tinytable as default output

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: 1.4.5
+Version: 1.9.9.9999
 Authors@R: c(person("Vincent", "Arel-Bundock", 
                    email = "[email protected]", 
                    role = c("aut", "cre"),
@@ -52,12 +52,11 @@ Imports:
     data.table,
     generics,
     glue,
-    kableExtra (>= 1.3.4),
     insight (>= 0.19.6),
     parameters (>= 0.21.2),
     performance (>= 0.10.5),
     tables (>= 0.9.17),
-    tinytable (>= 0.0.4)
+    tinytable (>= 0.0.5)
 Suggests: 
     AER,
     altdoc,
@@ -88,6 +87,7 @@ Suggests:
     huxtable,
     IRdisplay,
     ivreg,
+    kableExtra,
     knitr,
     lavaan,
     lfe,

Makefile

@@ -22,7 +22,7 @@ install: document ## devtools::install()
 deploy: ## pkgdown::deploy_to_branch()
 	Rscript -e "pkgdown::deploy_to_branch()"
 
-document: install ## devtools::document()
+document: ## devtools::document()
 	Rscript -e "devtools::document()"
 
 website: document ## render vignettes and website

NEWS.md

@@ -1,5 +1,20 @@
 # News 
 
+## 1.9.9.9999
+
+BREAKING CHANGE: The default output format is now `tinytable` instead of `kableExtra`. Learn more about `tinytable` here:
+
+https://vincentarelbundock.github.io/tinytable/
+
+To revert to the previous behavior persistently, users can call:
+
+library(modelsummary)
+config_modelsummary(factory_default = "kableExtra")
+
+Other breaking changes:
+
+* The `statistic_override` argument was replaced by `vcov` over 1 year ago, with appropriate deprecation warnings. It is now fully removed.
+
 ## 1.4.5
 
 * `tinytable` supports histograms in `datasummary_skim()`

R/config_modelsummary.R

@@ -1,6 +1,6 @@
 #' Persistent user settings for the `modelsummary` package
 #'
-#' @param factory_default Default output format: "kableExtra", "gt", "flextable", "huxtable", "DT", or "markdown" 
+#' @param factory_default Default output format: "tinytable", "kableExtra", "gt", "flextable", "huxtable", "DT", or "markdown" 
 #' @param factory_latex Name of package used to generate LaTeX output when `output="latex"`.
 #' @param factory_markdown Name of package used to generate LaTeX output when `output="markdown"`.
 #' @param factory_html Name of package used to generate LaTeX output when `output="html"`.

R/datasummary.R

@@ -37,7 +37,7 @@
 #' `x~mean*z` will print the `mean`-related header above the `z`-related
 #' header.`
 #' @param ... all other arguments are passed through to the table-making
-#' functions [kableExtra::kbl], [gt::gt], [DT::datatable], etc. depending on the `output` argument.
+#' functions [tinytable::tt], [kableExtra::kbl], [gt::gt], [DT::datatable], etc. depending on the `output` argument.
 #' This allows users to pass arguments directly to `datasummary` in order to
 #' affect the behavior of other functions behind the scenes.
 #' @template citation
@@ -124,6 +124,7 @@
 #' #datasummary(f, data = mtcars, output = 'latex')
 #'
 #' # Return a table object to customize using a table-making package
+#' #datasummary(f, data = mtcars, output = 'tinytable')
 #' #datasummary(f, data = mtcars, output = 'gt')
 #' #datasummary(f, data = mtcars, output = 'kableExtra')
 #' #datasummary(f, data = mtcars, output = 'flextable')
@@ -144,7 +145,7 @@
 #' found in the 'tables' package documentation: ?tables::tabular
 #'
 #' Hierarchical or "nested" column labels are only available for these output
-#' formats: kableExtra, gt, html, rtf, and LaTeX. When saving tables to other
+#' formats: tinytable, kableExtra, gt, html, rtf, and LaTeX. When saving tables to other
 #' formats, nested labels will be combined to a "flat" header.
 #' @export
 datasummary <- function(formula,
@@ -222,13 +223,6 @@ datasummary <- function(formula,
     }
   }
 
-  ## escape stub
-  sw <- attr(dse, "stub_width")
-  for (i in 1:sw) {
-    dse[, i] <- escape_string(dse[, i])
-  }
-  colnames(dse)[1:sw] <- escape_string(colnames(dse)[1:sw])
-
   # build
   out <- factory(dse,
     align = align,
@@ -239,6 +233,7 @@ datasummary <- function(formula,
     title = title,
     add_columns = add_columns,
     add_rows = add_rows,
+    escape = escape,
     ...)
 
   # invisible return

R/datasummary_balance.R

@@ -258,13 +258,6 @@ datasummary_balance <- function(formula,
                         strrep("r", ncol(tab) - attr(tab, "stub_width")))
     }
 
-    ## escape stub: re-sanitize because we called `datasummary()` a few times
-    sanitize_output(output) # before sanitize_escape
-    sanitize_escape(escape) # after sanitize_output
-    for (i in 1:attr(tab, "stub_width")) {
-      tab[[i]] <- escape_string(tab[[i]])
-    }
-
     ## weights warning
     if (isTRUE(any_factor) && "weights" %in% colnames(data)) {
       msg <- 'When the `data` used in `datasummary_balance` contains a "weights" column, the means, standard deviations, difference in means, and standard errors of numeric variables are adjusted to account for weights. However, the counts and percentages for categorical variables are not adjusted.'
@@ -339,7 +332,6 @@ DinM <- function(lhs, rhs, data, fmt, statistic, stars = TRUE, escape = TRUE) {
 
   if (identical(statistic, "p.value")) {
     out[[statistic]] <- rounding(out[[statistic]], pval = TRUE)
-    out[[statistic]] <- escape_string(out[[statistic]]) # <0.001 interpreted as html tag
   } else {
     out[[statistic]] <- rounding(out[[statistic]])
   }

