[skip vbump], preping for 0.9.4 release (#1227)

# Pull Request

<!--- Replace `#nnn` with your issue link for reference. -->

Fixes #nnn

---------

Signed-off-by: Joe Zhu <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.3.9035
+Version: 0.9.4
 Date: 2024-04-16
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
@@ -25,7 +25,7 @@ URL: https://insightsengineering.github.io/tern/,
 BugReports: https://github.com/insightsengineering/tern/issues
 Depends:
     R (>= 3.6),
-    rtables (>= 0.6.6)
+    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 (>= 0.5.5),
+    formatters (>= 0.5.6),
     ggplot2 (>= 3.5.0),
     grid,
     gridExtra (>= 2.0.0),

NEWS.md

@@ -1,12 +1,12 @@
-# tern 0.9.3.9035
+# tern 0.9.4
 
 ### New Features
-* Refactored `g_forest` to output a `ggplot` object instead of a `grob` object.
 * Added `h_glm_negbin` to `h_glm_count` to enable count data analysis using a negative binomial model.
 * Added argument `grade_groups_only` to `count_occurrences_by_grade` to allow users to only display rows for specified grade groups.
 * Added internal function `df2gg` that converts `data.frame` objects to `ggplot` objects.
 * Added functions `control_surv_med_annot` and `control_coxph_annot` to configure `g_km` annotation table sizes/positions.
 * Refactored `g_km` to output a `ggplot` object instead of a `grob` object.
+* Refactored `g_forest` to output a `ggplot` object instead of a `grob` object.
 
 ### Enhancements
 * Default format for mean p-values (`mean_pval`) updated from `"xx.xx"` to `"x.xxxx | (<0.0001)"`.
@@ -20,16 +20,16 @@
 
 ### Miscellaneous
 * Added function `expect_snapshot_ggplot` to test setup file to process plot snapshot tests and allow plot dimensions to be set.
-* Began deprecation of the named element `strat`, to be renamed to `strata`, within the `variables` argument to `h_rsp_to_logistic_variables`, `h_logistic_mult_cont_df`, `h_odds_ratio_subgroups_df`, `h_coxreg_mult_cont_df`, `h_coxph_subgroups_df`, `h_tbl_coxph_pairwise`, `extract_rsp_biomarkers`, `extract_rsp_subgroups`, `extract_survival_biomarkers`, and `extract_survival_subgroups`.
-* Began deprecation of the `strat` argument to `s_coxph_pairwise` and replaced it with the `strata` argument.
-* Adapt to argument renames introduced in `ggplot2` 3.5.0.
+* Adapted to argument renames introduced in `ggplot2` 3.5.0.
+* 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.
+* Began deprecation of the named element `strat`, to be renamed to `strata`, within the `variables` argument to `h_rsp_to_logistic_variables`, `h_logistic_mult_cont_df`, `h_odds_ratio_subgroups_df`, `h_coxreg_mult_cont_df`, `h_coxph_subgroups_df`, `h_tbl_coxph_pairwise`, `extract_rsp_biomarkers`, `extract_rsp_subgroups`, `extract_survival_biomarkers`, and `extract_survival_subgroups`.
+* Began deprecation of the `strat` argument to `s_coxph_pairwise` and replaced it with the `strata` argument.
 * Began deprecation of the `forest_grob`, `forest_dot_line`, `forest_viewport`, `vp_forest_table_part`, and `grid.forest` functions.
 * Began deprecation of no longer used Kaplan-Meier helper functions `h_ggkm`, `h_decompose_gg`, `h_km_layout`, `h_grob_tbl_at_risk`, `h_grob_median_surv`, `h_grob_y_annot`, and `h_grob_coxph`.
 * Began deprecation of `grob`/`grid` related functions `stack_grobs`, `arrange_grobs`, and `draw_grob` which are no longer used in `tern`.
-* Removed `vdiffr` package from Suggests in DESCRIPTION file.
-* Renamed `individual_patient_plot.R` to `g_ipp.R`. 
 
 # tern 0.9.3
 

R/utils_ggplot.R

@@ -136,14 +136,14 @@ rtable2gg <- function(tbl, fontsize = 12, colwidths = NULL, lbl_col_padding = 0)
 #' Given a `data.frame` object, performs basic conversion to a [ggplot2::ggplot()] object built using
 #' functions from the `ggplot2` package.
 #'
-#' @param tbl (`data.frame`)\cr a data frame.
+#' @param df (`data.frame`)\cr a data frame.
 #' @param colwidths (`numeric` or `NULL`)\cr a vector of column widths. Each element's position in
 #'   `colwidths` corresponds to the column of `df` in the same position. If `NULL`, column widths
 #'   are calculated according to maximum number of characters per column.
 #' @param font_size (`numeric(1)`)\cr font size.
 #' @param col_labels (`flag`)\cr whether the column names (labels) of `df` should be used as the first row
 #'   of the output table.
-#' @param col_labels_fontface (`string`)\cr font face to apply to the first row (of column labels
+#' @param col_lab_fontface (`string`)\cr font face to apply to the first row (of column labels
 #'   if `col_labels = TRUE`). Defaults to `"bold"`.
 #' @param hline (`flag`)\cr whether a horizontal line should be printed below the first row of the table.
 #' @param bg_fill (`string`)\cr table background fill color.

README.md

@@ -36,7 +36,7 @@ Data visualizations:
 
 Statistical model fit summaries:
 
--   Logistic regression ([`summarize_logistic`](https://insightsengineering.github.io/tern/latest-tag/reference/logistic_regression.html))
+-   Logistic regression ([`summarize_logistic`](https://insightsengineering.github.io/tern/latest-tag/reference/summarize_logistic.html))
 -   Cox regression ([`summarize_coxreg`](https://insightsengineering.github.io/tern/latest-tag/reference/cox_regression.html))
 
 Analysis tables: