page, test and coverage

.Rbuildignore

@@ -3,3 +3,7 @@
 ^data-raw$
 ^test-data$
 ^troubleshooting\.R$
+^setup\.R$
+^docs$
+^\.github$
+^codecov\.yml$

.github/.gitignore

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

.github/workflows/R-CMD-check.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:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapCAST
 Title: REDCap Castellated data handling
-Version: 23.3.1
+Version: 23.3.2
 Authors@R: c(
     person("Paul", "Egeler", email = "paul.egeler@spectrumhealth.org", role = c("aut")),
      person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", role = c("cre", "ctb","cph"),
@@ -19,13 +19,15 @@ Description: This package is based on REDCapRITS by Paul Egeler and Spectrum Hea
     4) procedures for data integration and interoperability with external sources
     (<doi:10.1016/j.jbi.2008.08.010>; <doi:10.1016/j.jbi.2019.103208>).
 Depends: R (>= 3.4.0)
-Suggests: 
+Suggests:
-    RCurl, 
+    spelling,
+    RCurl,
     httr,
     jsonlite,
     testthat,
     Hmisc,
-    readr
+    readr,
+    covr
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
@@ -43,3 +45,4 @@ Collate:
     'REDCap_split.r'
     'read_redcap_tables.R'
     'redcap_wider.R'
+Language: en-US

NEWS.md

@@ -1,3 +1,9 @@
+# REDCapCAST 23.3.2
+
+### Documentation:
+
+* Page added. Vignettes to follow.
+
 # REDCapCAST 23.3.1
 
 ### New name: REDCapCAST

R/utils.r

@@ -6,7 +6,6 @@
 #' @param vars_in_data Vector of variable names in the dataset
 #' @return A dataframe containing metadata for the variables in the dataset
 #' @export
-#' @examples
 #'
 focused_metadata <- function(metadata, vars_in_data) {
 
@@ -99,7 +98,6 @@ focused_metadata <- function(metadata, vars_in_data) {
 #'
 #' @export
 #'
-#' @examples
 #'
 sanitize_split <- function(l,
                            generic.names = c(
@@ -128,8 +126,6 @@ sanitize_split <- function(l,
 #'
 #' @export
 #'
-#' @examples
-#'
 #'
 match_fields_to_form <- function(metadata, vars_in_data) {
 

README.md

@@ -1,3 +1,8 @@
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/agdamsbo/REDCapCAST/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/agdamsbo/REDCapCAST/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/agdamsbo/REDCapCAST/branch/master/graph/badge.svg)](https://app.codecov.io/gh/agdamsbo/REDCapCAST?branch=master)
+<!-- badges: end -->
+
 # REDCapCAST
 REDCap Castellated data handling when using repeated instruments.
 

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

docs/bootstrap-toc.css

@@ -0,0 +1,60 @@
+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+
+/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
+
+/* All levels of nav */
+nav[data-toggle='toc'] .nav > li > a {
+  display: block;
+  padding: 4px 20px;
+  font-size: 13px;
+  font-weight: 500;
+  color: #767676;
+}
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+  padding-left: 19px;
+  color: #563d7c;
+  text-decoration: none;
+  background-color: transparent;
+  border-left: 1px solid #563d7c;
+}
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+  padding-left: 18px;
+  font-weight: bold;
+  color: #563d7c;
+  background-color: transparent;
+  border-left: 2px solid #563d7c;
+}
+
+/* Nav: second level (shown on .active) */
+nav[data-toggle='toc'] .nav .nav {
+  display: none; /* Hide by default, but at >768px, show it */
+  padding-bottom: 10px;
+}
+nav[data-toggle='toc'] .nav .nav > li > a {
+  padding-top: 1px;
+  padding-bottom: 1px;
+  padding-left: 30px;
+  font-size: 12px;
+  font-weight: normal;
+}
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+  padding-left: 29px;
+}
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+  padding-left: 28px;
+  font-weight: 500;
+}
+
+/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
+nav[data-toggle='toc'] .nav > .active > ul {
+  display: block;
+}

