Merge pull request datashield#611 from villegar/v6.3.4-dev

Update documentation prior to RC for CRAN

Author: StuartWheater

.Rbuildignore

@@ -22,3 +22,4 @@
 ^dsDanger_6.3.4.tar.gz$
 ^\.circleci$
 ^\.circleci/config\.yml$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: dsBaseClient
-Title: DataSHIELD Client Functions
+Title: 'DataSHIELD' Client Side Base Functions
 Version: 6.3.4
-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
+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.
+    the automated output checks. For more details, see 'citation("dsBaseClient")'.
 Authors@R: c(person(given = "Paul",
                     family = "Burton",
                     role = c("aut"),
@@ -77,6 +77,7 @@ Imports:
 Suggests:
     lme4,
     httr,
+    spelling,
     tibble,
     testthat,
     e1071,
@@ -86,3 +87,4 @@ Suggests:
     DSLite
 RoxygenNote: 7.3.3
 Encoding: UTF-8
+Language: en-GB

R/ds.asNumeric.R

@@ -5,7 +5,7 @@
 #' @details This function is based on the native R function \code{as.numeric}.
 #' However, it behaves differently with some specific classes of variables. For example, if the input 
 #' object is of class factor, it first converts its values into characters and then convert those to
-#' numerics. This behavior is important for the case where the input object is of class factor having
+#' numerics. This behaviour is important for the case where the input object is of class factor having
 #' numbers as levels. In that case, the native R 
 #' \code{as.numeric} function returns the underlying level codes and not the values as numbers. 
 #' For example \code{as.numeric} in R converts the factor vector: \cr

R/ds.corTest.R

@@ -10,7 +10,7 @@
 #' used for the test. One of "pearson", "kendall", or "spearman", can be abbreviated. 
 #' Default is set to "pearson".
 #' @param exact a logical indicating whether an exact p-value should be computed. Used for
-#' Kendall's tau and Spearman's rho. See ‘Details’ of R stats function \code{cor.test} for
+#' Kendall's tau and Spearman's rho. See \emph{Details} of R stats function \code{cor.test} for
 #' the meaning of NULL (the default).
 #' @param conf.level confidence level for the returned confidence interval. Currently
 #' only used for the Pearson product moment correlation coefficient if there are at least

R/ds.dataFrameSubset.R

@@ -12,7 +12,7 @@
 #' 
 #' Server functions called: \code{dataFrameSubsetDS1} and \code{dataFrameSubsetDS2}
 #' 
-#' @param df.name a character string providing the name of the data frame to be subseted. 
+#' @param df.name a character string providing the name of the data frame to be subset. 
 #' @param V1.name  A character string specifying the name of the vector 
 #' to which the Boolean operator is to be applied to define the subset.
 #' For more information see details. 

R/ds.dmtC2S.R

@@ -29,7 +29,7 @@
 #' wish to change the connections you wish to use by default the call
 #' datashield.connections_default('opals.a') will set 'default.connections'
 #' to be 'opals.a' and so in the absence of specific instructions to the contrary
-#' (e.g. by specifiying a particular dataset to be used via the <datasources>
+#' (e.g. by specifying a particular dataset to be used via the <datasources>
 #' argument) all subsequent function calls will be to the datasets held in opals.a.
 #' If the <datasources> argument is specified, it should be set without
 #' inverted commas: e.g. datasources=opals.a or datasources=default.connections.

R/ds.elspline.R

@@ -13,7 +13,7 @@
 #' @param x the name of the input numeric variable
 #' @param n integer greater than 2, knots are computed such that they cut n equally-spaced
 #' intervals along the range of x
-#' @param marginal logical, how to parametrize the spline, see Details
+#' @param marginal logical, how to parametrise the spline, see Details
 #' @param names character, vector of names for constructed variables
 #' @param newobj a character string that provides the name for the output 
 #' variable that is stored on the data servers. Default \code{elspline.newobj}. 

R/ds.forestplot.R

@@ -1,10 +1,10 @@
 #' @title Forestplot for SLMA models
-#' @description Draws a foresplot of the coefficients for Study-Level Meta-Analysis performed with
+#' @description Draws a forestplot of the coefficients for Study-Level Meta-Analysis performed with
 #' DataSHIELD
 #'
-#' @param mod \code{list} List outputed by any of the SLMA models of DataSHIELD (\code{ds.glmerSLMA}, 
+#' @param mod \code{list} List outputted by any of the SLMA models of DataSHIELD (\code{ds.glmerSLMA}, 
 #' \code{ds.glmSLMA}, \code{ds.lmerSLMA})
-#' @param variable \code{character} (default \code{NULL}) Variable to meta-analyze and visualize, by setting this 
+#' @param variable \code{character} (default \code{NULL}) Variable to meta-analyse and visualise, by setting this 
 #' argument to \code{NULL} (default) the first independent variable will be used.
 #' @param method \code{character} (Default \code{"ML"}) Method to estimate the between study variance. 
 #' See details from \code{?meta::metagen} for the different options.