Fix Issue #799

DESCRIPTION

@@ -9,7 +9,7 @@ Description: Create beautiful and customizable tables to summarize several
     RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or 'knitr'
     dynamic documents. Details can be found in Arel-Bundock (2022)
     <doi:10.18637/jss.v103.i01>.
-Version: 2.1.1.5
+Version: 2.1.1.6
 Authors@R: c(person("Vincent", "Arel-Bundock", 
                    email = "[email protected]", 
                    role = c("aut", "cre"),

NEWS.md

@@ -8,6 +8,10 @@
 * `kableExtra` escapes footnotes in HTML when `output="kableExtra")`. Thanks to @dmurdoch and @michaelherndon97 for report #793.
 * New `fmt_equivalence()` function to implement the rounding suggestion of Astier & Wolak (2024). Thanks to Nicolas Astier for code prototype.
 
+Bugs:
+
+* `datasummary_*()` functions can be called as arguments in another `datasummary_*()` arguments, like `add_columns`. Thanks to @mronkko for report #799 
+
 ## 2.1.1
 
 * Documentation improvements

R/datasummary.R

@@ -168,7 +168,10 @@ datasummary <- function(formula,
     ))
   }
 
-  sanitize_output(output) # before sanitize_escape
+  tmp <- sanitize_output(output)           # early
+  output_format <- tmp$output_format
+  output_factory <- tmp$output_factory
+  output_file <- tmp$output_file
   sanitize_escape(escape) # after sanitize_output
   sanity_align(align)
 
@@ -237,10 +240,13 @@ datasummary <- function(formula,
     add_columns = add_columns,
     add_rows = add_rows,
     escape = escape,
+    output_factory = output_factory,
+    output_format = output_format,
+    output_file = output_file,
     ...)
 
   # invisible return
-  if (!is.null(settings_get("output_file")) ||
+  if (!is.null(output_file) ||
       output == "jupyter" ||
       (output == "default" && settings_equal("output_default", "jupyter"))) {
     if (!isTRUE(list(...)[["internal_call"]])) settings_rm()

R/datasummary_balance.R

@@ -52,11 +52,15 @@ datasummary_balance <- function(formula,
     settings_init(settings = list("function_called" = "datasummary_balance"))
 
     ## sanity checks
-    sanitize_output(output) # before sanitize_escape
+    tmp <- sanitize_output(output) # before sanitize_escape
+    output_format <- tmp$output_format
+    output_factory <- tmp$output_factory
+    output_file <- tmp$output_file
+
     # this is going to be detected by fmt_mathmode() when we call
     # datasummary(output="dataframe") so we can get siunitx formatting even in
     # internal calls.
-    settings_set("output_format_ultimate", settings_get("output_format"))
+    settings_set("output_format_ultimate", output_format)
 
     sanity_align(align)
     sanitize_escape(escape) # after sanitize_output
@@ -156,7 +160,7 @@ datasummary_balance <- function(formula,
 
         ## datasummary(output="dataframe") changes the output format
         sanitize_output(output)
-        settings_set("output_format_ultimate", settings_get("output_format"))
+        settings_set("output_format_ultimate", output_format)
 
         ## enforce 2-column stub, even when there is only one factor
         idx <- grep("bad_factor_for_stub", tab_fac[[1]])
@@ -203,7 +207,7 @@ datasummary_balance <- function(formula,
 
         ## datasummary(output="dataframe") changes the output format
         sanitize_output(output)
-        settings_set("output_format_ultimate", settings_get("output_format"))
+        settings_set("output_format_ultimate", output_format)
     }
 
     ## combine
@@ -287,10 +291,13 @@ datasummary_balance <- function(formula,
         add_columns = add_columns,
         title = title,
         escape = escape,
+        output_factory = output_factory,
+        output_format = output_format,
+        output_file = output_file,
         ...)
 