docs/bootstrap-toc.js

@@ -0,0 +1,159 @@
+/*!
+ * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+(function() {
+  'use strict';
+
+  window.Toc = {
+    helpers: {
+      // return all matching elements in the set, or their descendants
+      findOrFilter: function($el, selector) {
+        // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
+        // http://stackoverflow.com/a/12731439/358804
+        var $descendants = $el.find(selector);
+        return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
+      },
+
+      generateUniqueIdBase: function(el) {
+        var text = $(el).text();
+        var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
+        return anchor || el.tagName.toLowerCase();
+      },
+
+      generateUniqueId: function(el) {
+        var anchorBase = this.generateUniqueIdBase(el);
+        for (var i = 0; ; i++) {
+          var anchor = anchorBase;
+          if (i > 0) {
+            // add suffix
+            anchor += '-' + i;
+          }
+          // check if ID already exists
+          if (!document.getElementById(anchor)) {
+            return anchor;
+          }
+        }
+      },
+
+      generateAnchor: function(el) {
+        if (el.id) {
+          return el.id;
+        } else {
+          var anchor = this.generateUniqueId(el);
+          el.id = anchor;
+          return anchor;
+        }
+      },
+
+      createNavList: function() {
+        return $('<ul class="nav"></ul>');
+      },
+
+      createChildNavList: function($parent) {
+        var $childList = this.createNavList();
+        $parent.append($childList);
+        return $childList;
+      },
+
+      generateNavEl: function(anchor, text) {
+        var $a = $('<a></a>');
+        $a.attr('href', '#' + anchor);
+        $a.text(text);
+        var $li = $('<li></li>');
+        $li.append($a);
+        return $li;
+      },
+
+      generateNavItem: function(headingEl) {
+        var anchor = this.generateAnchor(headingEl);
+        var $heading = $(headingEl);
+        var text = $heading.data('toc-text') || $heading.text();
+        return this.generateNavEl(anchor, text);
+      },
+
+      // Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
+      getTopLevel: function($scope) {
+        for (var i = 1; i <= 6; i++) {
+          var $headings = this.findOrFilter($scope, 'h' + i);
+          if ($headings.length > 1) {
+            return i;
+          }
+        }
+
+        return 1;
+      },
+
+      // returns the elements for the top level, and the next below it
+      getHeadings: function($scope, topLevel) {
+        var topSelector = 'h' + topLevel;
+
+        var secondaryLevel = topLevel + 1;
+        var secondarySelector = 'h' + secondaryLevel;
+
+        return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
+      },
+
+      getNavLevel: function(el) {
+        return parseInt(el.tagName.charAt(1), 10);
+      },
+
+      populateNav: function($topContext, topLevel, $headings) {
+        var $context = $topContext;
+        var $prevNav;
+
+        var helpers = this;
+        $headings.each(function(i, el) {
+          var $newNav = helpers.generateNavItem(el);
+          var navLevel = helpers.getNavLevel(el);
+
+          // determine the proper $context
+          if (navLevel === topLevel) {
+            // use top level
+            $context = $topContext;
+          } else if ($prevNav && $context === $topContext) {
+            // create a new level of the tree and switch to it
+            $context = helpers.createChildNavList($prevNav);
+          } // else use the current $context
+
+          $context.append($newNav);
+
+          $prevNav = $newNav;
+        });
+      },
+
+      parseOps: function(arg) {
+        var opts;
+        if (arg.jquery) {
+          opts = {
+            $nav: arg
+          };
+        } else {
+          opts = arg;
+        }
+        opts.$scope = opts.$scope || $(document.body);
+        return opts;
+      }
+    },
+
+    // accepts a jQuery object, or an options object
+    init: function(opts) {
+      opts = this.helpers.parseOps(opts);
+
+      // ensure that the data attribute is in place for styling
+      opts.$nav.attr('data-toggle', 'toc');
+
+      var $topContext = this.helpers.createChildNavList(opts.$nav);
+      var topLevel = this.helpers.getTopLevel(opts.$scope);
+      var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
+      this.helpers.populateNav($topContext, topLevel, $headings);
+    }
+  };
+
+  $(function() {
+    $('nav[data-toggle="toc"]').each(function(i, el) {
+      var $nav = $(el);
+      Toc.init($nav);
+    });
+  });
+})();

