diff --git a/DESCRIPTION b/DESCRIPTION
index 6a535a2ed159df5c660a02d46eebfce3003d1dc0..896a2ae5135dff346d8a2595720035cd7f516310 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: ufs
Type: Package
Title: A Collection of Utilities
-Version: 0.5.4
+Version: 0.5.5
Authors@R:
c(
person(given = "Gjalt-Jorn",
@@ -33,7 +33,7 @@ URL: https://r-packages.gitlab.io/ufs
BugReports: https://gitlab.com/r-packages/ufs/-/issues
Encoding: UTF-8
LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
Depends: R (>= 3.0.0)
Suggests:
bootES (>= 1.2),
diff --git a/R/ggSave.R b/R/ggSave.R
index f8cad0d3c11e770f88a92192418b68974b09162f..a994d022de557e516b284fa274330438eb11f981 100644
--- a/R/ggSave.R
+++ b/R/ggSave.R
@@ -13,6 +13,11 @@
#' @param type An additional arguments for the graphic device.
#' @param device The graphic device; is inferred from the file if not specified.
#' @param bg The background (e.g. 'white').
+#' @param preventType Whether to prevent passing a value for the `type` argument
+#' to [ggplot2::ggsave()]. This is prevented by default since {gglot} switched
+#' to using the ragg device by default, resulting in throwing a warning
+#' ("Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments")
+#' if something if passed for 'type'.
#' @param ... Any additional arguments are passed on to [ggplot2::ggsave()].
#'
#' @return The plot, invisibly.
@@ -25,7 +30,9 @@ ggSave <- function(file=NULL, plot = ggplot2::last_plot(),
height=ufs::opts$get("ggSaveFigHeight"),
units=ufs::opts$get("ggSaveUnits"),
dpi=ufs::opts$get("ggSaveDPI"),
- device=NULL, type=NULL, bg="transparent", ...) {
+ device=NULL, type=NULL, bg="transparent",
+ preventType = ufs::opts$get("ggSavePreventType"),
+ ...) {
extension <-
gsub("^.*\\.(.+)$", "\\1", file);
@@ -91,9 +98,18 @@ ggSave <- function(file=NULL, plot = ggplot2::last_plot(),
}
if (device[i]=="png") {
- ggplot2::ggsave(file=file[i], plot=plot, device=device[i],
- height=height[i], width=width[i], units=units[i],
- dpi=dpi[i], type=type[i], bg = bg[i], ...);
+ if (preventType) {
+ ### Preventing type by default since gglot uses the ragg device,
+ ### otherwise it throws
+ ### "Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments"
+ ggplot2::ggsave(file=file[i], plot=plot, device=device[i],
+ height=height[i], width=width[i], units=units[i],
+ dpi=dpi[i], bg = bg[i], ...);
+ } else{
+ ggplot2::ggsave(file=file[i], plot=plot, device=device[i],
+ height=height[i], width=width[i], units=units[i],
+ dpi=dpi[i], type=type[i], bg = bg[i], ...);
+ }
} else if (device[i]=="svg") {
### The 'svg' device doesn't have a 'type' argument
ggplot2::ggsave(file=file[i], plot=plot, device=device[i],
@@ -105,9 +121,18 @@ ggSave <- function(file=NULL, plot = ggplot2::last_plot(),
height=height[i], width=width[i], units=units[i],
dpi=dpi[i], bg = bg[i], ...);
} else {
- ggplot2::ggsave(file=file[i], plot=plot, device=device[i],
- height=height[i], width=width[i], units=units[i],
- dpi=dpi[i], type=type[i], bg = bg[i], ...);
+ if (preventType) {
+ ### Preventing type by default since gglot uses the ragg device,
+ ### otherwise it throws
+ ### "Warning: Using ragg device as default. Ignoring `type` and `antialias` arguments"
+ ggplot2::ggsave(file=file[i], plot=plot, device=device[i],
+ height=height[i], width=width[i], units=units[i],
+ dpi=dpi[i], bg = bg[i], ...);
+ } else {
+ ggplot2::ggsave(file=file[i], plot=plot, device=device[i],
+ height=height[i], width=width[i], units=units[i],
+ dpi=dpi[i], type=type[i], bg = bg[i], ...);
+ }
}
}
diff --git a/R/opts.R b/R/opts.R
index f8f70a61ff1400d52b09ed55f27509475faf02ec..5f9b85aa361a26aad75ec6e85d36eb509f5d1722 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -240,6 +240,8 @@ opts$defaults <-
knitAndSave.catPlot = FALSE,
knitFig.catPlot = FALSE,
+ ggSavePreventType = TRUE,
+
### Careless options
carelessDict = list(c("_chr", ""),
c("irv", "IRV "),
diff --git a/R/parallelSubscales.R b/R/parallelSubscales.R
index 4cf0a66cb8ef9e2ba8fa8d678b78855770fe20b5..7a0523ea2d5c4dc5c585c445b5cea66cd71c172d 100644
--- a/R/parallelSubscales.R
+++ b/R/parallelSubscales.R
@@ -10,7 +10,6 @@
#' and when printed shows the descriptives; or, for the print function, `x`,
#' invisibly.
