[2025.11]

Author: Bruce

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bruceR
 Title: Broadly Useful Convenient and Efficient R Functions
-Version: 2025.8
-Date: 2025-08-15
+Version: 2025.11
+Date: 2025-11-24
 Authors@R:
     c(person(given = "Han Wu Shuang",
              family = "Bao",
@@ -45,5 +45,5 @@ Suggests:
     cowplot, ggtext, see,
     car, lmtest, lme4, lmerTest, nnet, vars, phia, performance,
     MASS, MuMIn, BayesFactor, GGally, GPArotation
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,5 +1,9 @@
 **Please check the [latest news (change log)](https://psychbruce.github.io/bruceR/news/index.html) and keep this package updated.**
 
+# bruceR 2025.11
+
+-   Fixed `theme_bruce()` for `ggplot2` (\>= 3.4.0) warnings about its deprecated features.
+
 # bruceR 2025.8
 
 -   Rewrote all help pages in the style of Roxygen markdown, and refined most of them.
@@ -314,7 +318,7 @@
 ## Minor Changes
 
 -   Changed package title and description of `bruceR`: **BR**oadly **U**seful **C**onvenient and **E**fficient **R** functions that **BR**ing **U**sers **C**oncise and **E**legant **R** data analyses.
--   Reorganized [raw code files](https://github.com/psychbruce/bruceR/tree/master/R).
+-   Reorganized [raw code files](https://github.com/psychbruce/bruceR/tree/main/R).
 
 ## Bug Fixes
 
@@ -323,7 +327,7 @@
 
 ## Notes
 
--   Deprecated some useless/defective functions (see [details](https://github.com/psychbruce/bruceR/blob/master/R/deprecated.R)).
+-   Deprecated some useless/defective functions (see [details](https://github.com/psychbruce/bruceR/blob/main/R/deprecated.R)).
 
 # bruceR 0.5.0 (Aug 2020)
 

R/bruceR-stats_1_basic.R

@@ -424,8 +424,6 @@ Describe = function(
     names(desc)[2] = "(NA)"
     nsmalls = c(0, 0, rep(digits, 8))
   }
-  print_table(desc, digits=nsmalls, file=file,
-              title="Descriptive Statistics:")
 
   data.new = as.data.frame(data)
   vars.not.numeric = c()
@@ -437,8 +435,13 @@ Describe = function(
       }
     }
   }
-  if(length(vars.not.numeric)>0)
-    Print("\n\n\n<<yellow NOTE: `{paste(vars.not.numeric, collapse='`, `')}` transformed to numeric.>>")
+  if(length(vars.not.numeric)>0) {
+    Print("<<yellow NOTE: `{paste(vars.not.numeric, collapse='`, `')}` transformed to numeric.>>")
+    cat("\n")
+  }
+
+  print_table(desc, digits=nsmalls, file=file,
+              title="Descriptive Statistics:")
 
   p = NULL
   if(plot) {
@@ -643,7 +646,6 @@ Corr = function(
     if(p.adjust!="none")
       Print("<<blue <<italic p>> values and 95% CIs are adjusted using the \"{p.adjust}\" method.>>")
     print_table(COR, digits=0)
-    cat("\n")
   } else {
     Print("Descriptive Statistics and Correlation Matrix:")
     cor.mat = matrix(formatF(cor$r, digits),
@@ -754,12 +756,10 @@ Corr = function(
   if(is.null(plot.file)) {
     if(p.adjust!="none")
       Print("<<blue <<italic p>> values ABOVE the diagonal are adjusted using the \"{p.adjust}\" method.>>")
-    cat("\n")
   } else {
     ggsave(plot=p, filename=plot.file,
            width=plot.width, height=plot.height, dpi=plot.dpi)
     Print("<<green \u2714>> Plot saved to <<blue '{plot.file}'>>")
-    cat("\n")
   }
 
   invisible(list(corr=cor, plot=p))

