Merge branch 'datashield:refactor/perf-batch-2' into refactor/perf-batch-2

Author: StuartWheater

.Rbuildignore

@@ -23,3 +23,4 @@
 ^\.circleci$
 ^\.circleci/config\.yml$
 ^\.github$
+^man-roxygen$

DESCRIPTION

@@ -56,7 +56,12 @@ Authors@R: c(person(given = "Paul",
                     family = "Wheater",
                     role = c("aut", "cre"),
                     email = "stuart.wheater@arjuna.com",
-                    comment = c(ORCID = "0009-0003-2419-1964")))
+                    comment = c(ORCID = "0009-0003-2419-1964")),
+             person(given = "Tim",
+                    family = "Cadman",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0002-7682-5645",
+                                affiliation = "Genomics Coordination Centre, UMCG, Netherlands")))
 License: GPL-3
 Depends:
     R (>= 4.0.0),
@@ -70,8 +75,7 @@ Imports:
     gridExtra,
     data.table,
     methods,
-    dplyr, 
-    cli
+    dplyr
 Suggests:
     lme4,
     httr,

R/ds.dataFrameFill.R

@@ -21,7 +21,8 @@
 #' client-side indicating the name of the \code{newobj} that has been created in each data source
 #' and if it is in a valid form.
 #' @author Demetris Avraam for DataSHIELD Development Team
-#' 
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
+#'
 #' @examples 
 #' \dontrun{
 #' 

R/ds.numNA.R

@@ -6,7 +6,8 @@
 #' @details The number of missing entries are counted and the total for each study is returned.
 #' 
 #' Server function called: \code{numNaDS}
-#' @param x a character string specifying the name of the vector. 
+#' @param x a character string specifying the name of the vector.
+#' @template classConsistencyCheck
 #' @param datasources a list of \code{\link[DSI]{DSConnection-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}}.

R/ds.quantileMean.R

@@ -21,6 +21,7 @@
 #' @return \code{ds.quantileMean} returns to the client-side the quantiles and statistical mean
 #' of a server-side numeric vector. 
 #' @author DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @seealso \code{\link{ds.mean}} to compute the statistical mean.
 #' @seealso \code{\link{ds.summary}} to generate the summary of a variable.
 #' @export

R/ds.recodeLevels.R

@@ -19,6 +19,7 @@
 #' @return \code{ds.recodeLevels} returns to the server-side a variable of type factor
 #' with the replaces levels. 
 #' @author DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' @examples
 #' \dontrun{

R/ds.replaceNA.R

@@ -26,6 +26,7 @@
 #' with the missing values replaced by the specified values.
 #'  The class of the vector is the same as the initial vector. 
 #' @author DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' @examples
 #' \dontrun{

R/ds.rowColCalc.R

@@ -19,6 +19,7 @@
 #' 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
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @examples
 #' \dontrun{
 #' 

R/ds.subsetByClass.R

@@ -15,6 +15,7 @@
 #' 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.
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @seealso \link{ds.meanByClass} to compute mean and standard deviation across categories of a factor vectors.
 #' @seealso \link{ds.subset} to subset by complete cases (i.e. removing missing values), threshold, columns and rows.
 #' @export

R/ds.summary.R

@@ -19,6 +19,7 @@
 #' such as the minimum and maximum values of numeric vectors are not returned. 
 #' The summary is given for each study separately.
 #' @author DataSHIELD Development Team
+#' @author Tim Cadman, Genomics Coordination Centre, UMCG, Netherlands
 #' @export
 #' @examples
 #' \dontrun{