Revert "Merge branch 'main' into wasm-poc"

This reverts commit 21c7639, reversing
changes made to b6e6c86.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.4.9010
-Date: 2024-06-16
+Version: 0.9.4.9007
+Date: 2024-05-14
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
     person("Daniel", "Sabanés Bové", , "[email protected]", role = "aut"),
@@ -25,7 +25,7 @@ URL: https://insightsengineering.github.io/tern/,
 BugReports: https://github.com/insightsengineering/tern/issues
 Depends:
     R (>= 3.6),
-    rtables (>= 0.6.7.9004)
+    rtables (>= 0.6.7)
 Imports:
     broom (>= 0.5.4),
     car (>= 3.0-13),
@@ -34,7 +34,7 @@ Imports:
     dplyr (>= 1.0.0),
     emmeans (>= 1.8.0),
     forcats (>= 1.0.0),
-    formatters (>= 0.5.7.9000),
+    formatters (>= 0.5.6),
     ggplot2 (>= 3.5.0),
     grid,
     gridExtra (>= 2.0.0),

NEWS.md

@@ -1,14 +1,12 @@
-# tern 0.9.4.9010
+# tern 0.9.4.9007
 
 ### Enhancements
 * Added `facet_var` to `g_lineplot` to allow plot faceting by a factor variable.
 * Updated `g_lineplot` legend to follow factor levels set by users.
 * Added examples and tests for `label_all` parameter to `extract_survival_biomarkers` and `extract_survival_subgroups`.
-* Added the `xticks`, `xlim`, and `ylim` arguments to `g_lineplot` to allow for customization of the x and y axes.
 
 ### Bug Fixes
 * Fixed bug in `s_ancova` that prevented statistics from being printed when arm levels include special characters.
-* Fixed bug in `decorate_grob` that prevented the right margins to be respected when adding title and footers decorations.
 
 ### Miscellaneous
 * Began deprecation of the unused `label_all` parameter to `tabulate_survival_biomarkers` and `tabulate_survival_subgroups`, with redirection to the same parameter in their associated `extract_*` functions.
@@ -36,7 +34,7 @@
 ### Miscellaneous
 * Added function `expect_snapshot_ggplot` to test setup file to process plot snapshot tests and allow plot dimensions to be set.
 * Adapted to argument renames introduced in `ggplot2` 3.5.0.
-* Renamed `individual_patient_plot.R` to `g_ipp.R`.
+* Renamed `individual_patient_plot.R` to `g_ipp.R`. 
 * Removed all instances of deprecated parameters `time_unit_input`, `time_unit_output`, `na_level` and `indent_mod`.
 * Removed deprecated functions `summarize_vars`, `control_summarize_vars`, `a_compare`, `create_afun_summary`, `create_afun_compare`, and `summary_custom`.
 * Removed `vdiffr` package from Suggests in DESCRIPTION file.

R/argument_convention.R

@@ -67,11 +67,6 @@
 #' @param vars (`character`)\cr variable names for the primary analysis variable to be iterated over.
 #' @param var (`string`)\cr single variable name for the primary analysis variable.
 #' @param x (`numeric`)\cr vector of numbers we want to analyze.
-#' @param xlim (`numeric(2)`)\cr vector containing lower and upper limits for the x-axis, respectively.
-#'   If `NULL` (default), the default scale range is used.
-#' @param ylim (`numeric(2)`)\cr vector containing lower and upper limits for the y-axis, respectively.
-#'   If `NULL` (default), the default scale range is used.
-#'
 #'
 #' @details Although this function just returns `NULL` it has two uses, for
 #'   the `tern` users it provides a documentation of arguments that are

