Merge branch 'v6.3.2-test' into v6.3.2-test

Author: StuartWheater

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 <datasources>
-#' 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.

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 

R/ds.abs.R

@@ -10,9 +10,9 @@
 #' @param x a character string providing the name of a numeric or an integer vector.
 #' @param newobj a character string that provides the name for the output variable
 #' that is stored on the data servers. Default name is set to \code{abs.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. 
 #' If the \code{datasources} argument is not specified the default set of connections will be
-#' used: see \code{\link{datashield.connections_default}}.
+#' used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.abs} assigns a vector for each study that includes the absolute values of
 #' the input numeric or integer vector specified in the argument \code{x}. The created vectors
 #' are stored in the servers.

R/ds.asCharacter.R

@@ -9,9 +9,9 @@
 #' character.
 #' @param newobj a character string that provides the name for the output object
 #'  that is stored on the data servers. Default \code{ascharacter.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} 
 #' objects obtained after login. If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asCharacter} returns the object converted into a class character 
 #' that is written to the server-side. Also, two validity messages are returned to the client-side
 #' indicating the name of the \code{newobj} which has been created in each data source and if 

R/ds.asDataMatrix.R

@@ -8,9 +8,9 @@
 #' a matrix. 
 #' @param newobj a character string that provides the name for the output object
 #'  that is stored on the data servers. Default \code{asdatamatrix.newobj}.
-#' @param datasources a list of \code{\link{DSConnection-class}} 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} 
 #' objects obtained after login. If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asDataMatrix} returns the object converted into a matrix 
 #' that is written to the server-side. Also, two validity messages are returned 
 #' to the client-side

R/ds.asFactor.R

@@ -130,9 +130,9 @@
 #' to be used in the creation of the matrix with dummy variables. 
 #' If the \code{fixed.dummy.vars} is set to FALSE then any value of the baseline level is not taken
 #' into account.
-#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. 
 #' If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asFactor} returns the unique levels of the converted 
 #' variable in ascending order and a validity 
 #' message with the name of the created object on the client-side and 

R/ds.asFactorSimple.R

@@ -14,9 +14,9 @@
 #' the name of the variable to be converted to a factor. 
 #' @param newobj.name a character string that provides the name for the output variable 
 #' that is stored on the data servers. Default \code{asfactor.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. 
 #' If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return an output vector of class factor to the serverside. In addition, returns a validity 
 #' message with the name of the created object on the client-side and if creation fails an
 #' error message which can be viewed using datashield.errors().  
@@ -109,4 +109,4 @@ return(list(return.info=return.info,return.message=return.message))	 #
 
 
 }
-#ds.asFactorSimple
+#ds.asFactorSimple

R/ds.asInteger.R

@@ -22,9 +22,9 @@
 #' an integer.  
 #' @param newobj a character string that provides the name for the output object
 #'  that is stored on the data servers. Default \code{asinteger.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} 
 #' objects obtained after login. If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asInteger} returns the R object converted into an integer
 #' that is written to the server-side. Also, two validity messages are returned to the
 #' client-side indicating the name of the \code{newobj} which 

R/ds.asList.R

@@ -9,9 +9,9 @@
 #' a list.
 #' @param newobj a character string that provides the name for the output object
 #' that is stored on the data servers. Default \code{aslist.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} 
 #' objects obtained after login. If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asList} returns the R object converted into a list 
 #' which is written to the server-side. Also, two validity messages are returned to the
 #' client-side indicating the name of the \code{newobj} which has been created in each data 

R/ds.asLogical.R

@@ -8,9 +8,9 @@
 #' input object to be coerced to a logical. 
 #' @param newobj a character string that provides the name for the output object
 #'  that is stored on the data servers. Default \code{aslogical.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} 
 #' objects obtained after login. If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asLogical} returns the R object converted into a logical
 #' that is written to the server-side. Also, two validity messages are returned
 #' to the client-side indicating the name of the \code{newobj} which