From ad9d0e4e4cfd7a46edda8ff920c4ec83e9dda5f0 Mon Sep 17 00:00:00 2001 From: Carson Richardson Date: Sat, 5 Sep 2026 13:56:43 -0400 Subject: [PATCH] Misc doc changes --- NEWS.md | 86 ++++++++++++++++++++++++++++++++---------------- cran-comments.md | 2 +- revdep/README.md | 70 +++++++++++++++++++-------------------- 3 files changed, 93 insertions(+), 65 deletions(-) diff --git a/NEWS.md b/NEWS.md index db88d49..35f88ac 100644 --- a/NEWS.md +++ b/NEWS.md @@ -14,7 +14,7 @@ - Added explicit `subgroup` mappings for mixed hierarchical displays, allowing standalone covariates and contiguous categorical blocks to share a forest plot. Subgroup p-values can be delegated as "overall" or "level" via `p_method` - in `tidy_forest_model()` + in `tidy_forest_model()` (#11) - Added covariance-aware subgroup effects for fitted interaction models. `tidy_forest_model()` and fitted-model `as_forest_data()` methods now use `marginaleffects` to derive average slopes or comparisons from the original @@ -40,10 +40,10 @@ - Added the `forest_data` S3 class as the package's stable interchange format. It stores validated effect-scale, axis, confidence-level, reference-value, - source-model, source-package, and source-column metadata. + source-model, source-package, and source-column metadata. (#17) - Converted `as_forest_data()` into an S3 generic with methods for data frames, existing `forest_data` objects, linear and generalized linear models, Cox - models, and supported mixed-model classes. + models, and supported mixed-model classes. (#19) - Refactored `ggforestplot()` to consume the `forest_data` contract instead of determining plotting behavior from the original model class. - Added `forest_metadata()` for inspecting the semantic and provenance @@ -95,12 +95,12 @@ - Added mixed-model support for `tidy_forest_model()` and `ggforestplot()` when `broom.mixed` is installed. Mixed-model tidiers are restricted to fixed - effects so random-effect parameter rows are not plotted as terms. + effects so random-effect parameter rows are not plotted as terms. (#21) - Added confidence interval truncation support to `ggforestplot()` via `ci_limits`, with optional arrowheads for intervals extending beyond the - displayed range. + displayed range. (#18) - Added `bind_forest_models()` to stack multiple fitted models into one - grouped forest-plot data frame. + grouped forest-plot data frame. (#16) ## Minor Changes @@ -115,59 +115,87 @@ - Faceted `ggforestplot()` output now respects factor level order in the `facet` column, allowing users to control facet ordering directly from their data. -- Fixed faceted `ggforestplot()` output when users add `scale_y_discrete(limits = ...)`, preserving per-facet row filtering while accepting visible term labels. +- Fixed faceted `ggforestplot()` output when users add + `scale_y_discrete(limits = ...)`, preserving per-facet row filtering while + accepting visible term labels. (#20) # ggforestplotR 0.2.1 ## Breaking Changes -- Simplified the reference-line API in `ggforestplot()`: `ref_line` now takes the numeric reference value directly, and `NULL` hides the line. -- Replaced the older reference-line arguments with `ref_label`, `ref_linetype`, and `ref_color`. +- Simplified the reference-line API in `ggforestplot()`: `ref_line` now takes + the numeric reference value directly, and `NULL` hides the line. +- Replaced the older reference-line arguments with `ref_label`, `ref_linetype`, + and `ref_color`. ## Major Changes -- Added `facet` and `facet_strip_position` as clearer names for grouped plot panels. The older `grouping` and `grouping_strip_position` arguments now warn and continue to work. -- Added `linewidth` for confidence interval widths. The older `line_size` argument now warns and continues to work. -- Added deprecation warnings for table-display shortcuts in favor of explicit `columns`, `left_columns`, and `right_columns` selections. +- Added `facet` and `facet_strip_position` as clearer names for grouped plot + panels. The older `grouping` and `grouping_strip_position` arguments now warn + and continue to work. +- Added `linewidth` for confidence interval widths. The older `line_size` + argument now warns and continues to work. +- Added deprecation warnings for table-display shortcuts in favor of explicit + `columns`, `left_columns`, and `right_columns` selections. ## Minor Changes -- Added `stripe_alpha` to control row stripe transparency across plots, side tables, and split tables. -- Updated table helpers so they inherit custom y-axis ordering and filtering from the trained forest plot scale. -- Updated vignettes and tests to use the clearer faceting and geometry argument names. +- Added `stripe_alpha` to control row stripe transparency across plots, + side tables, and split tables. (#7) +- Updated table helpers so they inherit custom y-axis ordering and filtering + from the trained forest plot scale. (#9) +- Updated vignettes and tests to use the clearer faceting and geometry argument + names. # ggforestplotR 0.2.0 ## Major Changes -- Added separate table formatting controls for point estimates, confidence interval bounds, and p-values via `estimate_digits`, `interval_digits`, and `p_digits`. -- Added `ref_line`, `ref_line_value`, and `ref_line_label` to standardize reference-line naming while keeping `zero_line` arguments backward compatible. +- Added separate table formatting controls for point estimates, + confidence interval bounds, and p-values via `estimate_digits`, + `interval_digits`, and `p_digits`. +- Added `ref_line`, `ref_line_value`, and `ref_line_label` to standardize + reference-line naming while keeping `zero_line` arguments backward compatible. - Added `term_labels`, a named-vector relabeling helper for displayed model terms. -- Expanded `add_forest_table(columns = ...)` and split-table column selection to support arbitrary preserved data columns in addition to built-in columns. -- Added `column_labels`, a named-vector helper for relabeling displayed table column headers. -- Added a built-in `ci` table column and `ci_fmt` so users can display point estimates and confidence intervals in separate columns. `conf.low` and `conf.high` are accepted as aliases for `ci`. +- Expanded `add_forest_table(columns = ...)` and split-table column selection to + support arbitrary preserved data columns in addition to built-in columns. +- Added `column_labels`, a named-vector helper for relabeling displayed table + column headers. +- Added a built-in `ci` table column and `ci_fmt` so users can display point + estimates and confidence intervals in separate columns. `conf.low` and + `conf.high` are accepted as aliases for `ci`. ## Minor Changes -- Added model-aware default effect labels and scales, including odds ratios for binomial logit models and hazard ratios for Cox models. +- Added model-aware default effect labels and scales, including odds ratios for + binomial logit models and hazard ratios for Cox models. # ggforestplotR 0.1.1 ## Minor Changes -- Added `events` column support across `ggforestplot()`, `as_forest_data()`, `add_forest_table()`, and `add_split_table()`. (Thanks @sritchie73 for the suggestion) -- Added table header styling controls for font size, font face, and font family in both table helpers. (Thanks @sritchie73 for the suggestion) -- Split table composition code into dedicated source files to simplify maintenance of the public API. -- Refined split-table examples and documentation to match the expanded numeric column mapping. +- Added `events` column support across `ggforestplot()`, `as_forest_data()`, + `add_forest_table()`, and `add_split_table()`. (#2) (#3) + (Thanks @sritchie73 for the suggestion) +- Added table header styling controls for font size, font face, and font family + in both table helpers. (Thanks @sritchie73 for the suggestion) +- Split table composition code into dedicated source files