R/decorate_grob.R

@@ -11,22 +11,14 @@
 #'   according to the page width.
 #' @param footnotes (`character`)\cr footnotes. Uses the same formatting rules as `titles`.
 #' @param page (`string` or `NULL`)\cr page numeration. If `NULL` then no page number is displayed.
-#' @param width_titles (`grid::unit`)\cr width of titles. Usually defined as all the available space
-#'   `grid::unit(1, "npc")`, it is affected by the parameter `outer_margins`. Right margins (`outer_margins[4]`)
-#'   need to be subtracted to the allowed width.
-#' @param width_footnotes (`grid::unit`)\cr width of footnotes. Same default and margin correction as `width_titles`.
+#' @param width_titles (`grid::unit`)\cr width of titles.
+#' @param width_footnotes (`grid::unit`)\cr width of footnotes.
 #' @param border (`flag`)\cr whether a border should be drawn around the plot or not.
-#' @param padding (`grid::unit`)\cr padding. A unit object of length 4. Innermost margin between the plot (`grob`)
-#'   and, possibly, the border of the plot. Usually expressed in 4 identical values (usually `"lines"`). It defaults
-#'   to `grid::unit(rep(1, 4), "lines")`.
-#' @param margins (`grid::unit`)\cr margins. A unit object of length 4. Margins between the plot and the other
-#'   elements in the list (e.g. titles, plot, and footers). This is usually expressed in 4 `"lines"`, where the
-#'   lateral ones are 0s, while top and bottom are 1s. It defaults to `grid::unit(c(1, 0, 1, 0), "lines")`.
-#' @param outer_margins (`grid::unit`)\cr outer margins. A unit object of length 4. It defines the general margin of
-#'   the plot, considering also decorations like titles, footnotes, and page numbers. It defaults to
-#'   `grid::unit(c(2, 1.5, 3, 1.5), "cm")`.
-#' @param gp_titles (`gpar`)\cr a `gpar` object. Mainly used to set different `"fontsize"`.
-#' @param gp_footnotes (`gpar`)\cr a `gpar` object. Mainly used to set different `"fontsize"`.
+#' @param margins (`grid::unit`)\cr margins. A unit object of length 4.
+#' @param padding (`grid::unit`)\cr padding. A unit object of length 4.
+#' @param outer_margins (`grid::unit`)\cr outer margins. A unit object of length 4.
+#' @param gp_titles (`gpar`)\cr a `gpar` object.
+#' @param gp_footnotes (`gpar`)\cr a `gpar` object.
 #'
 #' @return A grid grob (`gTree`).
 #'
@@ -140,24 +132,17 @@ decorate_grob <- function(grob,
                           titles,
                           footnotes,
                           page = "",
-                          width_titles = grid::unit(1, "npc"),
-                          width_footnotes = grid::unit(1, "npc"),
+                          width_titles = grid::unit(1, "npc") - grid::unit(1.5, "cm"),
+                          width_footnotes = grid::unit(1, "npc") - grid::unit(1.5, "cm"),
                           border = TRUE,
-                          padding = grid::unit(rep(1, 4), "lines"),
                           margins = grid::unit(c(1, 0, 1, 0), "lines"),
+                          padding = grid::unit(rep(1, 4), "lines"),
                           outer_margins = grid::unit(c(2, 1.5, 3, 1.5), "cm"),
                           gp_titles = grid::gpar(),
                           gp_footnotes = grid::gpar(fontsize = 8),
                           name = NULL,
                           gp = grid::gpar(),
                           vp = NULL) {
-  # External margins need to be taken into account when defining the width of titles and footers
-  # because the text is split in advance depending on only the width of the viewport.
-  if (any(as.numeric(outer_margins) > 0)) {
-    width_titles <- width_titles - outer_margins[4]
-    width_footnotes <- width_footnotes - outer_margins[4]
-  }
-
   st_titles <- split_text_grob(
     titles,
     x = 0, y = 1,
@@ -184,45 +169,45 @@ decorate_grob <- function(grob,
     gp = gp_footnotes
   )
 
