Merge branch 'dev' into 'prod'

Bumped version to 0.4

See merge request !4

DESCRIPTION

 Package: ufs
 Type: Package
 Title: Quantitative Analysis Made Accessible
-Version: 0.3.3
+Version: 0.4.0
 Authors@R: 
     c(
         person(given = "Gjalt-Jorn",
@@ -44,8 +44,9 @@ Suggests:
     MBESS (>= 4.5.1),
     psych (>= 1.8),
     rio (>= 0.5),
-    rmarkdown,
-    rstudioapi
+    remotes (>= 0.2),
+    rmarkdown (>= 2.5),
+    rstudioapi (>= 0.11)
 Imports: digest (>= 0.6.19),
          diptest (>= 0.75.7),
          dplyr (>= 0.7.6),

NAMESPACE

@@ -178,6 +178,8 @@ export(qCohensd)
 export(qVec)
 export(qd)
 export(qomegaSq)
+export(quietGitLabUpdate)
+export(quietRemotesInstall)
 export(rCohensd)
 export(rawDataDiamondLayer)
 export(rd)

R/checkPkgs.R

@@ -25,7 +25,11 @@
 #'
 #' ### This will show the error message
 #' tryCatch(
-#'   ufs::checkPkgs(base = "99"),
+#'   ufs::checkPkgs(
+#'     base = "99",
+#'     stats = "42.5",
+#'     ufs = 20
+#'   ),
 #'   error = print
 #' );
 checkPkgs <- function(...,

R/quietRemotesInstall.R

+#' Quietly update a package from a remote repository
+#'
+#' Simple wrapper for `remotes` functions that fail gracefully (well, don't
+#' fail at all, just don't do what they're supposed to do) when there's no
+#' internet connection).
+#'
+#' @param x The repository name (e.g. "`r-packages/ufs`")
+#' @param func The `remotes` function to use
+#' @param unloadNamespace Whether to first unload the relevant namespace
+#' @param dependencies,upgrade Whether to install dependencies or upgrade
+#' @param quiet Whether to suppress messages and warnings
+#' @param errorInvisible Whether to suppress errors
+#' @param ... Additional arguments are passed on to the `remotes` function
+#'
+#' @return The result of the call to the `remotes` function
+#' @rdname quietRemotesInstall
+#' @export
+quietRemotesInstall <- function(x,
+                                func,
+                                unloadNamespace = TRUE,
+                                dependencies = FALSE,
+                                upgrade = FALSE,
+                                quiet = TRUE,
+                                errorInvisible = TRUE,
+                                ...) {
+
+  if (!requireNamespace("remotes", quietly = TRUE)) {
+    stop("This is a wrapper for `remotes` functions; ",
+         "you need to have `remotes` installed to use it.");
+  }
+
+  if (unloadNamespace) {
+    unloadNamespace(gsub(".*/", "", x));
+  }
+
+  if (quiet) {
+    silencefunc <- function(x) {
+      invisible(
+        suppressMessages(
+          suppressWarnings(
+            x
+          )
+        )
+      );
+    }
+  } else {
+    silencefunc <- function(x) {
+      x
+    };
+  }
+
+  remotesFunction <- utils::getFromNamespace(x = func,
+                                             ns = "remotes");
+
+  if (errorInvisible) {
+    silencefunc(tryCatch(
+      remotesFunction(x,
+                      dependencies=dependencies,
+                      quiet=quiet,
+                      upgrade=upgrade,
+                      ...),
+      error=invisible));
+  } else {
+    silencefunc(
+      remotesFunction(x,
+                      dependencies=dependencies,
+                      quiet=quiet,
+                      upgrade=upgrade,
+                      ...)
+      );
+  }
+
+
+}
+
+#' @rdname quietRemotesInstall
+#' @export
+quietGitLabUpdate <- function(x,
+                              unloadNamespace = TRUE,
+                              dependencies = FALSE,
+                              upgrade = FALSE,
+                              quiet = TRUE,
+                              errorInvisible = TRUE,
+                              ...) {
+  quietRemotesInstall(x,
+                      func = "install_gitlab",
+                      unloadNamespace = unloadNamespace,
+                      dependencies=dependencies,
+                      quiet=quiet,
+                      upgrade=upgrade,
+                      errorInvisible=errorInvisible,
+                      ...);
+}

man/IN.Rd

@@ -15,7 +15,7 @@ find \%IN\% table
 A logical vector.
 }
 \description{
-This is simply 'in', but applies \code{\link[base:toupper]{base::toupper()}} to both
+This is simply 'in', but applies \code{\link[base:chartr]{base::toupper()}} to both
 arguments, first.
 }
 \examples{

man/checkPkgs.Rd

@@ -12,9 +12,9 @@ checkPkgs(
 )
 }
 \arguments{
-\item{...}{A vector with packages. If this is a names vector, the
+\item{...}{A series of packages. If the packages are named, the
 names are the package names, and the values are the minimum required
-package versions.}
+package versions (see the second example).}
 
 \item{install}{Whether to install missing packages from \code{repos}.}
 
@@ -37,9 +37,16 @@ are installed, but their namespace won't attach to the search path.
 \examples{
 ufs::checkPkgs('base');
 
+### Require a version
+ufs::checkPkgs(ufs = "0.3.1");
+
 ### This will show the error message
 tryCatch(
-  ufs::checkPkgs(base = "99"),
+  ufs::checkPkgs(
+    base = "99",
+    stats = "42.5",
+    ufs = 20
+  ),
   error = print
 );
 }

man/descriptives.Rd

@@ -95,7 +95,7 @@ what SPSS's DESCRIPTIVES (often called with DESCR) does.
 \details{
 Note that R (of course) has many similar functions, such as
 \code{\link{summary}}, \code{\link[psych:describe]{psych::describe()}} in the excellent
-\link[psych:psych]{psych::psych} package.
+\link[psych:00.psych-package]{psych::psych} package.
 
 The Hartigans' Dip Test may be unfamiliar to users; it is a measure of uni-
 vs. multidimensionality, computed by \code{\link[diptest:dip.test]{diptest::dip.test()}} from the

man/faConfInt.Rd

@@ -8,7 +8,7 @@ faConfInt(fa)
 }
 \arguments{
 \item{fa}{The object produced by the \code{\link[psych:fa]{psych::fa()}} function from the
-\link[psych:psych-package]{psych::psych-package} package. It is important that the \code{n.iter} argument
+\link[psych:00.psych-package]{psych::psych-package} package. It is important that the \code{n.iter} argument
 of\code{\link[psych:fa]{psych::fa()}} was set to a realistic number, because otherwise, no
 confidence intervals will be available.}
 }
@@ -19,7 +19,7 @@ dataframe three variables: \item{lo}{lower bound of the confidence interval}
 the confidence interval}
 }
 \description{
-This function contains some code from a function in \link[psych:psych-package]{psych::psych-package}
+This function contains some code from a function in \link[psych:00.psych-package]{psych::psych-package}
 that's not exported \code{print.psych.fa.ci} but useful nonetheless. It
 basically takes the outcomes of a factor analysis and extracted the
 confidence intervals.
@@ -27,7 +27,7 @@ confidence intervals.
 \details{
 THis function extract confidence interval bounds and combines them with
 factor loadings using the code from the \code{print.psych.fa.ci} in
-\link[psych:psych-package]{psych::psych-package}.
+\link[psych:00.psych-package]{psych::psych-package}.
 }
 \examples{
 

man/factorLoadingDiamondCIplot.Rd

@@ -16,7 +16,7 @@ factorLoadingDiamondCIplot(
 }
 \arguments{
 \item{fa}{The object produced by the \code{\link[psych:fa]{psych::fa()}} function from the
-\link[psych:psych]{psych::psych} package. It is important that the \code{n.iter} argument
+\link[psych:00.psych-package]{psych::psych} package. It is important that the \code{n.iter} argument
 of \code{\link[psych:fa]{psych::fa()}} was set to a realistic number, because otherwise, no
 confidence intervals will be available.}
 

man/quietRemotesInstall.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/quietRemotesInstall.R
+\name{quietRemotesInstall}
+\alias{quietRemotesInstall}
+\alias{quietGitLabUpdate}
+\title{Quietly update a package from a remote repository}
+\usage{
+quietRemotesInstall(
+  x,
+  func,
+  unloadNamespace = TRUE,
+  dependencies = FALSE,
+  upgrade = FALSE,
+  quiet = TRUE,
+  errorInvisible = TRUE,
+  ...
+)
+
+quietGitLabUpdate(
+  x,
+  unloadNamespace = TRUE,
+  dependencies = FALSE,
+  upgrade = FALSE,
+  quiet = TRUE,
+  errorInvisible = TRUE,
+  ...
+)
+}
+\arguments{
+\item{x}{The repository name (e.g. "\code{r-packages/ufs}")}
+
+\item{func}{The \code{remotes} function to use}
+
+\item{unloadNamespace}{Whether to first unload the relevant namespace}
+
+\item{dependencies, upgrade}{Whether to install dependencies or upgrade}
+
+\item{quiet}{Whether to suppress messages and warnings}
+
+\item{errorInvisible}{Whether to suppress errors}
+
+\item{...}{Additional arguments are passed on to the \code{remotes} function}
+}
+\value{
+The result of the call to the \code{remotes} function
+}
+\description{
+Simple wrapper for \code{remotes} functions that fail gracefully (well, don't
+fail at all, just don't do what they're supposed to do) when there's no
+internet connection).
+}

public/404.html

@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">ufs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.0</span>
       </span>
     </div>
 
@@ -142,7 +142,7 @@ Content not found. Please use links in the navbar.
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>

public/articles/conceptual-independence-matrix.html

@@ -31,7 +31,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">ufs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.0</span>
       </span>
     </div>
 
@@ -83,7 +83,7 @@
       <h1 data-toc-skip>Conceptual Independence Matrix</h1>
                         <h4 class="author">Gjalt-Jorn Peters</h4>
             
-            <h4 class="date">2020-10-31</h4>
+            <h4 class="date">2020-11-03</h4>
       
       <small class="dont-index">Source: <a href="https://gitlab.com/r-packages/ufs/blob/master/vignettes/conceptual-independence-matrix.Rmd"><code>vignettes/conceptual-independence-matrix.Rmd</code></a></small>
       <div class="hidden name"><code>conceptual-independence-matrix.Rmd</code></div>
@@ -92,28 +92,29 @@
 
     
     
-<div class="sourceCode" id="cb1"><html><body><pre class="r">
+<div class="sourceCode" id="cb1"><pre class="downlit">
+
 <span class="co">### Load data from psych package</span>
-<span class="fu"><a href="https://rdrr.io/r/utils/data.html">data</a></span>(<span class="no">bfi</span>, <span class="kw">package</span><span class="kw">=</span> <span class="st">'psych'</span>);
+<span class="fu"><a href="https://rdrr.io/r/utils/data.html">data</a></span><span class="op">(</span><span class="va">bfi</span>, package<span class="op">=</span> <span class="st">'psych'</span><span class="op">)</span>;
 
 <span class="co">### Specify scales</span>
-<span class="no">bfiScales</span> <span class="kw">&lt;-</span>
-  <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="kw">Agreeableness</span>     <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"Agreeableness_item_"</span>, <span class="fl">1</span>:<span class="fl">5</span>),
-       <span class="kw">Conscientiousness</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"Conscientiousness_item_"</span>, <span class="fl">1</span>:<span class="fl">5</span>),
-       <span class="kw">Extraversion</span>      <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"Extraversion_item_"</span>, <span class="fl">1</span>:<span class="fl">5</span>),
-       <span class="kw">Neuroticism</span>       <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"Neuroticism_item_"</span>, <span class="fl">1</span>:<span class="fl">5</span>),
-       <span class="kw">Openness</span>          <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"Openness_item_"</span>, <span class="fl">1</span>:<span class="fl">5</span>));
+<span class="va">bfiScales</span> <span class="op">&lt;-</span>
+  <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>Agreeableness     <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"Agreeableness_item_"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span>,
+       Conscientiousness <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"Conscientiousness_item_"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span>,
+       Extraversion      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"Extraversion_item_"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span>,
+       Neuroticism       <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"Neuroticism_item_"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span>,
+       Openness          <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"Openness_item_"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span><span class="op">)</span>;
 
-<span class="fu"><a href="https://rdrr.io/r/base/names.html">names</a></span>(<span class="no">bfi</span>) <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/unlist.html">unlist</a></span>(<span class="no">bfiScales</span>),
-                <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">'gender'</span>, <span class="st">'education'</span>, <span class="st">'age'</span>));
+<span class="fu"><a href="https://rdrr.io/r/base/names.html">names</a></span><span class="op">(</span><span class="va">bfi</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/unlist.html">unlist</a></span><span class="op">(</span><span class="va">bfiScales</span><span class="op">)</span>,
+                <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">'gender'</span>, <span class="st">'education'</span>, <span class="st">'age'</span><span class="op">)</span><span class="op">)</span>;
 
 <span class="co">### Only select first two and the first three items to</span>
 <span class="co">### keep it quick; just pass the full 'bfiScales'</span>
 <span class="co">### object to run for all five the full scales</span>
-<span class="kw pkg">ufs</span><span class="kw ns">::</span><span class="fu"><a href="../reference/CIM.html">CIM</a></span>(<span class="no">bfi</span>,
-         <span class="kw">scales</span><span class="kw">=</span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html">lapply</a></span>(<span class="no">bfiScales</span>, <span class="no">head</span>, <span class="fl">3</span>)[<span class="fl">1</span>:<span class="fl">2</span>],
-         <span class="kw">n.iter</span><span class="kw">=</span><span class="fl">10</span>);
-<span class="co">#&gt; Loading required namespace: GPArotation</span></pre></body></html></div>
+<span class="fu">ufs</span><span class="fu">::</span><span class="fu"><a href="../reference/CIM.html">CIM</a></span><span class="op">(</span><span class="va">bfi</span>,
+         scales<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html">lapply</a></span><span class="op">(</span><span class="va">bfiScales</span>, <span class="va">head</span>, <span class="fl">3</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>,
+         n.iter<span class="op">=</span><span class="fl">10</span><span class="op">)</span>;
+<span class="co">#&gt; Loading required namespace: GPArotation</span></pre></div>
 <hr>
 <div class="conceptual-independence-matrix-start" style="display:block;clear:both;">
 
@@ -172,7 +173,7 @@
 <h3 class="hasAnchor">
 <a href="#conceptual-independence-of-agreeableness-and-conscientiousness" class="anchor"></a>Conceptual (in)dependence of Agreeableness and Conscientiousness</h3>
 <div class="figure">
-<img src="conceptual-independence-matrix_files/figure-html/1bba497af7_b1d3f2d4b4b2a944dc14bbfcaffa090a-1.png" alt="Factor loadings for Agreeableness and Conscientiousness" width="1344"><p class="caption">
+<img src="conceptual-independence-matrix_files/figure-html/1f692a2516_996508eb54fd6797b0c676d3770b67d2-1.png" alt="Factor loadings for Agreeableness and Conscientiousness" width="1344"><p class="caption">
 Factor loadings for Agreeableness and Conscientiousness
 </p>
 </div>
@@ -203,7 +204,7 @@ Factor loadings for Agreeableness and Conscientiousness
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>

public/articles/index.html

@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">ufs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.0</span>
       </span>
     </div>
 
@@ -141,7 +141,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>

public/authors.html

@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">ufs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.0</span>
       </span>
     </div>
 
@@ -145,7 +145,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>

public/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">ufs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.0</span>
       </span>
     </div>
 
@@ -100,9 +100,11 @@
 <h2 class="hasAnchor">
 <a href="#installation" class="anchor"></a>Installation</h2>
 <p>You can install the released version of <code>ufs</code> from <a href="https://CRAN.R-project.org">CRAN</a> with:</p>
-<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">'ufs'</span>);</pre></div>
+<div class="sourceCode" id="cb1"><pre class="downlit">
+<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">'ufs'</span><span class="op">)</span>;</pre></div>
 <p>You can install the development version of <code>ufs</code> from <a href="https://about.gitlab.com">GitLab</a> with:</p>
-<div class="sourceCode" id="cb2"><pre class="r"><span class="kw pkg">remotes</span><span class="kw ns">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_gitlab.html">install_gitlab</a></span>(<span class="st">'r-packages/ufs'</span>);</pre></div>
+<div class="sourceCode" id="cb2"><pre class="downlit">
+<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_gitlab.html">install_gitlab</a></span><span class="op">(</span><span class="st">'r-packages/ufs'</span><span class="op">)</span>;</pre></div>
 <p>(assuming you have <code>remotes</code> installed; otherwise, install that first using the <code><a href="https://rdrr.io/r/utils/install.packages.html">install.packages()</a></code> function)</p>
 </div>
 </div>
@@ -154,7 +156,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>

public/pkgdown.css

@@ -244,14 +244,14 @@ nav[data-toggle='toc'] .nav .nav > .active:focus > a {
 
 .ref-index th {font-weight: normal;}
 
-.ref-index td {vertical-align: top;}
+.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;}
+.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
 .ref-arguments .name {width: 20%;}
 .ref-arguments .desc {width: 80%;}
 

public/pkgdown.yml

 pandoc: 2.9.2.1
-pkgdown: 1.5.1
+pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
-  conceptual-independence-matrix: ../../../../../../B:/Data/R/ufs/vignettes/conceptual-independence-matrix.html
-last_built: 2020-10-31T10:06Z
+  conceptual-independence-matrix: conceptual-independence-matrix.html
+last_built: 2020-11-03T20:19Z
 

public/reference/A_VarghaDelaney.html

@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">ufs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.0</span>
       </span>
     </div>
 
@@ -129,13 +129,13 @@
     <p>Vargha &amp; Delaney's A</p>
     </div>
 
-    <pre class="usage"><span class='fu'>A_VarghaDelaney</span>(
-  <span class='no'>control</span>,
-  <span class='no'>experimental</span>,
-  <span class='kw'>bootstrap</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>conf.level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>,
-  <span class='kw'>warn</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
-)</pre>
+    <pre class="usage"><span class='fu'>A_VarghaDelaney</span><span class='op'>(</span>
+  <span class='va'>control</span>,
+  <span class='va'>experimental</span>,
+  bootstrap <span class='op'>=</span> <span class='cn'>NULL</span>,
+  conf.level <span class='op'>=</span> <span class='fl'>0.95</span>,
+  warn <span class='op'>=</span> <span class='cn'>FALSE</span>
+<span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -169,7 +169,8 @@ warnings, for example if ties are encountered.</p></td>
     <p>A numeric vector of length 1 with the A value, named 'A'.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='kw pkg'>ufs</span><span class='kw ns'>::</span><span class='fu'>A_VarghaDelaney</span>(<span class='fl'>1</span>:<span class='fl'>8</span>, <span class='fl'>3</span>:<span class='fl'>12</span>);</div><div class='output co'>#&gt;     A 
+    <pre class="examples"><div class='input'><span class='fu'>ufs</span><span class='fu'>::</span><span class='fu'>A_VarghaDelaney</span><span class='op'>(</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>8</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>12</span><span class='op'>)</span>;
+</div><div class='output co'>#&gt;     A 
 #&gt; 0.775 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -186,7 +187,7 @@ warnings, for example if ties are encountered.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>

public/reference/CIM.html

@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">ufs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.4.0</span>
       </span>
     </div>
 
@@ -129,46 +129,46 @@
     <p>Conceptual Independence Matrix</p>
     </div>
 
-    <pre class="usage"><span class='fu'>CIM</span>(
-  <span class='no'>data</span>,
-  <span class='no'>scales</span>,
-  <span class='kw'>conf.level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>,
-  <span class='kw'>colors</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"#440154FF"</span>, <span class='st'>"#7AD151FF"</span>),
-  <span class='kw'>outputFile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>outputWidth</span> <span class='kw'>=</span> <span class='fl'>100</span>,
-  <span class='kw'>outputHeight</span> <span class='kw'>=</span> <span class='fl'>100</span>,
-  <span class='kw'>outputUnits</span> <span class='kw'>=</span> <span class='st'>"cm"</span>,
-  <span class='kw'>faMethod</span> <span class='kw'>=</span> <span class='st'>"minres"</span>,
-  <span class='kw'>n.iter</span> <span class='kw'>=</span> <span class='fl'>100</span>,
-  <span class='kw'>n.repeatOnWarning</span>