docs/docsearch.js

@@ -0,0 +1,85 @@
+$(function() {
+
+  // register a handler to move the focus to the search bar
+  // upon pressing shift + "/" (i.e. "?")
+  $(document).on('keydown', function(e) {
+    if (e.shiftKey && e.keyCode == 191) {
+      e.preventDefault();
+      $("#search-input").focus();
+    }
+  });
+
+  $(document).ready(function() {
+    // do keyword highlighting
+    /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
+    var mark = function() {
+
+      var referrer = document.URL ;
+      var paramKey = "q" ;
+
+      if (referrer.indexOf("?") !== -1) {
+        var qs = referrer.substr(referrer.indexOf('?') + 1);
+        var qs_noanchor = qs.split('#')[0];
+        var qsa = qs_noanchor.split('&');
+        var keyword = "";
+
+        for (var i = 0; i < qsa.length; i++) {
+          var currentParam = qsa[i].split('=');
+
+          if (currentParam.length !== 2) {
+            continue;
+          }
+
+          if (currentParam[0] == paramKey) {
+            keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
+          }
+        }
+
+        if (keyword !== "") {
+          $(".contents").unmark({
+            done: function() {
+              $(".contents").mark(keyword);
+            }
+          });
+        }
+      }
+    };
+
+    mark();
+  });
+});
+
+/* Search term highlighting ------------------------------*/
+
+function matchedWords(hit) {
+  var words = [];
+
+  var hierarchy = hit._highlightResult.hierarchy;
+  // loop to fetch from lvl0, lvl1, etc.
+  for (var idx in hierarchy) {
+    words = words.concat(hierarchy[idx].matchedWords);
+  }
+
+  var content = hit._highlightResult.content;
+  if (content) {
+    words = words.concat(content.matchedWords);
+  }
+
+  // return unique words
+  var words_uniq = [...new Set(words)];
+  return words_uniq;
+}
+
+function updateHitURL(hit) {
+
+  var words = matchedWords(hit);
+  var url = "";
+
+  if (hit.anchor) {
+    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+  } else {
+    url = hit.url + '?q=' + escape(words.join(" "));
+  }
+
+  return url;
+}

docs/link.svg

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 19.2.1, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 viewBox="0 0 20 20" style="enable-background:new 0 0 20 20;" xml:space="preserve">
+<style type="text/css">
+	.st0{fill:#75AADB;}
+</style>
+<path class="st0" d="M4,11.3h1.3v1.3H4c-2,0-4-2.3-4-4.7s2.1-4.7,4-4.7h5.3c1.9,0,4,2.3,4,4.7c0,1.9-1.2,3.6-2.7,4.3v-1.5
+	C11.4,10.2,12,9.1,12,8c0-1.7-1.4-3.3-2.7-3.3H4C2.7,4.7,1.3,6.3,1.3,8S2.7,11.3,4,11.3z M16,7.3h-1.3v1.3H16c1.3,0,2.7,1.6,2.7,3.3
+	s-1.4,3.3-2.7,3.3h-5.3C9.4,15.3,8,13.7,8,12c0-1.1,0.6-2.2,1.3-2.8V7.7C7.9,8.4,6.7,10.1,6.7,12c0,2.4,2.1,4.7,4,4.7H16
+	c1.9,0,4-2.3,4-4.7S18,7.3,16,7.3z"/>
+</svg>

