fixed minor 'descr' bug

DESCRIPTION

 Package: ufs
 Type: Package
 Title: Quantitative Analysis Made Accessible
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: 
     c(
         person(given = "Gjalt-Jorn",

R/attenuate.d.R

@@ -12,7 +12,7 @@
 #' @references Bobko, P., Roth, P. L., & Bobko, C. (2001). Correcting
 #' the Effect Size of d for Range Restriction and Unreliability.
 #' *Organizational Research Methods, 4*(1), 46–61.
-#' \url{https://doi.org/10.1177/109442810141003}
+#' \doi{10.1177/109442810141003}
 #'
 #' @examples
 #' attenuate.d(.5, .8);

R/convert.d.to.nnc.R

@@ -25,7 +25,7 @@
 #' @seealso [behaviorchange::nnc()]
 #' @references Gruijters, S. L., & Peters, G. Y. (2019). Gauging the
 #' impact of behavior change interventions: A tutorial on the Numbers
-#' Needed to Treat. *PsyArXiv.* doi:[10.31234/osf.io/2bau7](https://doi.org/10.31234/osf.io/2bau7)
+#' Needed to Treat. *PsyArXiv.* \doi{10.31234/osf.io/2bau7}
 #' @keywords utilities
 #' @rdname nncConversion
 #' @examples

R/descr.R

@@ -43,7 +43,7 @@
 #' @author Gjalt-Jorn Peters
 #'
 #' Maintainer: Gjalt-Jorn Peters <gjalt-jorn@@userfriendlyscience.com>
-#' @seealso \code{\link{summary}}, [psych::describe()
+#' @seealso \code{\link{summary}}, [psych::describe()]
 #' @references Hartigan, J. A.; Hartigan, P. M. The Dip Test of Unimodality.
 #' Ann. Statist. 13 (1985), no. 1, 70--84. doi:10.1214/aos/1176346577.
 #' https://projecteuclid.org/euclid.aos/1176346577.
@@ -181,8 +181,36 @@ pander.descr <- function(x, headerPrefix = "",
 #' @method as.data.frame descr
 #' @rdname descriptives
 #' @export
-as.data.frame.descr <- function(x, row.names=NULL, optional=FALSE, ...) {
-  res <- as.data.frame(t(matrix(unlist(x)[c(1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18)])),
+as.data.frame.descr <- function(x, row.names=NULL,
+                                optional=FALSE, ...) {
+
+  if (!is.null(attr(x, 'digits'))) {
+    res <-
+      unlist(lapply(
+        x,
+        function(valList) {
+          return(
+            unlist(
+              lapply(
+                valList,
+                function(val) {
+                  if (is.numeric(val)) {
+                    return(round(val, attr(x, 'digits')));
+                  } else {
+                    return(val);
+                  }
+                }
+              )
+            )
+          );
+        }
+      ));
+  } else {
+    res <-
+      unlist(x);
+  }
+  res <- res[c(1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18)];
+  res <- as.data.frame(t(matrix(res)),
                        row.names=row.names,
                        optional=optional,
                        ...);

R/disattenuate.d.R

@@ -13,7 +13,7 @@
 #' @references Bobko, P., Roth, P. L., & Bobko, C. (2001). Correcting
 #' the Effect Size of d for Range Restriction and Unreliability.
 #' *Organizational Research Methods, 4*(1), 46–61.
-#' \url{https://doi.org/10.1177/109442810141003}
+#' \doi{10.1177/109442810141003}
 #'
 #' @examples
 #' disattenuate.d(.5, .8);

R/escapeRegex_(from_Hmisc).R

@@ -22,7 +22,7 @@
 #'
 #' Maintainer: Gjalt-Jorn Peters <gjalt-jorn@@userfriendlyscience.com>
 #' @seealso \code{\link[base]{grep}}, \code{Hmisc},
-#' \url{http://biostat.mc.vanderbilt.edu/wiki/Main/Hmisc},
+#' \url{https://hbiostat.org/R/Hmisc/},
 #' \url{https://github.com/harrelfe/Hmisc}
 #' @keywords manip character programming
 #' @examples

R/factorLoadingHeatmap.R

@@ -24,8 +24,13 @@
 #' arguments to [colorRamp()] (and therefore, to
 #' [col2rgb()]).
 #' @param labels The labels to use for the items (on the Y axis).
+#' @param showLoadings Whether to show the factor loadings or not.
+#' @param heatmap Whether to produce a heatmap or use diamond plots.
 #' @param theme The ggplot2 theme to use.
 #' @param sortAlphabetically Whether to sort the items alphabetically.
+#' @param digits Number of digits to round to.
+#' @param labs The labels to pass to ggplot2.
+#' @param themeArgs Additional theme arguments to pass to ggplot2.
 #' @param \dots Additional arguments will be passed to
 #' [ggDiamondLayer()]. This can be used to set, for example, the
 #' transparency (alpha value) of the diamonds to a lower value using e.g.

R/regrInfluential.R

@@ -43,7 +43,7 @@ regrInfluential <- function(formula, data, createPlot = TRUE) {
   res <- list(input = as.list(environment()), intermediate = list(),
               output = list())
   ### Get variables in formula
-  res$intermediate$variableNames <- all.vars(formula)
+  res$intermediate$variableNames <- all.vars(formula);
   ### Store temporary dataframe
   res$intermediate$dat <-
     data.frame(stats::na.omit(data[, res$intermediate$variableNames]));
@@ -56,20 +56,23 @@ regrInfluential <- function(formula, data, createPlot = TRUE) {
                                      indexOfInfluentiality = rowSums(res$intermediate$influence.measures$is.inf));
 
   ### Generate scattermatrix showing index fo influentiality
-  res$output$plot <-
-    GGally::ggpairs(data=res$intermediate$dat[,
-                                              c(res$intermediate$variableNames,
-                                                'indexOfInfluentiality')],
-            columns=1:length(res$intermediate$variableNames),
-            upper='blank',
-            lower=list(continuous=function(data, mapping, ...) {
-              res <- ggplot2::ggplot(data=data, mapping=mapping) +
-                ggplot2::geom_point(position="jitter") +
-                ggplot2::scale_colour_gradient(low='green', high='red') +
-                ggplot2::theme_bw();
-              return(res);
-            }),
-            mapping=ggplot2::aes_string(colour='indexOfInfluentiality'));
+  if (createPlot) {
+    res$output$plot <-
+      GGally::ggpairs(data=res$intermediate$dat[,
+                                                c(res$intermediate$variableNames,
+                                                  'indexOfInfluentiality')],
+              columns=1:length(res$intermediate$variableNames),
+              upper='blank',
+              lower=list(continuous=function(data, mapping, ...) {
+                res <- ggplot2::ggplot(data=data, mapping=mapping) +
+                  ggplot2::geom_point(position="jitter") +
+                  ggplot2::scale_colour_gradient(low='green', high='red') +
+                  ggplot2::theme_bw();
+                return(res);
+              }),
+              mapping=ggplot2::aes_string(colour='indexOfInfluentiality'));
+  }
+
   ### Conduct regression analyses for all levels of indexOfInfluentiality
   ### higher than 0
   res$output$regrObjects <- list();
@@ -96,7 +99,9 @@ print.regrInfluential <- function(x,
             repStr("#", headingLevel),
             " Influential cases:\n\n");
   print(x$output$dat.diagnostics);
-  print(x$output$plot);
+  if (!is.null(x$output$plot)) {
+    print(x$output$plot);
+  }
   ufs::cat0("\n",
             repStr("#", headingLevel + 1),
             " Regression analyses, repeated without influential cases\n\n");

