Merge pull request #421 from datashield/v6.3.4-dev

Update with changes to v6.3.4-dev

Author: StuartWheater

.github/workflows/dsBase_test_suite.yaml

@@ -13,7 +13,6 @@ name: dsBase tests' suite
 
 on:
   push:
-    branches: [master, v6.3.4-dev]
   schedule:
     - cron: '0 0 * * 0'   # Weekly
     - cron: '0 1 * * *'   # Nightly
@@ -153,10 +152,9 @@ jobs:
         working-directory: dsBase
 
       - name: Commit results to testStatus
-        # if: github.repository == 'villegar/dsBase' && github.event_name != 'pull_request'
         run: |
-          git config --global user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          git config --global user.name "$GITHUB_ACTOR"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions[bot]"
           cd testStatus
           git checkout master
           git pull

DESCRIPTION

@@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a
     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. For more details, see 'citation("dsBase")'.
-Version: 6.3.4-9000
+Version: 6.3.4
 Authors@R: c(person(given = "Paul",
                     family = "Burton",
                     role = c("aut"),
@@ -73,6 +73,8 @@ Imports:
     mice,
     childsds
 Suggests:
+    spelling,
     testthat
 RoxygenNote: 7.3.2
 Encoding: UTF-8
+Language: en-GB

R/asDataMatrixDS.R

@@ -3,7 +3,7 @@
 #' class for all columns in data.frames.
 #' @details This assign function is based on the native R function \code{data.matrix}
 #' If applied to a data.frame, the native R function \code{as.matrix}
-#' coverts all columns into character class. In contrast, if applied to
+#' converts all columns into character class. In contrast, if applied to
 #' a data.frame the native R function \code{data.matrix} converts
 #' the data.frame to a matrix but maintains all data columns in their
 #' original class

R/checkNegValueDS.R

@@ -1,7 +1,7 @@
 #'
 #' @title Checks if a numeric variable has negative values
 #' @description this function is only called by the client function \code{ds.glm}.
-#' @details if a user sets the parameter 'weights' on the client site function \code{ds.glm} this 
+#' @details if a user sets the parameter 'weights' on the client side function \code{ds.glm} this 
 #' server side function is called to verify that the 'weights' vector does not have negative values
 #' because no negative are allowed in weights.
 #' @param weights a numeric vector

R/densityGridDS.R

@@ -1,6 +1,6 @@
 #' 
 #' @title Generates a density grid with or without a priori defined limits
-#' @description Generates a density grid that can then be used for heatmap or countour plots.
+#' @description Generates a density grid that can then be used for heatmap or contour plots.
 #' @details Invalid cells (cells with count < to the set filter value for the minimum allowed
 #' counts in table cells) are turn to 0.
 #' @param xvect a numerical vector

R/dmtC2SDS.R

@@ -22,10 +22,10 @@
 #' @param ncols.transmit specifies the number of columns in the matrix to be created.
 #' Fixed by the clientside function as equal to the number of columns in
 #' the clientside DMT to be transferred.
-#' @param colnames.transmit a parser-transmissable vector specifying the name of each column
+#' @param colnames.transmit a parser-transmissible vector specifying the name of each column
 #' in the DMT being transferred from clientside to serverside.
 #' Generated automatically by clientside function from colnames of clientside DMT.
-#' @param colclass.transmit a parser-transmissable vector specifying the class of the
+#' @param colclass.transmit a parser-transmissible vector specifying the class of the
 #' vector representing each individual column in the DMT to be transferred.
 #' Generated automatically by clientside function. This allows the transmission of DMTs
 #' containing columns with different classes.If something is going to go wrong with

R/dsBase-package.R

@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/gamlssDS.R

@@ -1,5 +1,5 @@
 #'
-#' @title gamlssDS an aggregate function called by ds.galmss
+#' @title gamlssDS an aggregate function called by ds.gamlss
 #' @description This function calls the gamlssDS that is a wrapper function from 
 #' the gamlss R package. The function returns an object of class "gamlss", which 
 #' is a generalized additive model for location, scale and shape (GAMLSS). The 

R/glmerSLMADS.assign.R

@@ -5,7 +5,7 @@
 #' The analytic work engine is the glmer function in R which sits in the lme4 package.
 #' glmerSLMADS.assign fits a generalized linear mixed effects model (glme) - e.g. a logistic or
 #' Poisson regression model including both fixed and random effects - on data
-#' from each single data source and saves the regression outcomes on the serveside.
+#' from each single data source and saves the regression outcomes on the serverside.
 #' @param formula see help for ds.glmerSLMA
 #' @param offset see help for ds.glmerSLMA
 #' @param weights see help for ds.glmerSLMA

R/hetcorDS.R

@@ -1,7 +1,7 @@
 #' 
 #' @title Heterogeneous Correlation Matrix
 #' @description This function is based on the hetcor function from the R package \code{polycor}.
-#' @details Computes a heterogenous correlation matrix, consisting of Pearson product-moment
+#' @details Computes a heterogeneous correlation matrix, consisting of Pearson product-moment
 #' correlations between numeric variables, polyserial correlations between numeric and ordinal
 #' variables, and polychoric correlations between ordinal variables.
 #' @param data the name of a data frame consisting of factors, ordered factors, logical variables,