-  # Initial decoration of the grob -> border, paddings, and margins are used here
-  main_plot <- grid::gTree(
-    children = grid::gList(
-      if (border) grid::rectGrob(),
-      grid::gTree(
-        children = grid::gList(
-          grob
-        ),
-        vp = grid::plotViewport(margins = padding) # innermost margins of the grob plot
-      )
-    ),
-    vp = grid::vpStack(
-      grid::viewport(layout.pos.row = 2, layout.pos.col = 1),
-      grid::plotViewport(margins = margins) # margins around the border plot
-    )
-  )
-
   grid::gTree(
     grob = grob,
     titles = titles,
     footnotes = footnotes,
     page = page,
     width_titles = width_titles,
     width_footnotes = width_footnotes,
+    border = border,
+    margins = margins,
+    padding = padding,
     outer_margins = outer_margins,
     gp_titles = gp_titles,
     gp_footnotes = gp_footnotes,
     children = grid::gList(
       grid::gTree(
         children = grid::gList(
           st_titles,
-          main_plot, # main plot with border, padding, and margins
+          grid::gTree(
+            children = grid::gList(
+              if (border) grid::rectGrob(),
+              grid::gTree(
+                children = grid::gList(
+                  grob
+                ),
+                vp = grid::plotViewport(margins = padding)
+              )
+            ),
+            vp = grid::vpStack(
+              grid::viewport(layout.pos.row = 2, layout.pos.col = 1),
+              grid::plotViewport(margins = margins)
+            )
+          ),
           st_footnotes,
           pg_footnote
         ),
         childrenvp = NULL,
         name = "titles_grob_footnotes",
         vp = grid::vpStack(
-          grid::plotViewport(margins = outer_margins), # Main external margins
+          grid::plotViewport(margins = outer_margins),
           grid::viewport(
             layout = grid::grid.layout(
               nrow = 4, ncol = 1,
@@ -400,7 +385,6 @@ split_string <- function(text, width) {
     if (length(newline_str) > 1) {
       for (i in seq(2, length(newline_str))) {
         width_i <- grid::stringWidth(newline_str[i])
-        # Main conversion of allowed text width -> npc units are 0<npc<1. External viewport is used for conversion
         if (grid::convertWidth(linewidth + gapwidth + width_i, grid::unitType(width), valueOnly = TRUE) < availwidth) {
           sep <- " "
           linewidth <- linewidth + gapwidth + width_i

R/g_km.R

@@ -6,7 +6,7 @@
 #' including the number of patient at risk at given time and the median survival
 #' per group.
 #'
-#' @inheritParams argument_convention
+#' @param df (`data.frame`)\cr data set containing all analysis variables.
 #' @param variables (named `list`)\cr variable names. Details are:
 #'   * `tte` (`numeric`)\cr variable indicating time-to-event duration values.
 #'   * `is_event` (`logical`)\cr event variable. `TRUE` if event, `FALSE` if time to event is censored.
@@ -35,6 +35,8 @@
 #' @param yval (`string`)\cr type of plot, to be plotted on the y-axis. Options are `Survival` (default) and `Failure`
 #'   probability.
 #' @param ylab (`string`)\cr y-axis label.
+#' @param ylim (`numeric(2)`)\cr vector containing lower and upper limits for the y-axis, respectively.
+#'   If `NULL` (default), the minimum and maximum y-values displayed are used as limits.
 #' @param title (`string`)\cr plot title.
 #' @param footnotes (`string`)\cr plot footnotes.
 #' @param font_size (`numeric(1)`)\cr font size to use for all text.