#'
-#' @examples
#' @rdname parallelSubscales
#' @export
parallelSubscales <- function(dat, convertToNumeric = TRUE) {
diff --git a/R/scaleStructure.R b/R/scaleStructure.R
index b32dbfa5c3ea5af9104512c21baa6757e13ea5c8..88bee2eb1f39d7207bc7589810ded97ec5d47080 100644
--- a/R/scaleStructure.R
+++ b/R/scaleStructure.R
@@ -152,12 +152,15 @@
#'
#' ### Use all items (don't order confidence intervals to save time
#' ### during automated testing of the example)
-#' scaleStructure(dat=exampleData, ci=FALSE);
+#' ufs::scaleStructure(dat=exampleData, ci=FALSE);
#'
#' ### Use a selection of three variables (without confidence
#' ### intervals to save time
-#' scaleStructure(dat=exampleData, items=c('t0_item2', 't0_item3', 't0_item4'),
-#' ci=FALSE);
+#' ufs::scaleStructure(
+#' dat=exampleData,
+#' items=c('t0_item2', 't0_item3', 't0_item4'),
+#' ci=FALSE
+#' );
#'
#' ### Make the items resemble an ordered categorical (ordinal) scale
#' ordinalExampleData <- data.frame(apply(exampleData, 2, cut,
@@ -165,7 +168,7 @@
#' labels=as.character(1:5)));
#'
#' ### Now we also get estimates assuming the ordinal measurement level
-#' scaleStructure(ordinalExampleData, ci=FALSE);
+#' ufs::scaleStructure(ordinalExampleData, ci=FALSE);
#' }
#'
#'
@@ -294,29 +297,50 @@ scaleStructure <- scaleReliability <- function (data=NULL, items = 'all', digits
res$output$coefficientH <- 1 / (1 + res$intermediate$minorDenom);
### GLB
- suppressWarnings(res$intermediate$glb <-
- psych::glb(res$input$dat));
- res$output$glb <- res$intermediate$glb$glb.max;
- res$output$dat$glb <- res$intermediate$glb$glb.max;
+ tryCatch(
+ suppressWarnings(res$intermediate$glb <-
+ psych::glb(res$input$dat)),
+ error = function(e) {
+ warning("\n\nWhen calling `psych::glb`, it threw an ",
+ "error, specifically:\n\n", e,
+ "\nThis prevents me from providing an ",
+ "estimate for the Greatest Lower Bound (GLB). I am setting ",
+ "it to NA.");
+ }
+ )
+ if (is.null(res$intermediate$glb)) {
+ res$intermediate$glb <- list(glb.max = NA);
+ res$output$glb <- NA;
+ res$output$dat$glb <- NA;
+ } else {
+ res$output$glb <- res$intermediate$glb$glb.max;
+ res$output$dat$glb <- res$intermediate$glb$glb.max;
+ }
### Omega
if (requireNamespace("psych", quietly = TRUE)) {
- invisible(
- utils::capture.output(
- suppressMessages(
- suppressWarnings(
- res$intermediate$omega.psych <-
- psych::omega(res$input$dat,
- nfactors = omega.psych_nfactors,
- flip = omega.psych_flip,
- plot = FALSE)
+ if (requireNamespace("GPArotation", quietly = TRUE)) {
+ invisible(
+ utils::capture.output(
+ suppressMessages(
+ suppressWarnings(
+ res$intermediate$omega.psych <-
+ psych::omega(res$input$dat,
+ nfactors = omega.psych_nfactors,
+ flip = omega.psych_flip,
+ plot = FALSE)
+ )
)
)
- )
- );
- res$output$omega.psych <- res$intermediate$omega.psych$omega.tot;
- res$output$dat$omega.psych.tot <- res$output$omega.psych;
- res$output$dat$omega.psych.h <- res$intermediate$omega.psych$omega_h;
+ );
+ res$output$omega.psych <- res$intermediate$omega.psych$omega.tot;
+ res$output$dat$omega.psych.tot <- res$output$omega.psych;
+ res$output$dat$omega.psych.h <- res$intermediate$omega.psych$omega_h;
+ } else {
+ stop("\n\nIf you want to compute omega, you need the {psych} package, ",
+ "which in turn needs the {GPArotation} package. You can ",
+ "install it with:\n\ninstall.packages('GPArotation');\n\n");
+ }
}
if (requireNamespace("MBESS", quietly = TRUE)) {
res$intermediate$omega <-
diff --git a/man/aipedjmv.Rd b/man/aipedjmv.Rd
index 0a908e264f5c46dd4a3e24ab78420535b1aa787e..360a575f5bd9815c72876a4314da6595b50d0eb4 100644
--- a/man/aipedjmv.Rd
+++ b/man/aipedjmv.Rd
@@ -1,10 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/aipedjmv.h.R
+\docType{data}
\name{aipedjmv}
\alias{aipedjmv}
\title{Sample size for accuracy: d}
+\format{
+An object of class \code{NULL} of length 0.
