Merge branch 'main' into strengejacke/issue1135

Author: strengejacke

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.27.0.1
+Version: 0.27.0.5
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -202,6 +202,7 @@ Suggests:
     rms,
     rstan,
     rstanarm,
+    sampleSelection,
     sandwich,
     see (>= 0.8.1),
     serp,
@@ -230,3 +231,4 @@ Config/testthat/parallel: true
 Config/Needs/website: easystats/easystatstemplate
 Config/Needs/check: stan-dev/cmdstanr
 Config/rcmdcheck/ignore-inconsequential-notes: true
+Remotes: easystats/insight

NAMESPACE

@@ -128,10 +128,12 @@ S3method(display,parameters_efa_summary)
 S3method(display,parameters_model)
 S3method(display,parameters_omega)
 S3method(display,parameters_omega_summary)
+S3method(display,parameters_p_function)
 S3method(display,parameters_pca)
 S3method(display,parameters_pca_summary)
 S3method(display,parameters_sem)
 S3method(display,parameters_simulate)
+S3method(display,parameters_standardized)
 S3method(dof_satterthwaite,lmerMod)
 S3method(equivalence_test,MixMod)
 S3method(equivalence_test,feis)
@@ -611,6 +613,7 @@ S3method(print,parameters_sem)
 S3method(print,parameters_simulate)
 S3method(print,parameters_standardized)
 S3method(print_html,compare_parameters)
+S3method(print_html,equivalence_test_lm)
 S3method(print_html,parameters_brms_meta)
 S3method(print_html,parameters_efa)
 S3method(print_html,parameters_efa_summary)
@@ -981,7 +984,6 @@ export(pool_parameters)
 export(principal_components)
 export(print_html)
 export(print_md)
-export(print_table)
 export(random_parameters)
 export(reduce_data)
 export(reduce_parameters)

NEWS.md

@@ -1,3 +1,25 @@
+# parameters (devel)
+
+## Breaking Changes
+
+* The experimental `print_table()` function was removed. The aim of this function
+  was to test the implementation of the `tinytable` backend for printing. Now,
+  `tinytable` is fully supported by `insight::export_table()` and thereby also
+  by the various `print()` resp. `display()` methods for model parameters.
+
+## Changes
+
+* All `print_html()` methods get an `engine` argument, to either use the `gt`
+  package or the `tinytable` package for printing HTML tables. Since `tinytable`
+  not only produces HTML tables, but rather different formats depending on the
+  environment, `print_html()` may also generate a markdown table. Thus, the
+  generic `display()` method can be used, too, which has a `format` argument that
+  also supports `"tt"` for `tinytable`.
+
+## Bug fixes
+
+* Fixed issue with models of class `selection` with multiple outcomes.
+
 # parameters 0.27.0
 
