #' @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.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.rNorm.R b/R/ds.rNorm.R index 451d4a92..6100c850 100644 --- a/R/ds.rNorm.R +++ b/R/ds.rNorm.R @@ -52,7 +52,7 @@ #' 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[DSI]{datashield.connections_default}}. #' @return \code{ds.rNorm} returns random number vectors with a normal distribution for each diff --git a/R/ds.rUnif.R b/R/ds.rUnif.R index 132241f2..936a8070 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -58,7 +58,7 @@ #' 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[DSI]{datashield.connections_default}}. #' @return \code{ds.Unif} returns random number vectors with a uniform distribution for each study, 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.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..4746ce2c 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 diff --git a/man/ds.glmSLMA.Rd b/man/ds.glmSLMA.Rd index f64e6a5c..f2e7fdef 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 diff --git a/man/ds.glmerSLMA.Rd b/man/ds.glmerSLMA.Rd index 8ee7cdfd..19d5a55a 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. 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 0d075897..e236a0e9 100644 --- a/man/ds.hetcor.Rd +++ b/man/ds.hetcor.Rd @@ -36,7 +36,7 @@ compute each correlation using all observations with valid data for that pair of \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 c081a7b1..499220a2 100644 --- a/man/ds.igb_standards.Rd +++ b/man/ds.igb_standards.Rd @@ -41,7 +41,7 @@ that is stored on the data servers. Default name is set to \code{igb.newobj}.} \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 afbb1d92..ec6b2f6f 100644 --- a/man/ds.isNA.Rd +++ b/man/ds.isNA.Rd @@ -11,7 +11,7 @@ ds.isNA(x = NULL, datasources = NULL) \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 790b89e9..2f927ae2 100644 --- a/man/ds.isValid.Rd +++ b/man/ds.isValid.Rd @@ -11,7 +11,7 @@ ds.isValid(x = NULL, datasources = NULL) \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 658bef10..4b698adf 100644 --- a/man/ds.kurtosis.Rd +++ b/man/ds.kurtosis.Rd @@ -20,7 +20,7 @@ The default value is set to 'both'.} \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 60b95325..27e105bc 100644 --- a/man/ds.length.Rd +++ b/man/ds.length.Rd @@ -24,7 +24,7 @@ should only be undertaken once the function call has failed.} \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 1f1ad038..fbdab0c4 100644 --- a/man/ds.levels.Rd +++ b/man/ds.levels.Rd @@ -11,7 +11,7 @@ ds.levels(x = NULL, datasources = NULL) \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.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 c907e78c..70d9ba5d 100644 --- a/man/ds.listServersideFunctions.Rd +++ b/man/ds.listServersideFunctions.Rd @@ -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..3ea75c10 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. diff --git a/man/ds.ls.Rd b/man/ds.ls.Rd index 3f3a05ce..e1b5d324 100644 --- a/man/ds.ls.Rd +++ b/man/ds.ls.Rd @@ -28,7 +28,7 @@ For more information see \strong{Details}.} \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.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.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.mean.Rd b/man/ds.mean.Rd index 9c5ccdcd..d662a389 100644 --- a/man/ds.mean.Rd +++ b/man/ds.mean.Rd @@ -33,7 +33,7 @@ For more information see \strong{Details}.} \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.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.rNorm.Rd b/man/ds.rNorm.Rd index a8b80e75..f60071fb 100644 --- a/man/ds.rNorm.Rd +++ b/man/ds.rNorm.Rd @@ -37,7 +37,7 @@ 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[DSI]{datashield.connections_default}}.} } diff --git a/man/ds.rUnif.Rd b/man/ds.rUnif.Rd index 0d7a24eb..0ffd62aa 100644 --- a/man/ds.rUnif.Rd +++ b/man/ds.rUnif.Rd @@ -39,7 +39,7 @@ 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[DSI]{datashield.connections_default}}.} } From 6d66ea58145210de7384ef3aecbc41dfa3b85f11 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 10 Jun 2025 14:22:12 +0100 Subject: [PATCH 5/5] Remove 'save' file --- R/ds.hetcor.R.save | 60 ---------------------------------------------- 1 file changed, 60 deletions(-) delete mode 100644 R/ds.hetcor.R.save diff --git a/R/ds.hetcor.R.save b/R/ds.hetcor.R.save deleted file mode 100644 index 611335a9..00000000 --- a/R/ds.hetcor.R.save +++ /dev/null @@ -1,60 +0,0 @@ - -c - - -#' -#' @title Heterogeneous Correlation Matrix -#' @description This function is based on the hetcor function from the R package \code{polycor}. -#' @details Computes a heterogenous correlation matrix, consisting of Pearson product-moment -#' correlations between numeric variables, polyserial correlations between numeric and ordinal -#' variables, and polychoric correlations between ordinal variables. -#' @param data the name of a data frame consisting of factors, ordered factors, logical variables, -#' character variables, and/or numeric variables, or the first of several variables. -#' @param ML if TRUE, compute maximum-likelihood estimates; if FALSE (default), compute quick -#' two-step estimates. -#' @param std.err if TRUE (default), compute standard errors. -#' @param bins number of bins to use for continuous variables in testing bivariate normality; -#' the default is 4. -#' @param pd if TRUE (default) and if the correlation matrix is not positive-definite, an attempt -#' will be made to adjust it to a positive-definite matrix, using the nearPD function in the Matrix -#' package. Note that default arguments to nearPD are used (except corr=TRUE); for more control call -#' nearPD directly. -#' @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[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[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 -#' the correlations are based; p-values for tests of bivariate normality for each pair of variables; -#' the method by which any missing data were handled: "complete.obs" or "pairwise.complete.obs"; TRUE -#' for ML estimates, FALSE for two-step estimates. -#' @author Demetris Avraam for DataSHIELD Development Team -#' @export -#' -ds.hetcor <- function(data=NULL, ML=TRUE, std.err=TRUE, bins=4, pd=TRUE, use="complete.obs", datasources=NULL){ - - # look for DS connections - if(is.null(datasources)){ - datasources <- datashield.connections_find() - } - - # ensure datasources is a list of DSConnection-class - if(!(is.list(datasources) && all(unlist(lapply(datasources, function(d) {methods::is(d,"DSConnection")}))))){ - stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE) - } - - if(is.null(data)){ - stop("Please provide the name of the input object!", call.=FALSE) - } - - # check if the input object is defined in all the studies - defined <- isDefined(datasources, data) - - calltext <- call('hetcorDS', data, ML, std.err, bins, pd, use) - output <- DSI::datashield.aggregate(datasources, calltext) - - return(output) - -}