R/scaleStructure.R

@@ -95,41 +95,41 @@
 #' @references Crutzen, R., & Peters, G.-J. Y. (2015). Scale quality: alpha is
 #' an inadequate estimate and factor-analytic evidence is needed first of all.
 #' \emph{Health Psychology Review.}
-#' \url{https://doi.org/10.1080/17437199.2015.1124240}
+#' \doi{10.1080/17437199.2015.1124240}
 #'
 #' Dunn, T. J., Baguley, T., & Brunsden, V. (2014). From alpha to omega: A
 #' practical solution to the pervasive problem of internal consistency
 #' estimation. \emph{British Journal of Psychology}, 105(3), 399-412.
-#' \url{https://doi.org/10.1111/bjop.12046}
+#' \doi{10.1111/bjop.12046}
 #'
 #' Eisinga, R., Grotenhuis, M. Te, & Pelzer, B. (2013). The reliability of a
 #' two-item scale: Pearson, Cronbach, or Spearman-Brown? \emph{International
 #' Journal of Public Health}, 58(4), 637-42.
-#' \url{https://doi.org/10.1007/s00038-012-0416-3}
+#' \doi{10.1007/s00038-012-0416-3}
 #'
 #' Gadermann, A. M., Guhn, M., Zumbo, B. D., & Columbia, B. (2012). Estimating
 #' ordinal reliability for Likert-type and ordinal item response data: A
 #' conceptual, empirical, and practical guide. \emph{Practical Assessment,
-#' Research & Evaluation}, 17(3), 1-12. \url{https://doi.org/10.7275/n560-j767}
+#' Research & Evaluation}, 17(3), 1-12. \doi{10.7275/n560-j767}
 #'
 #' Peters, G.-J. Y. (2014). The alpha and the omega of scale reliability and
 #' validity: why and how to abandon Cronbach's alpha and the route towards more
 #' comprehensive assessment of scale quality. \emph{European Health
 #' Psychologist}, 16(2), 56-69.
-#' \url{https://doi.org/10.31234/osf.io/h47fv}
+#' \doi{10.31234/osf.io/h47fv}
 #'
 #' Revelle, W., & Zinbarg, R. E. (2009). Coefficients Alpha, Beta, Omega, and
 #' the glb: Comments on Sijtsma. \emph{Psychometrika}, 74(1), 145-154.
-#' \url{https://doi.org/10.1007/s11336-008-9102-z}
+#' \doi{10.1007/s11336-008-9102-z}
 #'
 #' Sijtsma, K. (2009). On the Use, the Misuse, and the Very Limited Usefulness
 #' of Cronbach's Alpha. \emph{Psychometrika}, 74(1), 107-120.
-#' \url{https://doi.org/10.1007/s11336-008-9101-0}
+#' \doi{10.1007/s11336-008-9101-0}
 #'
 #' Zinbarg, R. E., Revelle, W., Yovel, I., & Li, W. (2005). Cronbach's alpha,
 #' Revelle's beta and McDonald's omega H: Their relations with each other and
 #' two alternative conceptualizations of reliability. \emph{Psychometrika},
-#' 70(1), 123-133. \url{https://doi.org/10.1007/s11336-003-0974-7}
+#' 70(1), 123-133. \doi{10.1007/s11336-003-0974-7}
 #'
 #' @keywords utilities univar
 #' @rdname scaleStructure

README.Rmd

@@ -61,7 +61,7 @@ install.packages('", packagename, "');
 ```"));
 ```
 
-You can install the development version of ``r packagename`` from [GitLab](https://gitlab.com) with:
+You can install the development version of ``r packagename`` from [GitLab](https://about.gitlab.com) with:
 
 ```{r echo=FALSE, comment="", results="asis"}
 cat(paste0("``` r

README.md

@@ -30,7 +30,7 @@ install.packages('ufs');
 ```
 