R/g_lineplot.R

@@ -4,7 +4,7 @@
 #'
 #' Line plot with the optional table.
 #'
-#' @inheritParams argument_convention
+#' @param df (`data.frame`)\cr data set containing all analysis variables.
 #' @param alt_counts_df (`data.frame` or `NULL`)\cr data set that will be used (only)
 #'   to counts objects in groups for stratification.
 #' @param variables (named `character`) vector of variable names in `df` which should include:
@@ -46,9 +46,6 @@
 #' @param legend_position (`string`)\cr the position of the plot legend (`"none"`, `"left"`, `"right"`, `"bottom"`,
 #'   `"top"`, or a two-element numeric vector).
 #' @param ggtheme (`theme`)\cr a graphical theme as provided by `ggplot2` to control styling of the plot.
-#' @param xticks (`numeric` or `NULL`)\cr numeric vector of tick positions or a single number with spacing
-#'   between ticks on the x-axis, for use when `variables$x` is numeric. If `NULL` (default), [labeling::extended()] is
-#'   used to determine optimal tick positions on the x-axis. If `variables$x` is not numeric, this argument is ignored.
 #' @param x_lab (`string` or `NULL`)\cr x-axis label. If `NULL` then no label will be added.
 #' @param y_lab (`string` or `NULL`)\cr y-axis label. If `NULL` then no label will be added.
 #' @param y_lab_add_paramcd (`flag`)\cr whether `paramcd`, i.e. `unique(df[[variables["paramcd"]]])` should be added
@@ -143,9 +140,6 @@ g_lineplot <- function(df,
                        legend_title = NULL,
                        legend_position = "bottom",
                        ggtheme = nestcolor::theme_nest(),
-                       xticks = NULL,
-                       xlim = NULL,
-                       ylim = NULL,
                        x_lab = obj_label(df[[variables[["x"]]]]),
                        y_lab = NULL,
                        y_lab_add_paramcd = TRUE,
@@ -164,9 +158,7 @@ g_lineplot <- function(df,
   checkmate::assert_character(mid, null.ok = TRUE)
   checkmate::assert_character(interval, null.ok = TRUE)
   checkmate::assert_character(col, null.ok = TRUE)
-  checkmate::assert_numeric(xticks, null.ok = TRUE)
-  checkmate::assert_numeric(xlim, finite = TRUE, any.missing = FALSE, len = 2, sorted = TRUE, null.ok = TRUE)
-  checkmate::assert_numeric(ylim, finite = TRUE, any.missing = FALSE, len = 2, sorted = TRUE, null.ok = TRUE)
+
   checkmate::assert_string(title, null.ok = TRUE)
   checkmate::assert_string(subtitle, null.ok = TRUE)
 
@@ -361,13 +353,8 @@ g_lineplot <- function(df,
     }
   }
 
-  if (is.numeric(df_stats[[x]])) {
-    if (length(xticks) == 1) xticks <- seq(from = min(df_stats[[x]]), to = max(df_stats[[x]]), by = xticks)
-    p <- p + ggplot2::scale_x_continuous(breaks = if (!is.null(xticks)) xticks else waiver(), limits = xlim)
-  }
-
   p <- p +
-    ggplot2::scale_y_continuous(labels = scales::comma, limits = ylim) +
+    ggplot2::scale_y_continuous(labels = scales::comma) +
     ggplot2::labs(
       title = title,
       subtitle = subtitle,

README.md

@@ -31,7 +31,7 @@ Data visualizations:
 -   Kaplan-Meier plots ([`g_km`](https://insightsengineering.github.io/tern/latest-tag/reference/g_km.html))
 -   Forest plots ([`g_forest`](https://insightsengineering.github.io/tern/latest-tag/reference/g_forest.html))
 -   STEP graphs ([`g_step`](https://insightsengineering.github.io/tern/latest-tag/reference/g_step.html))
--   Individual patient plots ([`g_ipp`](https://insightsengineering.github.io/tern/latest-tag/reference/g_ipp.html))
+-   Individual patient plots ([`g_ipp`](https://insightsengineering.github.io/tern/latest-tag/reference/individual_patient_plot.html))
 -   Waterfall plots ([`g_waterfall`](https://insightsengineering.github.io/tern/latest-tag/reference/g_waterfall.html))
 
 Statistical model fit summaries:

inst/WORDLIST

@@ -7,7 +7,6 @@ ADTTE
 AE
 ANCOVA
 Agresti
-Bové
 Byar's
 CDISC
 CMH
@@ -27,7 +26,6 @@ Newcombe
 Pre
 Rua
 SMQ
-Sabanés
 Satterthwaite
 Schouten
 TLG