to simplify + maintenance of the public API. +- Refined split-table examples and documentation to match the expanded numeric + column mapping. # ggforestplotR 0.1.0 ## Major Changes -- Refined split-table layout logic, including dynamic panel widths from column counts, alignment controls, and cleaner stripe/background handling. -- `add_forest_table()` now allows for custom column ordering via the `columns` argument. -- Converted package documentation to roxygen-generated `NAMESPACE` and `.Rd` files. -- Reworked package documentation, including pkgdown configuration, README installation guidance, and the vignette set. +- Refined split-table layout logic, including dynamic panel widths from column + counts, alignment controls, and cleaner stripe/background handling. +- `add_forest_table()` now allows for custom column ordering via the `columns` + argument. +- Converted package documentation to roxygen-generated `NAMESPACE` and `.Rd` + files. +- Reworked package documentation, including pkgdown configuration, README + installation guidance, and the vignette set. # ggforestplotR 0.0.0.9000 diff --git a/cran-comments.md b/cran-comments.md index eaf65e5..023b49b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -4,7 +4,7 @@ ## R CMD check results -- `R CMD check ggforestplotR_0.3.1.tar.gz --as-cran` +- `R CMD check ggforestplotR_0.5.0.tar.gz --as-cran` - Status: OK 0 errors | 0 warnings | 0 notes diff --git a/revdep/README.md b/revdep/README.md index e212009..61a88a6 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,43 +1,43 @@ # Platform -|field |value | -|:--------|:-------------------------------------------------------------------------------------------------------------------------------------------------------| -|version |R version 4.6.0 (2026-04-24 ucrt) | -|os |Windows 11 x64 (build 26200) | -|system |x86_64, mingw32 | -|ui |RStudio | -|language |(EN) | -|collate |English_United States.utf8 | -|ctype |English_United States.utf8 | -|tz |America/New_York | -|date |2026-05-19 | -|rstudio |2026.04.0+526 Globemaster Allium (desktop) | -|pandoc |3.9 @ D:\pandoc\pandoc-3.9\pandoc.exe | -|quarto |ERROR: Unknown command "TMPDIR=C:/Users/Carso/AppData/Local/Temp/RtmpoFpwMI/file19fc4e91f46". Did you mean command "remove"? @ D:\Quarto\bin\quarto.exe | +|field |value | +|:--------|:------------------------------------------| +|version |R version 4.6.1 (2026-06-24 ucrt) | +|os |Windows 11 x64 (build 26200) | +|system |x86_64, mingw32 | +|ui |RStudio | +|language |(EN) | +|collate |English_United States.utf8 | +|ctype |English_United States.utf8 | +|tz |America/New_York | +|date |2026-09-02 | +|rstudio |2026.04.0+526 Globemaster Allium (desktop) | +|pandoc |3.9 @ D:\pandoc\pandoc-3.9\pandoc.exe | +|quarto |1.9.35 @ D:\Quarto\bin\quarto.exe | # Dependencies -|package |old |new |Δ | -|:-------------|:-----|:-----|:--| -|ggforestplotR |0.1.1 |0.2.0 |* | -|cli |3.6.6 |3.6.6 | | -|cpp11 |0.5.5 |0.5.5 | | -|farver |2.1.2 |2.1.2 | | -|ggplot2 |4.0.3 |4.0.3 | | -|glue |1.8.1 |1.8.1 | | -|gtable |0.3.6 |0.3.6 | | -|isoband |0.3.0 |0.3.0 | | -|labeling |0.4.3 |0.4.3 | | -|lifecycle |1.0.5 |1.0.5 | | -|patchwork |1.3.2 |1.3.2 | | -|R6 |2.6.1 |2.6.1 | | -|RColorBrewer |1.1-3 |1.1-3 | | -|rlang |1.2.0 |1.2.0 | | -|S7 |0.2.2 |0.2.2 | | -|scales |1.4.0 |1.4.0 | | -|vctrs |0.7.3 |0.7.3 | | -|viridisLite |0.4.3 |0.4.3 | | -|withr |3.0.2 |3.0.2 | | +|package |old |new |Δ | +|:-------------|:-----|:---|:--| +|ggforestplotR |0.3.1 |NA |* | +|cli |3.6.6 |NA |* | +|cpp11 |0.5.5 |NA |* | +|farver |2.1.2 |NA |* | +|ggplot2 |4.0.3 |NA |* | +|glue |1.8.1 |NA |* | +|gtable |0.3.6 |NA |* | +|isoband |0.3.0 |NA |* | +|labeling |0.4.3 |NA |* | +|lifecycle |1.0.5 |NA |* | +|patchwork |1.3.2 |NA |* | +|R6 |2.6.1 |NA |* | +|RColorBrewer |1.1-3 |NA |* | +|rlang |1.3.0 |NA |* | +|S7 |0.2.2 |NA |* | +|scales |1.4.0 |NA |* | +|vctrs |0.7.3 |NA |* | +|viridisLite |0.4.3 |NA |* | +|withr |3.0.3 |NA |* | # Revdeps