R/datasummary_correlation.R

@@ -184,9 +184,6 @@ datasummary_correlation <- function(data,
       align <- paste0('l', strrep('r', ncols - 1))
   }
 
-  out[, 1] <- escape_string(out[, 1])
-  colnames(out) <- escape_string(colnames(out))
-
   # labelled data
   dict <- get_variable_labels_data(data)
   out[, 1] <- replace_dict(out[, 1], dict)

R/datasummary_df.R

@@ -22,9 +22,6 @@ datasummary_df <- function(data,
 
   checkmate::assert_data_frame(data)
 
-  notes <- escape_string(notes)
-  title <- escape_string(title)
-
   for (n in colnames(data)) {
     fmt <- sanitize_fmt(fmt)
     data[[n]] <- fmt(data[[n]])

R/datasummary_extract.R

@@ -65,9 +65,6 @@ datasummary_extract <- function(tab,
   # stub_width attribute before return
   attr(main, 'stub_width') <- stub_width
 
-  # escape latex column names
-  colnames(main) <- escape_string(colnames(main))
-
   # 1 header level means colnames are sufficient. return output immediately.
   # this needs to go before definition of header_nocolnames
   if (nrow(header) == 1) {

R/datasummary_skim.R

@@ -11,7 +11,7 @@
 #' @param histogram include a histogram (TRUE/FALSE). Supported for:
 #' \itemize{
 #' \item type = "numeric"
-#' \item output is "html", "default", "jpg", "png", or "kableExtra"
+#' \item output is "html", "default", "jpg", "png", "tinytable", or "kableExtra"
 #' \item PDF and HTML documents compiled via Rmarkdown or knitr
 #' \item See the examples section below for an example of how to use
 #' `datasummary` to include histograms in other formats such as markdown.

R/factory_kableExtra.R

@@ -15,6 +15,24 @@ factory_kableExtra <- function(tab,
 
   insight::check_if_installed("kableExtra")
 
+  output_format <- settings_get("output_format")
+
+  span_list <- get_span_kableExtra(tab)
+
+  # escape
+  if (isTRUE(escape) && isTRUE(output_format %in% c("latex", "html", "typst"))) {
+    tmp <- escape_everything(
+      tab = tab,
+      output_format = output_format,
+      span_list = span_list,
+      title = title,
+      notes = notes)
+    tab <- tmp$tab
+    title <- tmp$title
+    notes <- tmp$notes
+    span_list <- tmp$span_list
+  }
+
   # new variable "kable_format" because "kableExtra" and "html" both produce
   # html, but we need to distinguish the two.
   if (settings_equal("output_format", c("latex", "latex_tabular"))) {
@@ -34,27 +52,16 @@ factory_kableExtra <- function(tab,
              "position", "centering", "vline", "toprule", "bottomrule",
              "midrule", "caption.short", "table.envir", "col.names")
 
-  # kableExtra::kbl and knitr::kable do not respect the `escape` argument for captions.
-  # this will never be fixed upstream because of backward compatibility
-  title <- escape_string(title)
-
-  # don't escape \\label{} calls
-  if (isTRUE(kable_format == "latex")) {
-    title <- sub("\\\\textbackslash\\{\\}label\\\\\\{(.*)\\\\}", "\\\\label{\\1}", title)
-  }
-
   arguments <- c(
     list(...),
     "caption"   = title,
     "format"    = kable_format,
     "booktabs"  = TRUE,
+    "escape" = FALSE, # never use kableExtra's default escape; inconsistent
     "linesep"   = "",
     "row.names" = NULL
   )
 
-  ## never use `kableExtra`'s default escape
-  arguments$escape <- FALSE
-
   ## siunitx in preamble
   extra_siunitx <- "
   \\newcolumntype{d}{S[
@@ -84,7 +91,6 @@ factory_kableExtra <- function(tab,
           tab[[i]] <- ifelse(grepl("[0-9]", tab[[i]]), sprintf("$%s$", tab[[i]]), tab[[i]])
         }
       }
-
     }
     if (any(grepl("d", align))) {
       ## protect column labels
@@ -93,17 +99,6 @@ factory_kableExtra <- function(tab,
     arguments[["align"]] <- align
   }
 
-  # span: compute
-  span_list <- get_span_kableExtra(tab)
-  if (!is.null(span_list) && settings_equal("output_format", c("kableExtra", "html", "latex"))) {
-    column_names <- attr(span_list, "column_names")
-    if (!is.null(column_names)) {
-      colnames(tab) <- column_names
-    }
-  } else {
-      colnames(tab) <- gsub("\\|{4}", " / ", colnames(tab))
-  }
-
   # Issue #669: <0.001 gets printed as a tag in HTML
   if (settings_equal("output_format", c("kableExtra", "html"))) {
     for (i in seq_along(tab)) {
@@ -181,6 +176,7 @@ factory_kableExtra <- function(tab,
   # span: apply (not supported in markdown)
   if (!is.null(span_list) && settings_equal("output_format", c("kableExtra", "latex", "html"))) {
     for (i in 1:length(span_list)) {
+      sp <- span_list[[i]]
       names(span_list[[i]]) <- gsub("&nbsp;", " ", names(span_list[[i]]))
       out <- kableExtra::add_header_above(out, span_list[[i]], escape = TRUE)
     }