Merge pull request #971 from strengejacke/strengejacke/issue970

Namespace clash with new ggplot2 version

Author: strengejacke

DESCRIPTION

@@ -2,7 +2,7 @@ Package: sjPlot
 Type: Package
 Encoding: UTF-8
 Title: Data Visualization for Statistics in Social Science
-Version: 2.8.17
+Version: 2.9.0
 Authors@R: c(
     person("Daniel", "Lüdecke", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8895-3206")),
     person("Alexander", "Bartel", role = "ctb", comment = c(ORCID = "0000-0002-1280-6138")),
@@ -21,7 +21,7 @@ Description: Collection of plotting and table output functions for data
     labelled data.
 License: GPL-3
 Depends:
-    R (>= 3.6)
+    R (>= 4.1)
 Imports:
     graphics,
     grDevices,
@@ -34,7 +34,6 @@ Imports:
     ggplot2 (>= 3.2.0),
     knitr,
     insight,
-    MASS,
     parameters,
     performance,
     purrr,
@@ -59,6 +58,7 @@ Suggests:
     ggridges,
     httr,
     lme4,
+    MASS,
     nFactors,
     pscl,
     psych,
@@ -73,3 +73,4 @@ URL: https://strengejacke.github.io/sjPlot/
 BugReports: https://github.com/strengejacke/sjPlot/issues
 RoxygenNote: 7.3.2
 VignetteBuilder: knitr
+Remotes: easystats/performance, easystats/parameters

NAMESPACE

@@ -30,7 +30,6 @@ export(plot_frq)
 export(plot_gpt)
 export(plot_grid)
 export(plot_grpfrq)
-export(plot_kfold_cv)
 export(plot_likert)
 export(plot_model)
 export(plot_models)
@@ -43,9 +42,7 @@ export(scale_color_sjplot)
 export(scale_fill_sjplot)
 export(set_theme)
 export(show_sjplot_pals)
-export(sjp.aov1)
 export(sjp.chi2)
-export(sjp.corr)
 export(sjp.poly)
 export(sjplot)
 export(sjplot_pal)
@@ -66,124 +63,8 @@ export(theme_blank)
 export(theme_sjplot)
 export(theme_sjplot2)
 export(view_df)
-import(ggplot2)
-importFrom(dplyr,"%>%")
-importFrom(dplyr,arrange)
-importFrom(dplyr,bind_rows)
-importFrom(dplyr,case_when)
-importFrom(dplyr,filter)
-importFrom(dplyr,group_by)
-importFrom(dplyr,group_modify)
-importFrom(dplyr,group_vars)
-importFrom(dplyr,if_else)
-importFrom(dplyr,mutate)
-importFrom(dplyr,n_distinct)
-importFrom(dplyr,select)
-importFrom(dplyr,slice)
-importFrom(dplyr,summarize)
-importFrom(ggeffects,ggeffect)
-importFrom(ggeffects,ggpredict)
-importFrom(grDevices,axisTicks)
-importFrom(grDevices,cm)
-importFrom(grDevices,colorRampPalette)
-importFrom(grDevices,dev.off)
-importFrom(grDevices,jpeg)
-importFrom(grDevices,png)
-importFrom(grDevices,rgb)
-importFrom(grDevices,svg)
-importFrom(grDevices,tiff)
-importFrom(graphics,plot)
-importFrom(insight,has_intercept)
-importFrom(insight,is_multivariate)
-importFrom(insight,model_info)
 importFrom(knitr,asis_output)
 importFrom(knitr,knit_print)
-importFrom(performance,cronbachs_alpha)
-importFrom(performance,performance_aic)
-importFrom(performance,performance_aicc)
-importFrom(purrr,as_vector)
-importFrom(purrr,flatten_chr)
-importFrom(purrr,map)
-importFrom(purrr,map_chr)
-importFrom(purrr,map_dbl)
-importFrom(purrr,map_df)
-importFrom(purrr,map_if)
-importFrom(purrr,map_lgl)
-importFrom(purrr,pmap)
 importFrom(rlang,.data)
 importFrom(rlang,enquo)
 importFrom(rlang,quo_name)
-importFrom(scales,brewer_pal)
-importFrom(scales,grey_pal)
-importFrom(scales,percent)
-importFrom(sjlabelled,copy_labels)
-importFrom(sjlabelled,drop_labels)
-importFrom(sjlabelled,get_label)
-importFrom(sjlabelled,get_labels)
-importFrom(sjlabelled,get_values)
-importFrom(sjlabelled,set_labels)
-importFrom(sjmisc,add_variables)
-importFrom(sjmisc,frq)
-importFrom(sjmisc,group_labels)
-importFrom(sjmisc,group_var)
-importFrom(sjmisc,is_empty)
-importFrom(sjmisc,is_even)
-importFrom(sjmisc,is_float)
-importFrom(sjmisc,is_num_fac)
-importFrom(sjmisc,to_value)
-importFrom(sjmisc,trim)
-importFrom(sjmisc,var_type)
-importFrom(sjmisc,word_wrap)
-importFrom(sjstats,cramer)
-importFrom(sjstats,crosstable_statistics)
-importFrom(sjstats,phi)
-importFrom(sjstats,table_values)
-importFrom(stats,aov)
-importFrom(stats,binomial)
-importFrom(stats,chisq.test)
-importFrom(stats,coef)
-importFrom(stats,complete.cases)
-importFrom(stats,confint)
-importFrom(stats,cor)
-importFrom(stats,cor.test)
-importFrom(stats,dchisq)
-importFrom(stats,deviance)
-importFrom(stats,df)
-importFrom(stats,dnorm)
-importFrom(stats,dt)
-importFrom(stats,fisher.test)
-importFrom(stats,fitted)
-importFrom(stats,ftable)
-importFrom(stats,glm)
-importFrom(stats,kruskal.test)
-importFrom(stats,lm)
-importFrom(stats,loess)
-importFrom(stats,logLik)
-importFrom(stats,na.omit)
-importFrom(stats,na.pass)
-importFrom(stats,pchisq)
-importFrom(stats,pf)
-importFrom(stats,pnorm)
-importFrom(stats,poly)
-importFrom(stats,ppoints)
-importFrom(stats,prcomp)
-importFrom(stats,predict)
-importFrom(stats,pt)
-importFrom(stats,qchisq)
-importFrom(stats,qf)
-importFrom(stats,qnorm)
-importFrom(stats,qt)
-importFrom(stats,quantile)
-importFrom(stats,reshape)
-importFrom(stats,residuals)
-importFrom(stats,rstudent)
-importFrom(stats,sd)
-importFrom(stats,summary.lm)
-importFrom(stats,weighted.mean)
-importFrom(stats,xtabs)
-importFrom(tidyr,gather)
-importFrom(tidyr,nest)
-importFrom(tidyr,spread)
-importFrom(utils,browseURL)
-importFrom(utils,setTxtProgressBar)
-importFrom(utils,txtProgressBar)