 ## Breaking Changes

R/display.R

@@ -2,42 +2,24 @@
 #' @name display.parameters_model
 #'
 #' @description Prints tables (i.e. data frame) in different output formats.
-#' `print_md()` is an alias for `display(format = "markdown")`, `print_html()`
-#' is an alias for `display(format = "html")`. `print_table()` is for specific
-#' use cases only, and currently only works for `compare_parameters()` objects.
+#' `print_md()` is an alias for `display(format = "markdown")` and
+#' `print_html()` is an alias for `display(format = "html")`. A third option is
+#' `display(format = "tt")`, which returns a `tinytable` object, which is either
+#' printed as markdown or HTML table, depending on the environment.
 #'
-#' @param x An object returned by [`model_parameters()`].
-#' @param object An object returned by [`model_parameters()`],[`simulate_parameters()`],
-#' [`equivalence_test()`] or [`principal_components()`].
+#' @param object An object returned by one of the package's function, for example
+#' [`model_parameters()`], [`simulate_parameters()`], [`equivalence_test()`] or
+#' [`principal_components()`].
 #' @param format String, indicating the output format. Can be `"markdown"`
-#' or `"html"`.
-#' @param align Only applies to HTML tables. May be one of `"left"`,
-#' `"right"` or `"center"`.
-#' @param digits,ci_digits,p_digits Number of digits for rounding or
-#' significant figures. May also be `"signif"` to return significant
-#' figures or `"scientific"` to return scientific notation. Control the
-#' number of digits by adding the value as suffix, e.g. `digits = "scientific4"`
-#' to have scientific notation with 4 decimal places, or `digits = "signif5"`
-#' for 5 significant figures (see also [signif()]).
-#' @param subtitle Table title (same as caption) and subtitle, as strings. If `NULL`,
-#' no title or subtitle is printed, unless it is stored as attributes (`table_title`,
-#' or its alias `table_caption`, and `table_subtitle`). If `x` is a list of
-#' data frames, `caption` may be a list of table captions, one for each table.
-#' @param font_size For HTML tables, the font size.
-#' @param line_padding For HTML tables, the distance (in pixel) between lines.
-#' @param column_labels Labels of columns for HTML tables. If `NULL`, automatic
-#' column names are generated. See 'Examples'.
-#' @param theme String, indicating the table theme. Can be one of `"default"`,
-#' `"grid"`, `"striped"`, `"bootstrap"` or `"darklines"`.
-#' @inheritParams print.parameters_model
-#' @inheritParams insight::format_table
-#' @inheritParams insight::export_table
-#' @inheritParams compare_parameters
+#' `"html"`, or `"tt"`. `format = "tt"` creates a `tinytable` object, which is
+#' either printed as markdown or HTML table, depending on the environment. See
+#' [`insight::export_table()`] for details.
+#' @param ... Arguments passed to the underlying functions, such as `print_md()`
+#' or `print_html()`.
 #'
 #' @return If `format = "markdown"`, the return value will be a character
 #' vector in markdown-table format. If `format = "html"`, an object of
-#' class `gt_tbl`. For `print_table()`, an object of class `tinytable` is
-#' returned.
+#' class `gt_tbl`. If `format = "tt"`, an object of class `tinytable`.
 #'
 #' @details `display()` is useful when the table-output from functions,
 #' which is usually printed as formatted text-table to console, should
@@ -46,15 +28,7 @@
 #' [vignette](https://easystats.github.io/parameters/articles/model_parameters_formatting.html)
 #' for examples.
 #'
-#' `print_table()` is a special function for `compare_parameters()` objects,
-#' which prints the output as a formatted HTML table. It is still somewhat
-#' experimental, thus, only a fixed layout-style is available at the moment
-#' (columns for estimates, confidence intervals and p-values). However, it
-#' is possible to include other model components, like zero-inflation, or random
-#' effects in the table. See 'Examples'. An alternative is to set `engine = "tt"`
-#' in `print_html()` to use the _tinytable_ package for creating HTML tables.
-#'
-#' @seealso [print.parameters_model()] and [print.compare_parameters()]
+#' @seealso [`print.parameters_model()`] and [`print.compare_parameters()`]
 #'
 #' @examplesIf require("gt", quietly = TRUE)
 #' model <- lm(mpg ~ wt + cyl, data = mtcars)
@@ -81,54 +55,36 @@
 #'   column_labels = c("Est. (95% CI)")
 #' )
 #' }
+#'
+#' @examplesIf all(insight::check_if_installed(c("glmmTMB", "lme4", "tinytable"), quietly = TRUE))
+#' \donttest{
+#' data(iris)
+#' data(Salamanders, package = "glmmTMB")
+#' m1 <- lm(Sepal.Length ~ Species * Petal.Length, data = iris)
+#' m2 <- lme4::lmer(
+#'   Sepal.Length ~ Petal.Length + Petal.Width + (1 | Species),
+#'   data = iris
+#' )
+#' m3 <- glmmTMB::glmmTMB(
+#'   count ~ spp + mined + (1 | site),
+#'   ziformula = ~mined,
+#'   family = poisson(),
+#'   data = Salamanders
+#' )
+#' out <- compare_parameters(m1, m2, m3, effects = "all", component = "all")
+#'
+#' display(out, format = "tt")
+#'
+#' display(out, select = "{estimate}|{ci}", format = "tt")
+#' }
 #' @export
-display.parameters_model <- function(object,
-                                     format = "markdown",
-                                     pretty_names = TRUE,
-                                     split_components = TRUE,
-                                     select = NULL,
-                                     caption = NULL,
-                                     subtitle = NULL,
-                                     footer = NULL,
-                                     align = NULL,
-                                     digits = 2,
-                                     ci_digits = digits,
-                                     p_digits = 3,
-                                     footer_digits = 3,
-                                     ci_brackets = c("(", ")"),
-                                     show_sigma = FALSE,
-                                     show_formula = FALSE,
-                                     zap_small = FALSE,
-                                     font_size = "100%",
-                                     line_padding = 4,
-                                     column_labels = NULL,
-                                     include_reference = FALSE,
-                                     verbose = TRUE,
-                                     ...) {
+display.parameters_model <- function(object, format = "markdown", ...) {
   format <- insight::validate_argument(format, c("markdown", "html", "md", "tt"))
 
-  fun_args <- list(
-    x = object, pretty_names = pretty_names, split_components = split_components,
-    select = select, digits = digits, caption = caption, subtitle = subtitle,
-    footer = footer, ci_digits = ci_digits, p_digits = p_digits,
-    footer_digits = footer_digits, ci_brackets = ci_brackets,
-    show_sigma = show_sigma, show_formula = show_formula, zap_small = zap_small,
-    include_reference = include_reference, verbose = verbose
-  )
-
   if (format %in% c("html", "tt")) {
-    fun_args <- c(
-      fun_args,
-      list(
-        column_labels = column_labels,
-        align = align,
-        font_size = font_size,
-        line_padding = line_padding
-      )
-    )
-    do.call(print_html, c(fun_args, list(...)))
+    print_html(x = object, backend = ifelse(format == "tt", "tt", "html"), ...)
   } else {
-    do.call(print_md, c(fun_args, list(...)))
+    print_md(x = object, ...)
   }
 }
 