docs/pkgdown.css

@@ -0,0 +1,384 @@
+/* Sticky footer */
+
+/**
+ * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
+ * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
+ *
+ * .Site -> body > .container
+ * .Site-content -> body > .container .row
+ * .footer -> footer
+ *
+ * Key idea seems to be to ensure that .container and __all its parents__
+ * have height set to 100%
+ *
+ */
+
+html, body {
+  height: 100%;
+}
+
+body {
+  position: relative;
+}
+
+body > .container {
+  display: flex;
+  height: 100%;
+  flex-direction: column;
+}
+
+body > .container .row {
+  flex: 1 0 auto;
+}
+
+footer {
+  margin-top: 45px;
+  padding: 35px 0 36px;
+  border-top: 1px solid #e5e5e5;
+  color: #666;
+  display: flex;
+  flex-shrink: 0;
+}
+footer p {
+  margin-bottom: 0;
+}
+footer div {
+  flex: 1;
+}
+footer .pkgdown {
+  text-align: right;
+}
+footer p {
+  margin-bottom: 0;
+}
+
+img.icon {
+  float: right;
+}
+
+/* Ensure in-page images don't run outside their container */
+.contents img {
+  max-width: 100%;
+  height: auto;
+}
+
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+  display: list-item;
+}
+
+/* Typographic tweaking ---------------------------------*/
+
+.contents .page-header {
+  margin-top: calc(-60px + 1em);
+}
+
+dd {
+  margin-left: 3em;
+}
+
+/* Section anchors ---------------------------------*/
+
+a.anchor {
+  display: none;
+  margin-left: 5px;
+  width: 20px;
+  height: 20px;
+
+  background-image: url(./link.svg);
+  background-repeat: no-repeat;
+  background-size: 20px 20px;
+  background-position: center center;
+}
+
+h1:hover .anchor,
+h2:hover .anchor,
+h3:hover .anchor,
+h4:hover .anchor,
+h5:hover .anchor,
+h6:hover .anchor {
+  display: inline-block;
+}
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+  padding-top: 60px;
+  margin-top: -40px;
+}
+
+/* Navbar submenu --------------------------*/
+
+.dropdown-submenu {
+  position: relative;
+}
+
+.dropdown-submenu>.dropdown-menu {
+  top: 0;
+  left: 100%;
+  margin-top: -6px;
+  margin-left: -1px;
+  border-radius: 0 6px 6px 6px;
+}
+
+.dropdown-submenu:hover>.dropdown-menu {
+  display: block;
+}
+
+.dropdown-submenu>a:after {
+  display: block;
+  content: " ";
+  float: right;
+  width: 0;
+  height: 0;
+  border-color: transparent;
+  border-style: solid;
+  border-width: 5px 0 5px 5px;
+  border-left-color: #cccccc;
+  margin-top: 5px;
+  margin-right: -10px;
+}
+
+.dropdown-submenu:hover>a:after {
+  border-left-color: #ffffff;
+}
+
+.dropdown-submenu.pull-left {
+  float: none;
+}
+
+.dropdown-submenu.pull-left>.dropdown-menu {
+  left: -100%;
+  margin-left: 10px;
+  border-radius: 6px 0 6px 6px;
+}
+
+/* Sidebar --------------------------*/
+
+#pkgdown-sidebar {
+  margin-top: 30px;
+  position: -webkit-sticky;
+  position: sticky;
+  top: 70px;
+}
+
+#pkgdown-sidebar h2 {
+  font-size: 1.5em;
+  margin-top: 1em;
+}
+
+#pkgdown-sidebar h2:first-child {
+  margin-top: 0;
+}
+
+#pkgdown-sidebar .list-unstyled li {
+  margin-bottom: 0.5em;
+}
+
+/* bootstrap-toc tweaks ------------------------------------------------------*/
+
+/* All levels of nav */
+
+nav[data-toggle='toc'] .nav > li > a {
+  padding: 4px 20px 4px 6px;
+  font-size: 1.5rem;
+  font-weight: 400;
+  color: inherit;
+}
+
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+  padding-left: 5px;
+  color: inherit;
+  border-left: 1px solid #878787;
+}
+
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+  padding-left: 5px;
