Merge branch 'dev' into 'prod'

Forgot to push from dev

See merge request !6

DESCRIPTION

@@ -39,6 +39,7 @@ Suggests:
     bootES (>= 1.2),
     car (>= 3.0),
     careless (>= 1.1),
+    GGally (>= 1.4.0),
     jmvcore (>= 1.2),
     lavaan (>= 0.6),
     MBESS (>= 4.5.1),
@@ -50,7 +51,6 @@ Suggests:
 Imports: digest (>= 0.6.19),
          diptest (>= 0.75.7),
          dplyr (>= 0.7.6),
-         GGally (>= 1.4.0),
          ggplot2 (>= 2.2.1),
          ggrepel (>= 0.8),
          ggridges (>= 0.5.0),

NAMESPACE

@@ -136,6 +136,7 @@ export(ggEasyRidge)
 export(ggProportionPlot)
 export(ggSave)
 export(ggqq)
+export(heading)
 export(ifelseObj)
 export(insertFigureCaption)
 export(insertNumberedCaption)

R/ggBoxplot.R

@@ -142,6 +142,9 @@ ggBoxplot <- function(dat, y = NULL, x = NULL,
                       datF$outlier <- iqrOutlier(datF[, y]);
                       return(datF);
                     });
+
+
+
       dat$outlier <- ifelse(dat$outlier,
                             1:nrow(dat),
                             as.numeric(NA));

R/heading.R

+#' Print a heading
+#'
+#' This is just a convenience function to print a markdown or HTML heading at
+#' a given 'depth'.
+#'
+#' @param ... The heading text: pasted together with no separator.
+#' @param headingLevel The level of the heading; the default can be set
+#' with e.g. `ufs::opts$set(defaultHeadingLevel=1)`.
+#' @param output Whether to output to HTML ("`html`") or markdown (anything
+#' else).
+#' @param cat Whether to cat (print) the heading or just invisibly return it.
+#'
+#' @return The heading, invisibly.
+#' @export
+#'
+#' @examples heading("Hello ", "World", headingLevel=5);
+#' ### This produces: "\\n\\n##### Hello World\\n\\n"
+heading <- function(...,
+                    headingLevel = ufs::opts$get("defaultHeadingLevel"),
+                    output = "markdown",
+                    cat = TRUE) {
+  text <- paste0(..., collapse="");
+  if (output == "html") {
+    res <- paste0(
+      "\n\n<h", headingLevel, "> ",
+      text, "</h", headingLevel, ">\n\n"
+    );
+  } else {
+    res <- paste0(
+      "\n\n",
+      repStr("#", headingLevel), " ",
+      text, "\n\n"
+    );
+  }
+  if (cat) {
+    cat(res);
+  }
+  return(invisible(res));
+}

R/opts.R

@@ -206,6 +206,9 @@ opts$defaults <-
 
     ggBaseSize = 11,
 
+    ### Default heading level, for convenience
+    defaultHeadingLevel = 3,
+
     ### Where to print tables; 'console', 'viewer', and/or
     ### one or more filenames in existing directories
     tableOutput = c("console", "viewer"),

R/quietRemotesInstall.R

@@ -82,6 +82,12 @@ quietGitLabUpdate <- function(x,
                               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.");
+  }
+
   quietRemotesInstall(x,
                       func = "install_gitlab",
                       unloadNamespace = unloadNamespace,

R/regrInfluential.R

@@ -11,6 +11,8 @@
 #'
 #' @param formula The formule of the regression analysis.
 #' @param data The data to use for the analysis.
+#' @param createPlot Whether to create the scattermatrix (requires the `GGally`
+#' package to be installed).
 #' @param x Object to print.
 #' @param headingLevel The number of hash symbols to prepend to the heading.
 #' @param ... Additional arguments are passed on to the `regr` print function.
@@ -25,7 +27,18 @@
 #' regrInfluential(mpg ~ hp, mtcars);
 #'
 #' @export regrInfluential
-regrInfluential <- function(formula, data) {
+regrInfluential <- function(formula, data, createPlot = TRUE) {
+
+  if (createPlot) {
+    suppressMessages(suppressWarnings(
+      if (!requireNamespace("GGally")) {
+        stop("You need the {GGally} package to use this function!\n\n",
+             "You can install it with the following command:\n\n",
+             "install.packages('GGally');");
+      }
+    ));
+  }
+
   ### Create object for results and store input
   res <- list(input = as.list(environment()), intermediate = list(),
               output = list())

R/scatterMatrix.R

@@ -65,11 +65,13 @@ scatterMatrix <- function(dat, items=NULL,
                           conf.level = .95,
                           ...) {
 
-  suppressMessages(
+  suppressMessages(suppressWarnings(
     if (!requireNamespace("GGally")) {
-      stop("You need the {GGally} package to use this function!");
+      stop("You need the {GGally} package to use this function!\n\n",
+           "You can install it with the following command:\n\n",
+           "install.packages('GGally');");
     }
-  );
+  ));
 
   if (is.null(items)) {
     items <- names(dat);

man/heading.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/heading.R
+\name{heading}
+\alias{heading}
+\title{Print a heading}
+\usage{
+heading(
+  ...,
+  headingLevel = ufs::opts$get("defaultHeadingLevel"),
+  output = "markdown",
+  cat = TRUE
+)
+}
+\arguments{
+\item{...}{The heading text: pasted together with no separator.}
+
+\item{headingLevel}{The level of the heading; the default can be set
+with e.g. \code{ufs::opts$set(defaultHeadingLevel=1)}.}
+
+\item{output}{Whether to output to HTML ("\code{html}") or markdown (anything
+else).}
+
+\item{cat}{Whether to cat (print) the heading or just invisibly return it.}
+}
+\value{
+The heading, invisibly.
+}
+\description{
+This is just a convenience function to print a markdown or HTML heading at
+a given 'depth'.
+}
+\examples{
+heading("Hello ", "World", headingLevel=5);
+### This produces: "\\n\\n##### Hello World\\n\\n"
+}

man/regrInfluential.Rd

@@ -5,7 +5,7 @@
 \alias{print.regrInfluential}
 \title{Detecting influential cases in regression analyses}
 \usage{
-regrInfluential(formula, data)
+regrInfluential(formula, data, createPlot = TRUE)
 
 \method{print}{regrInfluential}(x, headingLevel = 3, ...)
 }
@@ -14,6 +14,9 @@ regrInfluential(formula, data)
 
 \item{data}{The data to use for the analysis.}
 
+\item{createPlot}{Whether to create the scattermatrix (requires the \code{GGally}
+package to be installed).}
+
 \item{x}{Object to print.}
 
 \item{headingLevel}{The number of hash symbols to prepend to the heading.}