R/bruceR-stats_5_advance.R

@@ -265,7 +265,7 @@ boot_ci = function(boot,
 #'
 #' # Software Comparison
 #'
-#' To perform mediation, moderation, and conditional process (moderated mediation) analyses, people may use [Mplus](http://www.statmodel.com/index.shtml), [SPSS "PROCESS" macro](https://www.processmacro.org/index.html), or [SPSS "MLmed" macro](https://njrockwood.com/mlmed/). Some R packages and functions can also perform such analyses, in a somewhat complex way, including [mediation::mediate()], [interactions::sim_slopes()], and [lavaan::sem()].
+#' To perform mediation, moderation, and conditional process (moderated mediation) analyses, people may use [Mplus](http://www.statmodel.com/index.shtml), [SPSS "PROCESS" macro](https://www.processmacro.org/index.html), or [SPSS "MLmed" macro](https://njrockwood.com/mlmed/). Some R packages and functions can also perform such analyses, in a somewhat complex way, including `mediation::mediate()`, `interactions::sim_slopes()`, and `lavaan::sem()`.
 #'
 #' Furthermore, some other R packages or scripts/modules have been developed, including [jamovi module `jAMM`](https://jamovi-amm.github.io/) (by *Marcello Gallucci*, based on the `lavaan` package), [R package `processR`](https://CRAN.R-project.org/package=processR) (by *Keon-Woong Moon*, not official, also based on the `lavaan` package), and [R script file "process.R"](https://www.processmacro.org/download.html) (the official PROCESS R code by *Andrew F. Hayes*, but it is not yet an R package).
 #'
@@ -1645,7 +1645,7 @@ process_mod = function(
 #'
 #' Tidy report of mediation analysis, which is performed using [mediation::mediate()].
 #'
-#' @param model Mediation model built with [mediation::mediate()].
+#' @param model Mediation model built with `mediation::mediate()`.
 #' @param digits Number of decimal places of output. Defaults to `3`.
 #' @param file File name of MS Word (`".doc"`).
 #'

R/bruceR-stats_6_plot.R

@@ -15,7 +15,7 @@
 #' @param markdown Use `element_markdown()` instead of `element_text()`. Defaults to `FALSE`.
 #' If set to `TRUE`, then you should also use `element_markdown()` in `theme()` (if any).
 #' @param base.size Basic font size. Defaults to `12`.
-#' @param line.size Line width. Defaults to `0.5`.
+#' @param line.width Line width. Defaults to `0.5`.
 #' @param border `TRUE`, `FALSE`, or `"black"` (default).
 #' @param bg Background color of whole plot. Defaults to `"white"`.
 #' You can use any colors or choose from some pre-set color palettes:
@@ -72,7 +72,7 @@
 #' @export
 theme_bruce = function(
     markdown=FALSE,
-    base.size=12, line.size=0.5,
+    base.size=12, line.width=0.5,
     border="black",
     bg="white", panel.bg="white",
     tag="bold", plot.title="bold", axis.title="plain",
@@ -99,52 +99,52 @@ theme_bruce = function(
   if(!is.null(font)) grDevices::windowsFonts(FONT=grDevices::windowsFont(font))
   theme = theme_bw() +
     theme(
-      # text=element_markdown(),
-      # title=element_markdown(),
-      # legend.text=element_markdown(size=base.size-2),
-      # legend.title=element_markdown(size=base.size),
-      panel.grid.minor=element_blank(),
-      panel.grid.major.x=if(grid.x=="" | grid.x==FALSE) element_blank() else
-        element_line(size=line.size, color=grid.x),
-      panel.grid.major.y=if(grid.y=="" | grid.y==FALSE) element_blank() else
-        element_line(size=line.size, color=grid.y),
-      panel.border=if(border=="" | border==FALSE) element_blank() else
-        element_rect(size=line.size+0.4, color=border, fill=NA),
-      panel.background=element_rect(fill=panel.bg),
-      axis.line=element_line(size=line.size, color="black"),  # lineend="square"
-      axis.title=element_text(size=base.size+2, color="black", face=axis.title),
-      axis.title.x=element_text(margin=margin(0.5, 0, 0.4, 0, "lines")),
-      axis.title.y=element_text(margin=margin(0, 0.5, 0, 0.4, "lines")),
-      axis.ticks=element_line(size=line.size, color="black", lineend="square"),
-      axis.ticks.length=unit(0.3, "lines"),
-      axis.text=element_text(size=base.size, color="black"),
-      axis.text.x=element_text(margin=margin(ifelse(tick.x, 0.5, 0.3), 0, 0, 0, "lines")),
-      axis.text.y=element_text(margin=margin(0, ifelse(tick.y, 0.5, 0.3), 0, 0, "lines")),
-      strip.background=element_rect(color=NA),
-      strip.text=element_text(size=base.size-2),
-      legend.title=element_text(size=base.size),
-      legend.text=element_text(size=base.size-2),
-      plot.title=element_text(size=base.size+2, face=plot.title, hjust=title.pos,
-                              margin=margin(0.2, 0, 0.6, 0, "lines")),
-      plot.subtitle=element_text(size=base.size, face=plot.title, hjust=subtitle.pos,
-                                 margin=margin(0, 0, 0.6, 0, "lines")),
-      plot.caption=element_text(size=base.size-2, hjust=caption.pos,
-                                margin=margin(0, 0, 0.1, 0, "lines")),
-      plot.tag=element_text(size=base.size+2, face=tag),
-      plot.tag.position=c(0.005, 0.985),
-      plot.background=element_rect(color=bg, fill=bg),
-      plot.margin=margin(0.02, 0.02, 0.02, 0.02, "npc")
+      # text = element_markdown(),
+      # title = element_markdown(),
+      # legend.text = element_markdown(size=base.size-2),
+      # legend.title = element_markdown(size=base.size),
+      panel.grid.minor = element_blank(),
+      panel.grid.major.x = if(grid.x=="" | grid.x==FALSE) element_blank() else
+        element_line(linewidth=line.width, color=grid.x),
+      panel.grid.major.y = if(grid.y=="" | grid.y==FALSE) element_blank() else
+        element_line(linewidth=line.width, color=grid.y),
+      panel.border = if(border=="" | border==FALSE) element_blank() else
+        element_rect(linewidth=line.width+0.4, color=border, fill=NA),
+      panel.background = element_rect(fill=panel.bg),
+      axis.line = element_line(linewidth=line.width, color="black"),  # lineend="square"
+      axis.title = element_text(size=base.size+2, color="black", face=axis.title),
+      axis.title.x = element_text(margin=margin(0.5, 0, 0.4, 0, "lines")),
+      axis.title.y = element_text(margin=margin(0, 0.5, 0, 0.4, "lines")),
+      axis.ticks = element_line(linewidth=line.width, color="black", lineend="square"),
+      axis.ticks.length = unit(0.3, "lines"),
+      axis.text = element_text(size=base.size, color="black"),
+      axis.text.x = element_text(margin=margin(ifelse(tick.x, 0.5, 0.3), 0, 0, 0, "lines")),
+      axis.text.y = element_text(margin=margin(0, ifelse(tick.y, 0.5, 0.3), 0, 0, "lines")),
+      strip.background = element_rect(color=NA),
+      strip.text = element_text(size=base.size-2),
+      legend.title = element_text(size=base.size),
+      legend.text = element_text(size=base.size-2),
+      plot.title = element_text(size=base.size+2, face=plot.title, hjust=title.pos,
+                                margin=margin(0.2, 0, 0.6, 0, "lines")),
+      plot.subtitle = element_text(size=base.size, face=plot.title, hjust=subtitle.pos,
+                                   margin=margin(0, 0, 0.6, 0, "lines")),
+      plot.caption = element_text(size=base.size-2, hjust=caption.pos,
+                                  margin=margin(0, 0, 0.1, 0, "lines")),
+      plot.tag = element_text(size=base.size+2, face=tag),
+      plot.tag.position = c(0.005, 0.985),
+      plot.background = element_rect(color=bg, fill=bg),
+      plot.margin = margin(0.02, 0.02, 0.02, 0.02, "npc")
     )
   if(!is.null(font))
-    theme = theme + theme(text=element_text(family="FONT"))
+    theme = theme + theme(text = element_text(family="FONT"))
   if((border!="" & border!=FALSE) | line.x==FALSE)
-    theme = theme + theme(axis.line.x=element_blank())
+    theme = theme + theme(axis.line.x = element_blank())
   if((border!="" & border!=FALSE) | line.y==FALSE)
-    theme = theme + theme(axis.line.y=element_blank())
+    theme = theme + theme(axis.line.y = element_blank())
   if(!tick.x)
-    theme = theme + theme(axis.ticks.x=element_blank())
+    theme = theme + theme(axis.ticks.x = element_blank())
   if(!tick.y)
-    theme = theme + theme(axis.ticks.y=element_blank())
+    theme = theme + theme(axis.ticks.y = element_blank())
   return(theme)
 }
 

R/bruceR.R

@@ -66,12 +66,12 @@ if(FALSE) {
 #' - [Print()]
 #' - [Glue()]
 #' - [Run()]
-#' - [`%^%`]
-#' - [`%notin%`]
-#' - [`%allin%`]
-#' - [`%anyin%`]
-#' - [`%nonein%`]
-#' - [`%partin%`]
+#' - [`%^%`][bruceR::%^%]
+#' - [`%notin%`][bruceR::%notin%]
+#' - [`%allin%`][bruceR::%allin%]
+#' - [`%anyin%`][bruceR::%anyin%]
+#' - [`%nonein%`][bruceR::%nonein%]
+#' - [`%partin%`][bruceR::%partin%]
 #'
 #' ## 2. Multivariate Computation
 #'

R/bruceR_utils.R

@@ -61,11 +61,11 @@ data.table::`%notin%`
 #' @seealso
 #' [`%in%`][base::match]
 #'
-#' [`%anyin%`]
+#' [`%anyin%`][bruceR::%anyin%]
 #'
-#' [`%nonein%`]
+#' [`%nonein%`][bruceR::%nonein%]
 #'
-#' [`%partin%`]
+#' [`%partin%`][bruceR::%partin%]
 #'
 #' @examples
 #' 1:2 %allin% 1:3  # TRUE
@@ -87,11 +87,11 @@ data.table::`%notin%`
 #' @seealso
 #' [`%in%`][base::match]
 #'
-#' [`%allin%`]
+#' [`%allin%`][bruceR::%allin%]
 #'
-#' [`%nonein%`]
+#' [`%nonein%`][bruceR::%nonein%]
 #'
-#' [`%partin%`]
+#' [`%partin%`][bruceR::%partin%]
 #'
 #' @examples
 #' 3:4 %anyin% 1:3  # TRUE
@@ -113,11 +113,11 @@ data.table::`%notin%`
 #' @seealso
 #' [`%in%`][base::match]
 #'
-#' [`%allin%`]
+#' [`%allin%`][bruceR::%allin%]
 #'
-#' [`%anyin%`]
+#' [`%anyin%`][bruceR::%anyin%]
 #'
-#' [`%partin%`]
+#' [`%partin%`][bruceR::%partin%]
 #'
 #' @examples
 #' 3:4 %nonein% 1:3  # FALSE
@@ -140,11 +140,11 @@ data.table::`%notin%`
 #' @seealso
 #' [`%in%`][base::match]
 #'
-#' [`%allin%`]
+#' [`%allin%`][bruceR::%allin%]
 #'
-#' [`%anyin%`]
+#' [`%anyin%`][bruceR::%anyin%]
 #'
-#' [`%nonein%`]
+#' [`%nonein%`][bruceR::%nonein%]
 #'
 #' @examples
 #' "Bei" %partin% c("Beijing", "Shanghai")  # TRUE