+}
\usage{
-aipedjmv(d = 0.5, w = 0.1, conf.level = 95)
+aipedjmv
}
\arguments{
\item{d}{.}
@@ -23,3 +27,4 @@ A results object containing:
\description{
Sample size for accuracy: d
}
+\keyword{datasets}
diff --git a/man/aiperjmv.Rd b/man/aiperjmv.Rd
index 35782af038e8bfaf9963bcbf3f1b22a33a7ca021..b4912e48a85cb4c77aeb0947fab3962680286084 100644
--- a/man/aiperjmv.Rd
+++ b/man/aiperjmv.Rd
@@ -1,10 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/aiperjmv.h.R
+\docType{data}
\name{aiperjmv}
\alias{aiperjmv}
\title{Sample size for accuracy: r}
+\format{
+An object of class \code{NULL} of length 0.
+}
\usage{
-aiperjmv(r = 0.3, w = 0.1, conf.level = 95)
+aiperjmv
}
\arguments{
\item{r}{.}
@@ -23,3 +27,4 @@ A results object containing:
\description{
Sample size for accuracy: r
}
+\keyword{datasets}
diff --git a/man/confintdjmv.Rd b/man/confintdjmv.Rd
index b0b46a532fbd43b2ee2a5f5992d16ad11fc8b550..2b8d7703a84ae7111f68769628ae58359fb364b7 100644
--- a/man/confintdjmv.Rd
+++ b/man/confintdjmv.Rd
@@ -1,10 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/confintdjmv.h.R
+\docType{data}
\name{confintdjmv}
\alias{confintdjmv}
\title{Effect Size Confidence Interval: Cohens's d}
+\format{
+An object of class \code{NULL} of length 0.
+}
\usage{
-confintdjmv(d = 0.5, n = 128, conf.level = 95)
+confintdjmv
}
\arguments{
\item{d}{.}
@@ -23,3 +27,4 @@ A results object containing:
\description{
Effect Size Confidence Interval: Cohens's d
}
+\keyword{datasets}
diff --git a/man/confintrjmv.Rd b/man/confintrjmv.Rd
index c3003c54417395cda1a76e892f75d76c4a5fb9d8..6423060609ab39815e5fa758dc45ef2cff422b60 100644
--- a/man/confintrjmv.Rd
+++ b/man/confintrjmv.Rd
@@ -1,10 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/confintrjmv.h.R
+\docType{data}
\name{confintrjmv}
\alias{confintrjmv}
\title{Effect Size Confidence Interval: Pearson's r}
+\format{
+An object of class \code{NULL} of length 0.
+}
\usage{
-confintrjmv(r = 0.3, N = 400, conf.level = 95)
+confintrjmv
}
\arguments{
\item{r}{.}
@@ -23,3 +27,4 @@ A results object containing:
\description{
Effect Size Confidence Interval: Pearson's r
}
+\keyword{datasets}
diff --git a/man/descriptives.Rd b/man/descriptives.Rd
index 80ab2e608262af8f949dfe8103e080e8ccaed304..09055323d1f758169507d7b05aa495ac4f364b5f 100644
--- a/man/descriptives.Rd
+++ b/man/descriptives.Rd
@@ -14,8 +14,7 @@ descr(
x,
digits = 4,
errorOnFactor = FALSE,
- include = c("central tendency", "spread", "range", "distribution shape",
- "sample size"),
+ include = c("central tendency", "spread", "range", "distribution shape", "sample size"),
maxModes = 1,
t = FALSE,
conf.level = 0.95,
@@ -26,8 +25,7 @@ descr(
x,
digits = 4,
errorOnFactor = FALSE,
- include = c("central tendency", "spread", "range", "distribution shape",
- "sample size"),
+ include = c("central tendency", "spread", "range", "distribution shape", "sample size"),
maxModes = 1,
t = FALSE,
conf.level = 0.95,
diff --git a/man/ggSave.Rd b/man/ggSave.Rd
index 8c3baadfc504f094cf48e78bbbebf081b0cf2803..b90939b196a0b242a8e59f8c77e30e38c143bd04 100644
--- a/man/ggSave.Rd
+++ b/man/ggSave.Rd
@@ -14,6 +14,7 @@ ggSave(
device = NULL,
type = NULL,
bg = "transparent",
+ preventType = ufs::opts$get("ggSavePreventType"),
...