 You can install the development version of `ufs` from
-[GitLab](https://gitlab.com) with:
+[GitLab](https://about.gitlab.com) with:
 
 ``` r
 remotes::install_gitlab('r-packages/ufs');

man/attenuate.d.Rd

@@ -25,7 +25,7 @@ attenuate.d(.5, .8);
 Bobko, P., Roth, P. L., & Bobko, C. (2001). Correcting
 the Effect Size of d for Range Restriction and Unreliability.
 \emph{Organizational Research Methods, 4}(1), 46–61.
-\url{https://doi.org/10.1177/109442810141003}
+\doi{10.1177/109442810141003}
 }
 \author{
 Gjalt-Jorn Peters & Stefan Gruijters

man/disattenuate.d.Rd

@@ -26,7 +26,7 @@ disattenuate.d(.5, .8);
 Bobko, P., Roth, P. L., & Bobko, C. (2001). Correcting
 the Effect Size of d for Range Restriction and Unreliability.
 \emph{Organizational Research Methods, 4}(1), 46–61.
-\url{https://doi.org/10.1177/109442810141003}
+\doi{10.1177/109442810141003}
 }
 \author{
 Gjalt-Jorn Peters & Stefan Gruijters

man/escapeRegex.Rd

@@ -41,7 +41,7 @@ if(!any(grep(escapeRegex(string), string))) {
 }
 \seealso{
 \code{\link[base]{grep}}, \code{Hmisc},
-\url{http://biostat.mc.vanderbilt.edu/wiki/Main/Hmisc},
+\url{https://hbiostat.org/R/Hmisc/},
 \url{https://github.com/harrelfe/Hmisc}
 }
 \author{

man/factorLoadingHeatmap.Rd

@@ -37,10 +37,20 @@ arguments to \code{\link[=colorRamp]{colorRamp()}} (and therefore, to
 
 \item{labels}{The labels to use for the items (on the Y axis).}
 
+\item{showLoadings}{Whether to show the factor loadings or not.}
+
+\item{heatmap}{Whether to produce a heatmap or use diamond plots.}
+
 \item{theme}{The ggplot2 theme to use.}
 
 \item{sortAlphabetically}{Whether to sort the items alphabetically.}
 
+\item{digits}{Number of digits to round to.}
+
+\item{labs}{The labels to pass to ggplot2.}
+
+\item{themeArgs}{Additional theme arguments to pass to ggplot2.}
+
 \item{\dots}{Additional arguments will be passed to
 \code{\link[=ggDiamondLayer]{ggDiamondLayer()}}. This can be used to set, for example, the
 transparency (alpha value) of the diamonds to a lower value using e.g.

man/nncConversion.Rd

@@ -77,7 +77,7 @@ convert.d.to.nnc(d=.5, cer=.25);
 \references{
 Gruijters, S. L., & Peters, G. Y. (2019). Gauging the
 impact of behavior change interventions: A tutorial on the Numbers
-Needed to Treat. \emph{PsyArXiv.} doi:\href{https://doi.org/10.31234/osf.io/2bau7}{10.31234/osf.io/2bau7}
+Needed to Treat. \emph{PsyArXiv.} \doi{10.31234/osf.io/2bau7}
 }
 \seealso{
 \code{\link[behaviorchange:nnc]{behaviorchange::nnc()}}

man/scaleStructure.Rd

@@ -196,41 +196,41 @@ scaleStructure(ordinalExampleData, ci=FALSE);
 Crutzen, R., & Peters, G.-J. Y. (2015). Scale quality: alpha is
 an inadequate estimate and factor-analytic evidence is needed first of all.
 \emph{Health Psychology Review.}
-\url{https://doi.org/10.1080/17437199.2015.1124240}
+\doi{10.1080/17437199.2015.1124240}
 
 Dunn, T. J., Baguley, T., & Brunsden, V. (2014). From alpha to omega: A
 practical solution to the pervasive problem of internal consistency
 estimation. \emph{British Journal of Psychology}, 105(3), 399-412.
-\url{https://doi.org/10.1111/bjop.12046}
+\doi{10.1111/bjop.12046}
 
 Eisinga, R., Grotenhuis, M. Te, & Pelzer, B. (2013). The reliability of a
 two-item scale: Pearson, Cronbach, or Spearman-Brown? \emph{International
 Journal of Public Health}, 58(4), 637-42.
-\url{https://doi.org/10.1007/s00038-012-0416-3}
+\doi{10.1007/s00038-012-0416-3}
 
 Gadermann, A. M., Guhn, M., Zumbo, B. D., & Columbia, B. (2012). Estimating
 ordinal reliability for Likert-type and ordinal item response data: A
 conceptual, empirical, and practical guide. \emph{Practical Assessment,
-Research & Evaluation}, 17(3), 1-12. \url{https://doi.org/10.7275/n560-j767}
+Research & Evaluation}, 17(3), 1-12. \doi{10.7275/n560-j767}
 
 Peters, G.-J. Y. (2014). The alpha and the omega of scale reliability and
 validity: why and how to abandon Cronbach's alpha and the route towards more
 comprehensive assessment of scale quality. \emph{European Health
 Psychologist}, 16(2), 56-69.
-\url{https://doi.org/10.31234/osf.io/h47fv}
+\doi{10.31234/osf.io/h47fv}
 
 Revelle, W., & Zinbarg, R. E. (2009). Coefficients Alpha, Beta, Omega, and
 the glb: Comments on Sijtsma. \emph{Psychometrika}, 74(1), 145-154.
-\url{https://doi.org/10.1007/s11336-008-9102-z}
+\doi{10.1007/s11336-008-9102-z}
 
 Sijtsma, K. (2009). On the Use, the Misuse, and the Very Limited Usefulness
 of Cronbach's Alpha. \emph{Psychometrika}, 74(1), 107-120.
-\url{https://doi.org/10.1007/s11336-008-9101-0}
+\doi{10.1007/s11336-008-9101-0}
 
 Zinbarg, R. E., Revelle, W., Yovel, I., & Li, W. (2005). Cronbach's alpha,
 Revelle's beta and McDonald's omega H: Their relations with each other and
 two alternative conceptualizations of reliability. \emph{Psychometrika},
-70(1), 123-133. \url{https://doi.org/10.1007/s11336-003-0974-7}
+70(1), 123-133. \doi{10.1007/s11336-003-0974-7}
 }
 \seealso{
 \code{\link[psych:omega]{psych::omega()}}, \code{\link[psych:alpha]{psych::alpha()}}, and