@@ -138,137 +94,32 @@ display.parameters_simulate <- display.parameters_model
 #' @export
 display.parameters_brms_meta <- display.parameters_model
 
-
-# Compare Parameters ------------------------
-
-
 #' @export
-display.compare_parameters <- function(object,
-                                       format = "markdown",
-                                       digits = 2,
-                                       ci_digits = digits,
-                                       p_digits = 3,
-                                       select = NULL,
-                                       column_labels = NULL,
-                                       ci_brackets = c("(", ")"),
-                                       font_size = "100%",
-                                       line_padding = 4,
-                                       zap_small = FALSE,
-                                       ...) {
-  format <- insight::validate_argument(format, c("markdown", "html", "md", "tt"))
-
-  fun_args <- list(
-    x = object,
-    digits = digits,
-    ci_digits = ci_digits,
-    p_digits = p_digits,
-    ci_brackets = ci_brackets,
-    select = select,
-    zap_small = zap_small
-  )
-
-  if (format %in% c("html", "tt")) {
-    fun_args <- c(
-      fun_args,
-      list(
-        column_labels = column_labels,
-        font_size = font_size,
-        line_padding = line_padding
-      )
-    )
-    do.call(print_html, c(fun_args, list(...)))
-  } else {
-    do.call(print_md, c(fun_args, list(...)))
-  }
-}
+display.compare_parameters <- display.parameters_model
 
-
-# SEM models ------------------------
-
-
-#' @rdname display.parameters_model
 #' @export
-display.parameters_sem <- function(object,
-                                   format = "markdown",
-                                   digits = 2,
-                                   ci_digits = digits,
-                                   p_digits = 3,
-                                   ci_brackets = c("(", ")"),
-                                   ...) {
-  format <- insight::validate_argument(format, c("markdown", "html", "md", "tt"))
-
-  fun_args <- list(
-    x = object,
-    digits = digits,
-    ci_digits = ci_digits,
-    p_digits = p_digits,
-    ci_brackets = ci_brackets
-  )
+display.parameters_sem <- display.parameters_model
 
-  if (format %in% c("html", "tt")) {
-    do.call(print_html, c(fun_args, list(...)))
-  } else {
-    do.call(print_md, c(fun_args, list(...)))
-  }
-}
-
-
-# PCA /EFA  models ------------------------
-
-
-#' @rdname display.parameters_model
 #' @export
-display.parameters_efa_summary <- function(object, format = "markdown", digits = 3, ...) {
-  format <- insight::validate_argument(format, c("markdown", "html", "md", "tt"))
-  fun_args <- list(x = object, digits = digits)
-
-  if (format %in% c("html", "tt")) {
-    do.call(print_html, c(fun_args, list(...)))
-  } else {
-    do.call(print_md, c(fun_args, list(...)))
-  }
-}
+display.parameters_efa_summary <- display.parameters_model
 
 #' @export
-display.parameters_pca_summary <- display.parameters_efa_summary
+display.parameters_pca_summary <- display.parameters_model
 
 #' @export
-display.parameters_omega_summary <- display.parameters_efa_summary
+display.parameters_omega_summary <- display.parameters_model
 
-
-#' @inheritParams model_parameters.principal
-#' @rdname display.parameters_model
 #' @export
-display.parameters_efa <- function(object, format = "markdown", digits = 2, sort = FALSE, threshold = NULL, labels = NULL, ...) {
-  format <- insight::validate_argument(format, c("markdown", "html", "md", "tt"))
-
-  fun_args <- list(
-    x = object,
-    digits = digits,
-    sort = sort,
-    threshold = threshold,
-    labels = labels
-  )
-
-  if (format %in% c("html", "tt")) {
-    do.call(print_html, c(fun_args, list(...)))
-  } else {
-    do.call(print_md, c(fun_args, list(...)))
-  }
-}
+display.parameters_efa <- display.parameters_model
 
 #' @export
-display.parameters_pca <- display.parameters_efa
+display.parameters_pca <- display.parameters_model
 
 #' @export
-display.parameters_omega <- display.parameters_efa
-
-
-# Equivalence tests ------------------------
+display.parameters_omega <- display.parameters_model
 
+#' @export
+display.equivalence_test_lm <- display.parameters_model
 
-#' @rdname display.parameters_model
 #' @export
-display.equivalence_test_lm <- function(object, format = "markdown", digits = 2, ...) {
-  print_md(x = object, digits = digits, ...)
-}
+display.parameters_p_function <- display.parameters_model