+  font-size: 1.5rem;
+  font-weight: 400;
+  color: inherit;
+  border-left: 2px solid #878787;
+}
+
+/* Nav: second level (shown on .active) */
+
+nav[data-toggle='toc'] .nav .nav {
+  display: none; /* Hide by default, but at >768px, show it */
+  padding-bottom: 10px;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a {
+  padding-left: 16px;
+  font-size: 1.35rem;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+  padding-left: 15px;
+}
+
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+  padding-left: 15px;
+  font-weight: 500;
+  font-size: 1.35rem;
+}
+
+/* orcid ------------------------------------------------------------------- */
+
+.orcid {
+  font-size: 16px;
+  color: #A6CE39;
+  /* margins are required by official ORCID trademark and display guidelines */
+  margin-left:4px;
+  margin-right:4px;
+  vertical-align: middle;
+}
+
+/* Reference index & topics ----------------------------------------------- */
+
+.ref-index th {font-weight: normal;}
+
+.ref-index td {vertical-align: top; min-width: 100px}
+.ref-index .icon {width: 40px;}
+.ref-index .alias {width: 40%;}
+.ref-index-icons .alias {width: calc(40% - 40px);}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+  display: block;
+  overflow: auto;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+pre, code, pre code {
+  background-color: #f8f8f8;
+  color: #333;
+}
+pre, pre code {
+  white-space: pre-wrap;
+  word-break: break-all;
+  overflow-wrap: break-word;
+}
+
+pre {
+  border: 1px solid #eee;
+}
+
+pre .img, pre .r-plt {
+  margin: 5px 0;
+}
+
+pre .img img, pre .r-plt img {
+  background-color: #fff;
+}
+
+code a, pre a {
+  color: #375f84;
+}
+
+a.sourceLine:hover {
+  text-decoration: none;
+}
+
+.fl      {color: #1514b5;}
+.fu      {color: #000000;} /* function */
+.ch,.st  {color: #036a07;} /* string */
+.kw      {color: #264D66;} /* keyword */
+.co      {color: #888888;} /* comment */
+
+.error   {font-weight: bolder;}
+.warning {font-weight: bolder;}
+
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+  position: relative;
+}
+
+.btn-copy-ex {
+  position: absolute;
+  right: 0;
+  top: 0;
+  visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+  visibility: visible;
+}
+
+/* headroom.js ------------------------ */
+
+.headroom {
+  will-change: transform;
+  transition: transform 200ms linear;
+}
+.headroom--pinned {
+  transform: translateY(0%);
+}
+.headroom--unpinned {
+  transform: translateY(-100%);
+}
+
+/* mark.js ----------------------------*/
+
+mark {
+  background-color: rgba(255, 255, 51, 0.5);
+  border-bottom: 2px solid rgba(255, 153, 51, 0.3);
+  padding: 1px;
+}
+
+/* vertical spacing after htmlwidgets */
+.html-widget {
+  margin-bottom: 10px;
+}
+
+/* fontawesome ------------------------ */
+
+.fab {
+    font-family: "Font Awesome 5 Brands" !important;
+}
+
+/* don't display links in code chunks when printing */
+/* source: https://stackoverflow.com/a/10781533 */
+@media print {
+  code a:link:after, code a:visited:after {
+    content: "";
+  }
+}
+
+/* Section anchors ---------------------------------
+   Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71
+*/
+
+div.csl-bib-body { }
+div.csl-entry {
+  clear: both;
+}
+.hanging-indent div.csl-entry {
+  margin-left:2em;
+  text-indent:-2em;
+}
+div.csl-left-margin {
+  min-width:2em;
+  float:left;
+}
+div.csl-right-inline {
+  margin-left:2em;
+  padding-left:1em;
+}
+div.csl-indent {
+  margin-left: 2em;
+}