)
}
@@ -34,6 +35,12 @@ ggSave(
\item{bg}{The background (e.g. 'white').}
+\item{preventType}{Whether to prevent passing a value for the \code{type} argument
+to \code{\link[ggplot2:ggsave]{ggplot2::ggsave()}}. This is prevented by default since {gglot} switched
+to using the ragg device by default, resulting in throwing a warning
+("Warning: Using ragg device as default. Ignoring \code{type} and \code{antialias} arguments")
+if something if passed for 'type'.}
+
\item{...}{Any additional arguments are passed on to \code{\link[ggplot2:ggsave]{ggplot2::ggsave()}}.}
}
\value{
diff --git a/man/meansDiamondPlotjmv.Rd b/man/meansDiamondPlotjmv.Rd
index a794313fbee10301bd56039e556bbd6e97b6fbc7..a8523ce9c27a392e8986a395e3427d6abc9c165f 100644
--- a/man/meansDiamondPlotjmv.Rd
+++ b/man/meansDiamondPlotjmv.Rd
@@ -1,10 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/meansdiamondplotjmv.h.R
+\docType{data}
\name{meansDiamondPlotjmv}
\alias{meansDiamondPlotjmv}
\title{Diamond plot: means}
+\format{
+An object of class \code{NULL} of length 0.
+}
\usage{
-meansDiamondPlotjmv(data, items, conf.level = 95, showData = TRUE)
+meansDiamondPlotjmv
}
\arguments{
\item{data}{.}
@@ -25,3 +29,4 @@ A results object containing:
\description{
Diamond plot: means
}
+\keyword{datasets}
diff --git a/man/multiResponsejmv.Rd b/man/multiResponsejmv.Rd
index 7a003245c3a1a0c02d6360cf682f35b0eccb3c71..f2bb75ea01275c485ea9739a9ea1449772577675 100644
--- a/man/multiResponsejmv.Rd
+++ b/man/multiResponsejmv.Rd
@@ -1,10 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/multiresponsejmv.h.R
+\docType{data}
\name{multiResponsejmv}
\alias{multiResponsejmv}
\title{Multi Response}
+\format{
+An object of class \code{NULL} of length 0.
+}
\usage{
-multiResponsejmv(data, items, endorsedOption = 1)
+multiResponsejmv
}
\arguments{
\item{data}{.}
@@ -28,3 +32,4 @@ Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.f
\description{
Multi Response
}
+\keyword{datasets}
diff --git a/man/scaleStructure.Rd b/man/scaleStructure.Rd
index db78339ad453979950108fc8055861508949a435..82e293c97b3c8ec30b441ed77c6560cee38bcb30 100644
--- a/man/scaleStructure.Rd
+++ b/man/scaleStructure.Rd
@@ -174,12 +174,15 @@ exampleData <- testRetestSimData[2:6];
### Use all items (don't order confidence intervals to save time
### during automated testing of the example)
-scaleStructure(dat=exampleData, ci=FALSE);
+ufs::scaleStructure(dat=exampleData, ci=FALSE);
### Use a selection of three variables (without confidence
### intervals to save time
-scaleStructure(dat=exampleData, items=c('t0_item2', 't0_item3', 't0_item4'),
- ci=FALSE);
+ufs::scaleStructure(
+ dat=exampleData,
+ items=c('t0_item2', 't0_item3', 't0_item4'),
+ ci=FALSE
+);
### Make the items resemble an ordered categorical (ordinal) scale
ordinalExampleData <- data.frame(apply(exampleData, 2, cut,
@@ -187,7 +190,7 @@ ordinalExampleData <- data.frame(apply(exampleData, 2, cut,
labels=as.character(1:5)));
### Now we also get estimates assuming the ordinal measurement level
-scaleStructure(ordinalExampleData, ci=FALSE);
+ufs::scaleStructure(ordinalExampleData, ci=FALSE);
}
diff --git a/man/testRetestReliability.Rd b/man/testRetestReliability.Rd
index 9391dbeee1d8976a02b7c3f6867800325d30ee9d..23435ea16e9df9fc08b711b422c7330b91f6e9b3 100644
--- a/man/testRetestReliability.Rd
+++ b/man/testRetestReliability.Rd
@@ -52,6 +52,10 @@ order of the items at each measurement moment is the same.}
vectors in the dataframes to numeric.}
\item{digits}{Number of digits to show when printing the output}
+
+\item{x}{The object to print}
+
+\item{...}{Passed on to the print function}
}
\value{
An object with the input and several output variables. Most notably: