Merge pull request #30 from datashield/v6.4.0-dev

V6.4.0 dev

Author: davraam

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsBaseClient
 Title: DataSHIELD Client Functions
-Version: 6.3.1
+Version: 6.4.0.9000
 Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
 Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
 Description: DataSHIELD client functions for the client side.

NAMESPACE

@@ -56,7 +56,6 @@ export(ds.lexis)
 export(ds.list)
 export(ds.listClientsideFunctions)
 export(ds.listDisclosureSettings)
-export(ds.listOpals)
 export(ds.listServersideFunctions)
 export(ds.lmerSLMA)
 export(ds.log)
@@ -100,11 +99,9 @@ export(ds.rowColCalc)
 export(ds.sample)
 export(ds.scatterPlot)
 export(ds.seq)
-export(ds.setDefaultOpals)
 export(ds.setSeed)
 export(ds.skewness)
 export(ds.sqrt)
-export(ds.subset)
 export(ds.subsetByClass)
 export(ds.summary)
 export(ds.table)

R/.Rapp.history

@@ -31,7 +31,6 @@
 #' @export
 #' @author DataSHIELD Development Team
 #' @seealso \code{\link{ds.subsetByClass}} to subset by the classes of factor vector(s).
-#' @seealso \code{\link{ds.subset}} to subset by complete cases (i.e. removing missing values), threshold, columns and rows.
 #' @examples
 #' \dontrun{
 #'

R/ds.listOpals.R

@@ -68,9 +68,6 @@
 #' across studies and/or separately for each study, depending on the argument \code{type}. 
 #' 
 #' @author DataSHIELD Development Team
-#' @seealso \code{\link{ds.subsetByClass}} to subset by the classes of factor vector(s).
-#' @seealso \code{\link{ds.subset}} to subset by complete cases (i.e. removing missing values), threshold,
-#' columns and rows.
 #' @export
 #' @examples
 #' \dontrun{

R/ds.meanByClass.R

@@ -110,15 +110,9 @@
 #' For further details see help for \code{sample} in native R.
 #' @param newobj This a character string providing a name for the output
 #' data.frame which defaults to 'newobj.sample' if no name is specified.
-#' @param datasources specifies the particular opal object(s) to use. If the <datasources>
-#' argument is not specified the default set of opals will be used. The default opals
-#' are called default.opals and the default can be set using the function
-#' \code{ds.setDefaultOpals}. If the <datasources> is to be specified, it should be set without
-#' inverted commas: e.g. datasources=opals.em or datasources=default.opals. If you wish to
-#' apply the function solely to e.g. the second opal server in a set of three,
-#' the argument can be specified as: e.g. datasources=opals.em[2].
-#' If you wish to specify the first and third opal servers in a set you specify:
-#' e.g. datasources=opals.em[c(1,3)]
+#' @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}}.
 #' @param notify.of.progress specifies if console output should be produce to indicate
 #' progress. The default value for notify.of.progress is FALSE.
 #' @return the object specified by the <newobj> argument (or default name

R/ds.meanSdGp.R

@@ -16,7 +16,6 @@
 #' @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.
-#' @seealso \link{ds.subset} to subset by complete cases (i.e. removing missing values), threshold, columns and rows.
 #' @export
 #' @examples
 #' \dontrun{