docs/pkgdown.js

@@ -0,0 +1,108 @@
+/* http://gregfranko.com/blog/jquery-best-practices/ */
+(function($) {
+  $(function() {
+
+    $('.navbar-fixed-top').headroom();
+
+    $('body').css('padding-top', $('.navbar').height() + 10);
+    $(window).resize(function(){
+      $('body').css('padding-top', $('.navbar').height() + 10);
+    });
+
+    $('[data-toggle="tooltip"]').tooltip();
+
+    var cur_path = paths(location.pathname);
+    var links = $("#navbar ul li a");
+    var max_length = -1;
+    var pos = -1;
+    for (var i = 0; i < links.length; i++) {
+      if (links[i].getAttribute("href") === "#")
+        continue;
+      // Ignore external links
+      if (links[i].host !== location.host)
+        continue;
+
+      var nav_path = paths(links[i].pathname);
+
+      var length = prefix_length(nav_path, cur_path);
+      if (length > max_length) {
+        max_length = length;
+        pos = i;
+      }
+    }
+
+    // Add class to parent <li>, and enclosing <li> if in dropdown
+    if (pos >= 0) {
+      var menu_anchor = $(links[pos]);
+      menu_anchor.parent().addClass("active");
+      menu_anchor.closest("li.dropdown").addClass("active");
+    }
+  });
+
+  function paths(pathname) {
+    var pieces = pathname.split("/");
+    pieces.shift(); // always starts with /
+
+    var end = pieces[pieces.length - 1];
+    if (end === "index.html" || end === "")
+      pieces.pop();
+    return(pieces);
+  }
+
+  // Returns -1 if not found
+  function prefix_length(needle, haystack) {
+    if (needle.length > haystack.length)
+      return(-1);
+
+    // Special case for length-0 haystack, since for loop won't run
+    if (haystack.length === 0) {
+      return(needle.length === 0 ? 0 : -1);
+    }
+
+    for (var i = 0; i < haystack.length; i++) {
+      if (needle[i] != haystack[i])
+        return(i);
+    }
+
+    return(haystack.length);
+  }
+
+  /* Clipboard --------------------------*/
+
+  function changeTooltipMessage(element, msg) {
+    var tooltipOriginalTitle=element.getAttribute('data-original-title');
+    element.setAttribute('data-original-title', msg);
+    $(element).tooltip('show');
+    element.setAttribute('data-original-title', tooltipOriginalTitle);
+  }
+
+  if(ClipboardJS.isSupported()) {
+    $(document).ready(function() {
+      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>";
+
+      $("div.sourceCode").addClass("hasCopyButton");
+
+      // Insert copy buttons:
+      $(copyButton).prependTo(".hasCopyButton");
+
+      // Initialize tooltips:
+      $('.btn-copy-ex').tooltip({container: 'body'});
+
+      // Initialize clipboard:
+      var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
+        text: function(trigger) {
+          return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, "");
+        }
+      });
+
+      clipboardBtnCopies.on('success', function(e) {
+        changeTooltipMessage(e.trigger, 'Copied!');
+        e.clearSelection();
+      });
+
+      clipboardBtnCopies.on('error', function() {
+        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      });
+    });
+  }
+})(window.jQuery || window.$)

docs/pkgdown.yml

@@ -0,0 +1,6 @@
+pandoc: 2.19.2
+pkgdown: 2.0.7
+pkgdown_sha: ~
+articles: {}
+last_built: 2023-03-07T20:04Z
+

docs/sitemap.xml

@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
+  <url>
+    <loc>/404.html</loc>
+  </url>
+  <url>
+    <loc>/authors.html</loc>
+  </url>
+  <url>
+    <loc>/index.html</loc>
+  </url>
+  <url>
+    <loc>/news/index.html</loc>
+  </url>
+  <url>
+    <loc>/reference/REDCap_split.html</loc>
+  </url>
+  <url>
+    <loc>/reference/focused_metadata.html</loc>
+  </url>
+  <url>
+    <loc>/reference/index.html</loc>
+  </url>
+  <url>
+    <loc>/reference/match_fields_to_form.html</loc>
+  </url>
+  <url>
+    <loc>/reference/read_redcap_tables.html</loc>
+  </url>
+  <url>
+    <loc>/reference/redcap_wider.html</loc>
+  </url>
+  <url>
+    <loc>/reference/sanitize_split.html</loc>
+  </url>
+  <url>
+    <loc>/reference/split_non_repeating_forms.html</loc>
+  </url>
+</urlset>

inst/WORDLIST

@@ -0,0 +1,21 @@
+DataDictionary
+GStat
+JSON
+README
+REDCap
+REDCapR
+REDCapRITS
+SpectrumHealthResearch
+Splitter
+api
+doi
+dplyr
+github
+https
+jbi
+matadata
+md
+nad
+og
+thorugh
+uri

tests/spelling.R

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)