     # invisible return
-    if (!is.null(settings_get("output_file")) ||
+    if (!is.null(output_file) ||
         output == "jupyter" ||
         (output == "default" && settings_equal("output_default", "jupyter"))) {
       settings_rm()

R/datasummary_correlation.R

@@ -126,7 +126,10 @@ datasummary_correlation <- function(data,
   ))
 
   # sanity checks
-  sanitize_output(output) # before sanitize_escape
+  tmp <- sanitize_output(output) # before sanitize_escape
+  output_format <- tmp$output_format
+  output_factory <- tmp$output_factory
+  output_file <- tmp$output_file
   sanitize_escape(escape) # after sanitize_output
   sanity_add_columns(add_columns)
   sanity_align(align)
@@ -244,10 +247,13 @@ datasummary_correlation <- function(data,
     notes = notes,
     title = title,
     escape = escape,
+    output_factory = output_factory,
+    output_format = output_format,
+    output_file = output_file,
     ...)
 
   # invisible return
-  if (!is.null(settings_get("output_file")) ||
+  if (!is.null(output_file) ||
       output == "jupyter" ||
       (output == "default" && settings_equal("output_default", "jupyter"))) {
     settings_rm()

R/datasummary_crosstab.R

@@ -76,7 +76,10 @@ datasummary_crosstab <- function(formula,
 
 
     # argument checking
-    sanitize_output(output) # before sanitize_escape
+    tmp <- sanitize_output(output) # before sanitize_escape
+    output_format <- tmp$output_format
+    output_factory <- tmp$output_factory
+    output_file <- tmp$output_file
     sanitize_escape(escape) # after sanitize_output
 
     checkmate::assert_formula(formula)
@@ -182,7 +185,7 @@ Note that the `datasummary()` function supports the `=` sign and the `Heading()`
                 escape = escape,
                 ...)
 
-    if (!is.null(settings_get("output_file"))) {
+    if (!is.null(output_file)) {
         settings_rm()
         return(invisible(out))
     } else {

R/datasummary_df.R

@@ -19,7 +19,10 @@ datasummary_df <- function(data,
 
   settings_init(settings = list("function_called" = "datasummary_df"))
 
-  sanitize_output(output) # before sanitize_escape
+  tmp <- sanitize_output(output) # before sanitize_escape
+  output_format <- tmp$output_format
+  output_factory <- tmp$output_factory
+  output_file <- tmp$output_file
   sanitize_escape(escape) # after sanitize_output
   sanity_align(align)
 
@@ -39,6 +42,9 @@ datasummary_df <- function(data,
           escape = escape,
           add_rows = add_rows,
           add_columns = add_columns,
+          output_factory = output_factory,
+          output_format = output_format,
+          output_file = output_file,
           ...)
 
   settings_rm()

R/datasummary_skim.R

@@ -44,7 +44,10 @@ datasummary_skim <- function(data,
 
   ## settings 
   settings_init(settings = list("function_called" = "datasummary_skim"))
-  sanitize_output(output) # before sanitize_escape
+  tmp <- sanitize_output(output) # before sanitize_escape
+  output_format <- tmp$output_format
+  output_factory <- tmp$output_factory
+  output_file <- tmp$output_file
   sanitize_escape(escape) # after sanitize_output
   sanity_align(align)
   checkmate::assert_list(fun_numeric, min.len = 1, names = "unique")
@@ -99,7 +102,7 @@ datasummary_skim <- function(data,
       out <- tinytable::rbind2(a, b, use_names = FALSE)
       out <- tinytable::format_tt(out, replace = "")
       out <- tinytable::style_tt(out, i = nrow(a) + 1, line = "t", line_size = .3)
-      if (settings_equal("output_format", "html")) {
+      if (identical(output_format, "html")) {
           out <- tinytable::style_tt(out, i = nrow(a) + 1, bold = TRUE, line = "bt", line_color = "#d3d8dc")
       }
     } else if (!inherits(a, "tinytable") && !inherits(b, "tinytable")) {
@@ -110,11 +113,11 @@ datasummary_skim <- function(data,
       out <- b
     }
 
-    ofmt <- settings_get("output_format")
+    ofmt <- output_format
     if (isTRUE(ofmt %in% c("latex", "markdown", "html", "typst", "dataframe"))) {
       out@output <- ofmt
     }
-    ofile <- settings_get("output_file")
+    ofile <- output_file
     if (!is.null(ofile)) {
       tinytable::save_tt(out, output = ofile, overwrite = TRUE)
     }
@@ -154,7 +157,7 @@ datasummary_skim <- function(data,
     }
   }
 
