Merge pull request datashield#629 from datashield/v6.3.5-dev

Current v6.3.5 dev integrated with v7.0-dev

Author: StuartWheater

.Rbuildignore

@@ -17,8 +17,8 @@
 ^R/secure.global.ranking.md$
 ^_pkgdown\.yml$
 ^docs$
-^dsBase_6.3.4.tar.gz$
-^dsBase_6.3.4-permissive.tar.gz$
+^dsBase_6.3.5.tar.gz$
+^dsBase_6.3.5-permissive.tar.gz$
 ^dsDanger_6.3.4.tar.gz$
 ^\.circleci$
 ^\.circleci/config\.yml$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsBaseClient
 Title: 'DataSHIELD' Client Side Base Functions
-Version: 6.3.4
+Version: 6.3.5-9000
 Description: Base 'DataSHIELD' functions for the client side. 'DataSHIELD' is a software package which allows
     you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
     been designed to only share non disclosive summary statistics, with built in automated output
@@ -36,10 +36,6 @@ Authors@R: c(person(given = "Paul",
                     family = "Avraam",
                     role = c("aut"),
                     comment = c(ORCID = "0000-0001-8908-2441")),
-             person(given = "Demetris",
-                    family = "Avraam",
-                    role = c("aut"),
-                    comment = c(ORCID = "0000-0001-8908-2441")),
              person(given = "Yannick",
                     family = "Marcon",
                     role = c("aut"),

NAMESPACE

@@ -73,6 +73,7 @@ export(ds.matrixDimnames)
 export(ds.matrixInvert)
 export(ds.matrixMult)
 export(ds.matrixTranspose)
+export(ds.mdPattern)
 export(ds.mean)
 export(ds.meanByClass)
 export(ds.meanSdGp)

R/ds.asFactor.R

@@ -48,7 +48,7 @@
 #' \code{baseline.level = 1} and \code{forced.factor.levels = c(1,2,3,4,5)}. 
 #' The input vector is converted to the following matrix of dummy variables: 
 #'
-#' \tabular{rrrrr}{
+#' \tabular{rrrr}{
 #'   \strong{DV2} \tab \strong{DV3} \tab \strong{DV4} \tab \strong{DV5} \cr
 #'     0   \tab  0  \tab  0  \tab  0\cr
 #'     1   \tab  0  \tab  0  \tab  0\cr

R/ds.colnames.R

@@ -1,51 +1,51 @@
 #'
 #' @title Produces column names of the R object in the server-side
-#' @description Retrieves column names of an R object on the server-side.  
+#' @description Retrieves column names of an R object on the server-side.
 #' This function is similar to R function \code{colnames}.
-#' @details The input is restricted to the object of type \code{data.frame} or \code{matrix}. 
-#' 
+#' @details The input is restricted to the object of type \code{data.frame} or \code{matrix}.
+#'
 #' 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[DSI]{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.colnames} returns the column names of 
-#' the specified server-side data frame or matrix. 
+#' @return \code{ds.colnames} returns the column names of
+#' the specified server-side data frame or matrix.
 #' @author DataSHIELD Development Team
 #' @seealso \code{\link{ds.dim}} to obtain the dimensions of a matrix or a data frame.
-#' @examples 
+#' @examples
 #' \dontrun{
-#' 
+#'
 #'   ## Version 6, for version 5 see the Wiki
 #'   # Connecting to the Opal servers
-#' 
+#'
 #'   require('DSI')
 #'   require('DSOpal')
 #'   require('dsBaseClient')
-#' 
+#'
 #'   builder <- DSI::newDSLoginBuilder()
-#'   builder$append(server = "study1", 
-#'                  url = "http://192.168.56.100:8080/", 
-#'                  user = "administrator", password = "datashield_test&", 
+#'   builder$append(server = "study1",
+#'                  url = "http://192.168.56.100:8080/",
+#'                  user = "administrator", password = "datashield_test&",
 #'                  table = "CNSIM.CNSIM1", driver = "OpalDriver")
-#'   builder$append(server = "study2", 
-#'                  url = "http://192.168.56.100:8080/", 
-#'                  user = "administrator", password = "datashield_test&", 
+#'   builder$append(server = "study2",
+#'                  url = "http://192.168.56.100:8080/",
+#'                  user = "administrator", password = "datashield_test&",
 #'                  table = "CNSIM.CNSIM2", driver = "OpalDriver")
 #'   builder$append(server = "study3",
-#'                  url = "http://192.168.56.100:8080/", 
-#'                  user = "administrator", password = "datashield_test&", 
+#'                  url = "http://192.168.56.100:8080/",
+#'                  user = "administrator", password = "datashield_test&",
 #'                  table = "CNSIM.CNSIM3", driver = "OpalDriver")
 #'   logindata <- builder$build()
-#'   
+#'
 #'   # Log onto the remote Opal training servers
-#'   connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
-#' 
+#'   connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
+#'
 #'   # Getting column names of the R objects stored in the server-side
 #'   ds.colnames(x = "D",
 #'               datasources = connections[1]) #only the first server ("study1") is used
 #'   # Clear the Datashield R sessions and logout
-#'   datashield.logout(connections) 
+#'   datashield.logout(connections)
 #' }
 #' @export
 #'
@@ -65,17 +65,6 @@ ds.colnames <- function(x=NULL, datasources=NULL) {
     stop("Please provide the name of a data.frame or matrix!", call.=FALSE)
   }
 
-  # check if the input object(s) is(are) defined in all the studies
-  defined <- isDefined(datasources, x)
-
-  # call the internal function that checks the input object is of the same class in all studies.
-  typ <- checkClass(datasources, x)
-
-  # if the input object is not a matrix or a dataframe stop
-  if(!('data.frame' %in% typ) & !('matrix' %in% typ)){
-    stop("The input vector must be of type 'data.frame' or a 'matrix'!", call.=FALSE)
-  }
-
   cally <- call("colnamesDS", x)
   column_names <- DSI::datashield.aggregate(datasources, cally)