NEWS.md

@@ -1,3 +1,15 @@
+# sjPlot 2.9.0
+
+* Fix namespace clash with new ggplot2 version.
+
+* Fix confusing warning message.
+
+* Fix incorrect labeling of coefficients when `transform = NULL` with a probit
+  model.
+
+* Corrected documentation for `tab_model()` and `plot_model()` regarding the
+  `p.adjust` argument.
+
 # sjPlot 2.8.17
 
 ## Bug fixes

R/S3-methods.R

@@ -1,4 +1,3 @@
-#' @importFrom utils browseURL
 #' @export
 print.sjTable <- function(x, ...) {
   # check if we have filename specified
@@ -20,7 +19,6 @@ print.sjTable <- function(x, ...) {
   }
 }
 
-
 #' @importFrom knitr knit_print asis_output
 #' @export
 knit_print.sjTable <-  function(x, ...) {
@@ -209,7 +207,6 @@ pgrpmean <- function(x, ...) {
 }
 
 
-#' @importFrom purrr map_chr
 pgrpmeans <- function(x, ...) {
   uv <- attr(x, "print", exact = TRUE) == "viewer"
   enc <- attr(x, "encoding", exact = TRUE)
@@ -221,7 +218,7 @@ pgrpmeans <- function(x, ...) {
     "Mean for %s by %s<br><span class=\"subtitle\">grouped by %s</span>",
     attr(.x, "dv.label", exact = TRUE),
     attr(.x, "grp.label", exact = TRUE),
-    gsub(pattern = "\n", replacement = "<br>", attr(.x, "group", exact = TRUE), fixed = T)
+    gsub(pattern = "\n", replacement = "<br>", attr(.x, "group", exact = TRUE), fixed = TRUE)
   ))
 
   footnotes <- purrr::map_chr(x, ~ sprintf(
@@ -343,13 +340,11 @@ preliab <- function(x, ...) {
 }
 
 
-#' @importFrom purrr map_if
-#' @importFrom sjmisc is_float
 pdescr <- function(x, ...) {
   digits <- 2
 
   # do we have digits argument?
-  add.args <- lapply(match.call(expand.dots = F)$`...`, function(x) x)
+  add.args <- lapply(match.call(expand.dots = FALSE)$`...`, function(x) x)
   if ("digits" %in% names(add.args)) digits <- eval(add.args[["digits"]])
 
   uv <- attr(x, "print", exact = TRUE) == "viewer"
@@ -376,8 +371,8 @@ pdescr <- function(x, ...) {
   present_columns <- c("var", "type", "label", "n", "NA.prc", "mean", "sd", "se", "md", "trimmed", "range", "skew")
   chead <- chead[which(present_columns %in% colnames(x))]
 
-  x <- x %>%
-    purrr::map_if(sjmisc::is_float, ~ round(.x, digits)) %>%
+  x <- x |>
+    purrr::map_if(sjmisc::is_float, ~ round(.x, digits)) |>
     as.data.frame()
 
   tab_df(
@@ -404,18 +399,16 @@ pdescr <- function(x, ...) {
 }
 
 
-#' @importFrom purrr map_if map_chr map
-#' @importFrom sjmisc is_float
 pgdescr <- function(x, ...) {
   titles <- purrr::map_chr(x, ~ sprintf(
     "Basic descriptives<br><span class=\"subtitle\"><em>grouped by</em> %s</span>",
-    gsub(pattern = "\n", replacement = "<br>", attr(.x, "group", exact = TRUE), fixed = T)
+    gsub(pattern = "\n", replacement = "<br>", attr(.x, "group", exact = TRUE), fixed = TRUE)
   ))
 
   digits <- 2
 
   # do we have digits argument?
-  add.args <- lapply(match.call(expand.dots = F)$`...`, function(x) x)
+  add.args <- lapply(match.call(expand.dots = FALSE)$`...`, function(x) x)
   if ("digits" %in% names(add.args)) digits <- eval(add.args[["digits"]])
 
   uv <- attr(x, "print", exact = TRUE) == "viewer"
@@ -439,12 +432,12 @@ pgdescr <- function(x, ...) {
     "Skewness"
   )
 
-  x <- x %>%
+  x <- x |>
     purrr::map(~ purrr::map_if(
       .x,
       sjmisc::is_float,
       ~ round(.x, digits)
-    ) %>% as.data.frame())
+    ) |> as.data.frame())
 
   tab_dfs(
     x = x,
@@ -468,9 +461,6 @@ pgdescr <- function(x, ...) {
 }
 
 
-#' @importFrom purrr map_if map_chr map
-#' @importFrom dplyr n_distinct select
-#' @importFrom sjmisc is_empty
 pfrq <- function(x, ...) {
 
   uv <- attr(x, "print", exact = TRUE) == "viewer"
@@ -485,8 +475,8 @@ pfrq <- function(x, ...) {
     ret <- ""
 
     # get variable label
-    lab <- attr(i, "label", exact = T)
-    vt <- attr(i, "vartype", exact = T)
+    lab <- attr(i, "label", exact = TRUE)
+    vt <- attr(i, "vartype", exact = TRUE)
 
     # fix variable type string
     if (!sjmisc::is_empty(vt))
@@ -497,21 +487,21 @@ pfrq <- function(x, ...) {
     if (!is.null(lab)) ret <- sprintf("%s%s", lab, vt)
 
     # get grouping title label
-    grp <- attr(i, "group", exact = T)
+    grp <- attr(i, "group", exact = TRUE)
 
     if (!is.null(grp))
       ret <- sprintf("%s<br><span class=\"subtitle\"><em>grouped by:</em><br>%s</span>", ret, grp)
 
-    gsub(pattern = "\n", replacement = "<br>", x = ret, fixed = T)
+    gsub(pattern = "\n", replacement = "<br>", x = ret, fixed = TRUE)
   })
 
 
   footnotes <- purrr::map_chr(x, ~ sprintf(
     "total N=%i &middot; valid N=%i &middot; x&#772;=%.2f &middot; &sigma;=%.2f\n",
     sum(.x$frq, na.rm = TRUE),
     sum(.x$frq[1:(nrow(.x) - 1)], na.rm = TRUE),
-    attr(.x, "mean", exact = T),
-    attr(.x, "sd", exact = T)
+    attr(.x, "mean", exact = TRUE),
+    attr(.x, "sd", exact = TRUE)
   )
   )
 
@@ -549,7 +539,6 @@ pfrq <- function(x, ...) {
 }
 
 
-#' @importFrom stats na.omit kruskal.test
 pmwu <- function(x, ...) {
   fn <- NULL
 

R/color_utils.R

@@ -57,7 +57,7 @@ get_sjplot_colorpalette <- function(pal, len) {
   col <- sjplot_colors[[pal]]
 
   if (len > length(col)) {
-    warning("More colors requested than length of color palette.", call. = F)
+    warning("More colors requested than length of color palette.", call. = FALSE)
     len <- length(col)
   }