-  if (!is.null(settings_get("output_file"))) {
+  if (!is.null(output_file)) {
     settings_rm()
     return(invisible(out))
   } else {

R/escape.R

@@ -1,11 +1,14 @@
 #' Make sure LaTeX and HTML are safe to compile
 #'
 #' @keywords internal
-escape_string <- function(x) {
+escape_string <- function(x, output_format = NULL) {
+    if (is.null(output_format)) {
+        output_format <- settings_get("output_format")
+    }
     if (settings_equal("escape", TRUE)) {
-        if (identical(Sys.getenv("pkgdown"),  "true") || settings_equal("output_format", c("html", "kableExtra"))) {
+        if (identical(Sys.getenv("pkgdown"),  "true") || output_format %in% c("html", "kableExtra")) {
             out <- escape_html(x)
-        } else if (settings_equal("output_format", c("latex", "latex_tabular"))) {
+        } else if (output_format %in% c("latex", "latex_tabular")) {
             out <- escape_latex(x)
         } else {
             out <- x

R/factory.R

@@ -16,34 +16,36 @@ factory <- function(tab,
                     add_rows = NULL,
                     add_columns = NULL,
                     escape = TRUE,
+                    output_factory = "tinytable",
+                    output_format = "tinytable",
+                    output_file = NULL,
                     ...) {
 
 
   # sanity check functions are hosted in R/sanity_checks.R
   sanity_title(title, ...)
   sanity_notes(notes)
-  # sanitize_output(output) # do not override (otherwise this breaks quarto for shape="rbind")
 
   # parse output
   if (isTRUE(output == "data.frame")) { # internal calls from datasummary_skim()
     factory_fun <- factory_dataframe
-  } else if (settings_equal("output_factory", "gt")) {
+  } else if (output_factory == "gt") {
     factory_fun <- factory_gt
-  } else if (settings_equal("output_factory", "tinytable")) {
+  } else if (output_factory == "tinytable") {
     factory_fun <- factory_tinytable
-  } else if (settings_equal("output_factory", "kableExtra")) {
+  } else if (output_factory == "kableExtra") {
     factory_fun <- factory_kableExtra
-  } else if (settings_equal("output_factory", "flextable")) {
+  } else if (output_factory == "flextable") {
     factory_fun <- factory_flextable
-  } else if (settings_equal("output_factory", "huxtable")) {
+  } else if (output_factory == "huxtable") {
     factory_fun <- factory_huxtable
-  } else if (settings_equal("output_factory", "DT")) {
+  } else if (output_factory == "DT") {
     factory_fun <- factory_DT
-  } else if (settings_equal("output_factory", "dataframe")) {
+  } else if (output_factory == "dataframe") {
     factory_fun <- factory_dataframe
-  } else if (settings_equal("output_factory", "modelsummary")) {
+  } else if (output_factory == "modelsummary") {
     factory_fun <- factory_markdown
-  } else if (settings_equal("output_factory", "typst")) {
+  } else if (output_factory == "typst") {
     factory_fun <- factory_typst
   }
 
@@ -52,8 +54,8 @@ factory <- function(tab,
   if (!is.null(flat_header)) {
     flat_factories <- c('huxtable', 'dataframe', 'typst')
     flat_formats <- c('markdown', 'word', 'powerpoint', 'typst')
-    if (settings_get("output_factory") %in% flat_factories ||
-        settings_get("output_format") %in% flat_formats) {
+    if (output_factory %in% flat_factories ||
+        output_format %in% flat_formats) {
         attr(tab, "header_bottom") <- colnames(tab)
 
       # datasummary_balance with dinm produces more cols than flat_header
@@ -65,7 +67,7 @@ factory <- function(tab,
   }
 
   # de-duplicate columns with whitespace
-  colnames(tab) <- pad(colnames(tab))
+  colnames(tab) <- pad(colnames(tab), output_format = output_format)
 
   # add_columns
   if (!is.null(add_columns)) {
@@ -124,7 +126,7 @@ factory <- function(tab,
   if (!is.null(add_rows)) {
 
     # data.frame includes metadata columns
-    if (settings_equal("output_format", "dataframe")) {
+    if (identical(output_format, "dataframe")) {
       # only for modelsummary, not for datasummary
 
       if (all(c("term", "statistic") %in% colnames(tab))) {
@@ -173,10 +175,10 @@ factory <- function(tab,
   align <- strsplit(align, "")[[1]]
 
   # dot align with unicode spaces (latex has its own mechanism)
-  if (!settings_equal("output_format", c("latex", "tinytable"))) {
+  if (!output_format %in% c("latex", "tinytable")) {
     align_d <- grep("d", align)
     for (i in align_d) {
-      tab[[i]] <- pad(tab[[i]], style = "character")
+      tab[[i]] <- pad(tab[[i]], style = "character", output_format = output_format)
     }
     align[align == "d"] <- "c"
   }
@@ -188,6 +190,8 @@ factory <- function(tab,
     notes = notes,
     title = title,
     escape = escape,
+    output_format = output_format,
+    output_file = output_file,
     ...)
 
 

R/factory_dataframe.R

@@ -8,10 +8,10 @@ factory_dataframe <- function(tab,
                               align = NULL,
                               hrule = NULL,
                               notes = NULL,
-                              output_file = NULL,
-                              output_format = NULL,
                               add_rows = NULL,
                               title = NULL,
+                              output_file = NULL,
+                              output_format = NULL,
                               ...) {
 
   out <- tab
@@ -24,7 +24,7 @@ factory_dataframe <- function(tab,
   if (!isTRUE(list(...)$internal_call)) {
     colnames(out) <- gsub("\\|\\|\\|\\|", " / ", colnames(out))
     colnames(out) <- ifelse(colnames(out) == " ", colnames(out), trimws(colnames(out)))
-    colnames(out) <- pad(trimws(colnames(out)))
+    colnames(out) <- pad(trimws(colnames(out)), output_format = output_format)
   }
 
   # factor -> character (useful for R<4.0.0)
@@ -49,7 +49,6 @@ factory_dataframe <- function(tab,
   out <- theme_ms(out)
 
   # write spreadsheet to file
-  output_file <- settings_get("output_file")
   if (isTRUE(tools::file_ext(output_file) == "csv")) {
     utils::write.csv(out, file = output_file, row.names = FALSE)
   } else if (isTRUE(tools::file_ext(output_file) == "xlsx")) {

R/factory_flextable.R

@@ -8,13 +8,15 @@ factory_flextable <- function(tab,
                               hrule = NULL,
                               notes = NULL,
                               title = NULL,
+                              output_format = "flextable",
+                              output_file = NULL,
                               ...) {
 
   insight::check_if_installed("flextable")
 
   span <- get_span_kableExtra(tab)
   colnames(tab) <- gsub(".*\\|\\|\\|\\|", "", colnames(tab))
-  colnames(tab) <- pad(colnames(tab))
+  colnames(tab) <- pad(colnames(tab), output_format = output_format)
 
   # measurements
   table_width <- ncol(tab)
@@ -51,15 +53,15 @@ factory_flextable <- function(tab,
 
 
   # output
-  if (is.null(settings_get("output_file"))) {
+  if (is.null(output_file)) {
     return(out)
-  } else if (settings_equal("output_format", "word")) {
-    flextable::save_as_docx(out, path = settings_get("output_file"))
-  } else if (settings_equal("output_format", "powerpoint")) {
-    flextable::save_as_pptx(out, path = settings_get("output_file"))
-  } else if (settings_equal("output_format", "png")) {
-    flextable::save_as_image(out, path = settings_get("output_file"))
-  } else if (settings_equal("output_format", "html")) {
-    flextable::save_as_html(out, path = settings_get("output_file"))
+  } else if (identical(output_format, "word")) {
+    flextable::save_as_docx(out, path = output_file)
+  } else if (identical(output_format, "powerpoint")) {
+    flextable::save_as_pptx(out, path = output_file)
+  } else if (identical(output_format, "png")) {
+    flextable::save_as_image(out, path = output_file)
+  } else if (identical(output_format, "html")) {
+    flextable::save_as_html(out, path = output_file)
   }
 }