Merge pull request datashield#600 from StuartWheater/v6.4.0-dev

Update with v6.3.3-dev changes

Author: StuartWheater

.Rbuildignore

@@ -17,8 +17,8 @@
 ^R/secure.global.ranking.md$
 ^_pkgdown\.yml$
 ^docs$
-^dsBase_6.3.1.tar.gz$
-^dsBase_6.3.1-permissive.tar.gz$
+^dsBase_6.3.2.tar.gz$
+^dsBase_6.3.2-permissive.tar.gz$
 ^dsDanger_6.3.1.tar.gz$
 ^\.circleci$
 ^\.circleci/config\.yml$

.circleci/config.yml

@@ -47,7 +47,6 @@ jobs:
               sudo Rscript -e "install.packages('ggplot2', dependencies=TRUE)"
               sudo Rscript -e "install.packages('gridExtra', dependencies=TRUE)"
               sudo Rscript -e "install.packages('data.table', dependencies=TRUE)"
-              sudo Rscript -e "install.packages('panelaggregation', dependencies=TRUE)"
               sudo Rscript -e "install.packages('methods', dependencies=TRUE)"
               sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
               sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"

DESCRIPTION

@@ -1,9 +1,47 @@
 Package: dsBaseClient
 Title: DataSHIELD Client Functions
 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.
+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
+    checking based on statistical disclosure control. With data sites setting the threshold values for
+    the automated output checks.
+Authors@R: c(person(given = "Paul",
+                    family = "Burton",
+                    role = c("aut")),
+             person(given = "Rebecca",
+                    family = "Wilson",
+                    role = c("aut")),
+             person(given = "Olly",
+                    family = "Butters",
+                    role = c("aut")),
+             person(given = "Patricia",
+                    family = "Ryser-Welch",
+                    role = c("aut")),
+             person(given = "Alex",
+                    family = "Westerberg",
+                    role = c("aut")),
+             person(given = "Leire",
+                    family = "Abarrategui",
+                    role = c("aut")),
+             person(given = "Roberto",
+                    family = "Villegas-Diaz",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-5036-8661")),
+             person(given = "Demetris",
+                    family = "Avraam",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-8908-2441")),
+             person(given = "Yannick",
+                    family = "Marcon",
+                    role = c("aut"),
+                    email = "yannick.marcon@obiba.org",
+                    comment = c(ORCID = "0000-0003-0138-2023")),
+             person(given = "Stuart",
+                    family = "Wheater",
+                    role = c("aut", "cre"),
+                    email = "stuart.wheater@arjuna.com",
+                    comment = c(ORCID = "0009-0003-2419-1964")))
 License: GPL-3
 Depends:
     R (>= 4.0.0),
@@ -15,7 +53,6 @@ Imports:
     ggplot2,
     gridExtra,
     data.table,
-    panelaggregation,
     methods,
     dplyr
 Suggests:

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(computeWeightedMeans)
 export(ds.Boole)
 export(ds.abs)
 export(ds.asCharacter)
@@ -116,3 +117,7 @@ export(ds.var)
 export(ds.vectorCalc)
 import(DSI)
 import(data.table)
+importFrom(stats,as.formula)
+importFrom(stats,na.omit)
+importFrom(stats,ts)
+importFrom(stats,weighted.mean)

R/checkClass.R

@@ -3,8 +3,8 @@
 #' @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 <datasources>
-#' 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 <datasources>
+#' 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/computeWeightedMeans.R

@@ -0,0 +1,25 @@
+#' Compute Weighted Mean by Group
+#' 
+#' This function is originally from the panelaggregation package.
+#' It has been ported here in order to bypass the package being
+#' kicked off CRAN.
+#' 
+#' @author Matthias Bannert, Gabriel Bucur
+#' @param data_table a data.table
+#' @param variables character name of the variable(s) to focus on. The variables must be in the data.table
+#' @param weight character name of the data.table column that contains a weight. 
+#' @param by character vector of the columns to group by
+#' @import data.table
+#' @importFrom stats as.formula na.omit ts weighted.mean
+#' @export
+computeWeightedMeans <- function(data_table, variables, weight, by) {
+  
+  if (is.null(weight)) {
+    res_dt <- data_table[, lapply(.SD, mean, na.rm = TRUE), .SDcols = variables, by = by]
+  } else {
+    res_dt <- data_table[, lapply(.SD, weighted.mean, weight = eval(as.name(weight)), na.rm = TRUE),
+                         .SDcols = variables, by = by]
+  }
+  
+  res_dt
+}

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