From 189f4cc2e06f3475148e654bbdee44a79c55ee2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Wed, 19 Jul 2023 15:46:23 +0200 Subject: [PATCH 01/15] docs: adds minimum version to dependencies --- DESCRIPTION | 49 ++++++++++++++++++++++++++++++---------- NEWS.md | 64 ++++++++++++++++++++++++++++------------------------- 2 files changed, 71 insertions(+), 42 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9af9f0e991..dd7b9882ac 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,11 +23,11 @@ Depends: R (>= 3.6), rtables (>= 0.6.5) Imports: - broom, - car, - checkmate, + broom (>= 0.5.1), + car (>= 3.0-13), + checkmate (>= 2.1.0), cowplot, - dplyr, + dplyr (>= 1.0.0), emmeans (>= 1.4.5), forcats (>= 1.0.0), formatters (>= 0.5.4), @@ -36,31 +36,56 @@ Imports: gridExtra, gtable, labeling, - lifecycle, - magrittr, + lifecycle (>= 0.2.0), + magrittr (>= 1.5), methods, Rdpack, rlang, scales, stats, survival (>= 3.2-13), - tibble, - tidyr, + tibble (>= 2.0.0), + tidyr (>= 0.8.3), utils Suggests: - knitr, + knitr (>= 1.34), lattice, lubridate, nestcolor (>= 0.1.1), - rmarkdown, - stringr, - testthat (>= 3.0), + rmarkdown (>= 2.19), + stringr (>= 1.4.1), + testthat (>= 3.1.5), vdiffr (>= 1.0.0) VignetteBuilder: knitr RdMacros: lifecycle, Rdpack +Config/Needs/verdepcheck: + insightsengineering/rtables, + tidymodels/broom, + cran/car, + mllg/checkmate, + wilkelab/cowplot, + tidyverse/dplyr, + rvlenth/emmeans, + tidyverse/forcats, + insightsengineering/formatters, + tidyverse/ggplot2, + r-lib/gtable, + r-lib/lifecycle, + tidyverse/magrittr, + GeoBosh/Rdpack, + r-lib/rlang, + r-lib/scales, + tidyverse/tibble, + tidyverse/tidyr, + yihui/knitr, + tidyverse/lubridate, + insightsengineering/nestcolor, + rstudio/rmarkdown, + tidyverse/stringr, + r-lib/testthat Config/Needs/website: insightsengineering/nesttemplate Config/testthat/edition: 3 Encoding: UTF-8 diff --git a/NEWS.md b/NEWS.md index 2a6d0f2443..68dcb33766 100644 --- a/NEWS.md +++ b/NEWS.md @@ -39,6 +39,10 @@ * Renamed statistical method for `p-value` in the discrete case to `pval_counts`. * Removed `a_summary_internal()` in favor of only one main `a_summary()`. +## Miscellaneous + +* Specify minimal version of dependent packages. + # tern 0.9.0 ### New Features @@ -65,7 +69,7 @@ ### Enhancements * Added `ylim` argument to `g_km` to allow the user to set custom limits for the y-axis. * Added assertion to `g_km` which checks whether there is one arm present in the data when `annot_coxph` is true. -* Added `flag_labels` argument to `s_count_patients_with_flags` to enable more label handling options in `count_patients_by_flags`. +* Added `flag_labels` argument to `s_count_patients_with_flags` to enable more label handling options in `count_patients_by_flags`. * Added the `nested` argument to `analyze` wrapper functions `count_abnormal`, `count_abnormal_by_baseline`, `count_abnormal_by_marked`, `count_abnormal_by_worst_grade`, `count_abnormal_lab_worsen_by_baseline`, `count_cumulative`, `count_missed_doses`, `count_occurrences`, `count_occurrences_by_grade`, `count_patients_with_event`, `count_patients_with_flags`, `count_values`, `estimate_multinomial_response`, `estimate_proportion`, `estimate_incidence_rate`, `estimate_odds_ratio`, `estimate_proportion_diff`, `test_proportion_diff`, `summarize_ancova`, `summarize_change`, `summarize_glm_count`, `analyze_num_patients`, `coxph_pairwise`, `surv_time`, and `surv_timepoint`. ## Miscellaneous @@ -139,7 +143,7 @@ ### Enhancements * Added `summarize_glm_count` function to analyze count data using a linear model. * Added legend to `g_step`. -* Added formatting functions `format_fraction_fixed_dp` and +* Added formatting functions `format_fraction_fixed_dp` and `format_count_fraction_fixed_dp` with fixed single decimal place in percentages. * Added `na_level` and `labelstr` arguments to `summarize_vars_in_cols`. * Added `analyze_num_patients` to include summary at the beginning that does not @@ -147,11 +151,11 @@ * Added `h_row_first_values` function as a more general helper function to retrieve first values from specific rows. * Added option to remove `"(n)"` suffix from `unique_count` labels for `s_num_patients`. -* Added options to `g_km` to annotate with statistics (`annot_stats`) and add corresponding +* Added options to `g_km` to annotate with statistics (`annot_stats`) and add corresponding vertical lines (`annot_stats_lines`). ### Bug Fixes -* Fixed bug causing incorrect ordering of numeric grade levels when missing +* Fixed bug causing incorrect ordering of numeric grade levels when missing grades are present in `s_count_occurrences_by_grade`. * Refactored `summarize_vars_in_cols` to work with pagination machinery. * Fixed bug to allow passing of `conf_level` argument to `emmeans::contrast()` in `s_ancova`. @@ -166,11 +170,11 @@ * Added more tests to increase code coverage. * Created separate documentation files for functions in different sections of `pkgdown` reference. * Created separate `.R` files for logistic regression and cox regression helper functions. -* Fixed table tests using `analyze_num_patients` to generate an initial summary so there is no +* Fixed table tests using `analyze_num_patients` to generate an initial summary so there is no repetition when paginating. * Updated tests to use `testthat` 3rd edition and replaced applicable tests with snapshot testing. * Updated `summarize_ancova` examples to use `iris` dataset instead of `scda` data. -* Created vignette which saves cached synthetic `CDISC` dataset files to the `data/` folder and +* Created vignette which saves cached synthetic `CDISC` dataset files to the `data/` folder and generated cached synthetic datasets. * Updated all examples/tests to use datasets from the `data/` folder instead of `scda` datasets. * Removed all template tests from `tern`. These tests are in internal repo `scda.test`. @@ -189,40 +193,40 @@ ### New Features * Added stratified `Newcombe` and stratified Wilson statistics to `estimate_proportion` and `estimate_proportion_diff` with relative tests. -* Added `stat_mean_pval`, a new summary statistic to calculate the p-value of +* Added `stat_mean_pval`, a new summary statistic to calculate the p-value of the mean. -* Added statistic `mean_se` (mean with standard error) for `summarize_variables` +* Added statistic `mean_se` (mean with standard error) for `summarize_variables` and related functions. * Introduced again `Rdpack` for references. -### Enhancements -* Redesign of data handling in tests by removing repetitive data loads and +### Enhancements +* Redesign of data handling in tests by removing repetitive data loads and library calls. * Added `DescTools::BinomDiffCI` function within `tern`. -* Added new parameter to `summarize_logistic` to specify which pivoted value +* Added new parameter to `summarize_logistic` to specify which pivoted value to use during analysis. -* Updated `s_coxph_pairwise` to generate log-rank p-value using original +* Updated `s_coxph_pairwise` to generate log-rank p-value using original log-rank test instead of Cox Proportional-Hazards Model. -* Implemented `nestcolor` in all examples by adapting `g_km`, `g_ipp`, +* Implemented `nestcolor` in all examples by adapting `g_km`, `g_ipp`, `g_waterfall`, `g_step`, `g_lineplot`, and `g_forest`. -* Added parameters `interaction_y` and `interaction_item` in `ANCOVA` to make the +* Added parameters `interaction_y` and `interaction_item` in `ANCOVA` to make the interaction calculations available. * Added new parameter `footnotes` to add footnotes to `g_km`. ### Migration from `assertthat` to `checkmate` -* Implemented `checkmate::assert_vector`, `checkmate::assert_set_equal`, and +* Implemented `checkmate::assert_vector`, `checkmate::assert_set_equal`, and `checkmate::assert_int` to check vector type, length, and values. * Replaced with standard assertions from `checkmate` the following functions: - `all_elements_in_ref`, `is_df_with_nlevels_factor`, `is_df_with_no_na_level`, - `is_proportion_vector`, `is_quantiles_vector`, `is_character_or_factor`, - `is_nonnegative_count`, `is_valid_character`, `assert_character_or_factor`, + `all_elements_in_ref`, `is_df_with_nlevels_factor`, `is_df_with_no_na_level`, + `is_proportion_vector`, `is_quantiles_vector`, `is_character_or_factor`, + `is_nonnegative_count`, `is_valid_character`, `assert_character_or_factor`, `assert_equal_length` and `has_tabletree_colnames`. -* Modified `is_proportion`, `is_equal_length`, `is_df_with_no_na_level`, - `is_df_with_nlevels_factor`, `is_variables`, `is_df_with_variables`, +* Modified `is_proportion`, `is_equal_length`, `is_df_with_no_na_level`, + `is_df_with_nlevels_factor`, `is_variables`, `is_df_with_variables`, `is_df_with_factors`, `is_valid_factor` to use assertion logic. * Added more verbose warnings from `as_factor_keep_attributes`. * Made `assert_df_with_factors` and `assert_proportion_value` internal functions. -* Renamed `assertthat.R` and `test-assertthat.R` to `utils_checkmate.R` and +* Renamed `assertthat.R` and `test-assertthat.R` to `utils_checkmate.R` and `test-utils_checkmate.R`. ### Documentation and NAMESPACE Polishing @@ -252,7 +256,7 @@ `estimate_multinomial_rsp`, `decorate_grob_set`, `extreme_format`, `fit_rsp_step`, `fit_survival_step`, `footnotes`, `footnotes-set`, `format_count_fraction`, `format_fraction_threshold`, `formatting_functions`, - `format_fraction`, `combination_function` (S4 method), `compare_variables` (S3 method), + `format_fraction`, `combination_function` (S4 method), `compare_variables` (S3 method), `kaplan_meier`. * Internal keywords added, export removed, `_pkgdown.yml` updated, and `tern:::` added for tests/examples/vignettes where present for the following functions: @@ -287,24 +291,24 @@ * Fixed empty vector exception for `cut_quantile_bins`. * Fixed exception error when empty strings are present in pivoted columns (`rtables` split functions) -* Fixed bug in `s_ancova` causing an error when the first level of the arm - factor is not the control arm. +* Fixed bug in `s_ancova` causing an error when the first level of the arm + factor is not the control arm. * Fixed bug in `s_abnormal_by_worst_grade` when there is one `PARAM` level. * Fixed bug in `prop_diff_wald` when selecting all responders, updated tests accordingly. * Fixed bug in `h_ancova` that caused an error when deselecting all covariates. ### Miscellaneous * Added deprecated badge to `g_mmrm`. -* Removed internal function calls in examples (`tern:::`) and added `dontrun` +* Removed internal function calls in examples (`tern:::`) and added `dontrun` to internal function examples. * Removed warnings and messages to console occurring in examples and tests. -* Deprecated functions `color_palette` and `h_set_nest_theme` in favor of +* Deprecated functions `color_palette` and `h_set_nest_theme` in favor of `nestcolor::color_palette` and `nestcolor::theme_nest`, respectively. -* Removed deprecated functions: `color_palette`, `color_palette_core`, +* Removed deprecated functions: `color_palette`, `color_palette_core`, `h_set_nest_theme`, `s_cox_univariate`. -* Removed deprecated `mmrm` functions: `fit_mmrm`, `g_mmrm_diagnostic`, - `g_mmrm_lsmeans`, `as.rtable.mmrm`, `h_mmrm_fixed`, `h_mmrm_cov`, - `h_mmrm_diagnostic`, `tidy.mmrm`, `s_mmrm_lsmeans`, `s_mmrm_lsmeans_single`, +* Removed deprecated `mmrm` functions: `fit_mmrm`, `g_mmrm_diagnostic`, + `g_mmrm_lsmeans`, `as.rtable.mmrm`, `h_mmrm_fixed`, `h_mmrm_cov`, + `h_mmrm_diagnostic`, `tidy.mmrm`, `s_mmrm_lsmeans`, `s_mmrm_lsmeans_single`, `summarize_lsmeans`. * Renamed functions `arm` to `study_arm` and `extract` to `extract_by_name`. * Renamed `rtables.R` to `utils_rtables.R`. From b26ecde239dadad79f250d8c7cc89caa28efc249 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Wed, 19 Jul 2023 15:46:33 +0200 Subject: [PATCH 02/15] ci: adds temporary action on push --- .github/workflows/scheduled.yaml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index 62afcda85a..8a2d9ad324 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -5,14 +5,20 @@ on: schedule: - cron: '45 3 * * 0' workflow_dispatch: + # Section to be removed before action is merged + # note: branch below needs to point to main instead of new-verdepcheck-strategy + push: + branches: + - verdepcheck_action + # end of section to be removed jobs: dependency-test: strategy: fail-fast: false matrix: - test-strategy: ["min", "release", "max"] - uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main + test-strategy: ["min_cohort", "min_isolated", "release", "max"] + uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@new-verdepcheck-strategy name: Dependency Test - ${{ matrix.test-strategy }} đŸ”¢ secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} From 228dcd1d5e6c9a99364a599a76676763594f6fba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Wed, 26 Jul 2023 00:29:59 +0200 Subject: [PATCH 03/15] docs: add minimal version of deps --- DESCRIPTION | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index dd7b9882ac..f0606bc580 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,25 +23,25 @@ Depends: R (>= 3.6), rtables (>= 0.6.5) Imports: - broom (>= 0.5.1), + broom (>= 0.5.4), car (>= 3.0-13), checkmate (>= 2.1.0), - cowplot, + cowplot (>= 0.7.0), dplyr (>= 1.0.0), emmeans (>= 1.4.5), forcats (>= 1.0.0), formatters (>= 0.5.4), ggplot2 (>= 3.4.0), grid, - gridExtra, - gtable, + gridExtra (>= 2.0.0), + gtable (>= 0.3.0), labeling, lifecycle (>= 0.2.0), magrittr (>= 1.5), methods, - Rdpack, - rlang, - scales, + Rdpack (>= 2.4), + rlang (>= 1.1.0), + scales (>= 1.2.0), stats, survival (>= 3.2-13), tibble (>= 2.0.0), @@ -49,8 +49,8 @@ Imports: utils Suggests: knitr (>= 1.34), - lattice, - lubridate, + lattice (>= 0.18-4), + lubridate (>= 1.7.9), nestcolor (>= 0.1.1), rmarkdown (>= 2.19), stringr (>= 1.4.1), @@ -85,7 +85,8 @@ Config/Needs/verdepcheck: insightsengineering/nestcolor, rstudio/rmarkdown, tidyverse/stringr, - r-lib/testthat + r-lib/testthat, + r-lib/vdiffr Config/Needs/website: insightsengineering/nesttemplate Config/testthat/edition: 3 Encoding: UTF-8 From 549d98f4baecd9f671ffd81d58fa6c2b61c94458 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 1 Sep 2023 15:52:42 +0200 Subject: [PATCH 04/15] docs: update versions --- .github/workflows/scheduled.yaml | 2 +- DESCRIPTION | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index 8a2d9ad324..e696caac63 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -18,7 +18,7 @@ jobs: fail-fast: false matrix: test-strategy: ["min_cohort", "min_isolated", "release", "max"] - uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@new-verdepcheck-strategy + uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main name: Dependency Test - ${{ matrix.test-strategy }} đŸ”¢ secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} diff --git a/DESCRIPTION b/DESCRIPTION index f0606bc580..cbcf97b6b3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -81,6 +81,7 @@ Config/Needs/verdepcheck: tidyverse/tibble, tidyverse/tidyr, yihui/knitr, + deepayan/lattice, tidyverse/lubridate, insightsengineering/nestcolor, rstudio/rmarkdown, From 951c23e20305cd07b7bde681a509993cd91fa672 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 1 Sep 2023 15:56:59 +0200 Subject: [PATCH 05/15] docs: remove rmarkdown in favor or recent knitr --- DESCRIPTION | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cbcf97b6b3..f459f1c27c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -48,11 +48,10 @@ Imports: tidyr (>= 0.8.3), utils Suggests: - knitr (>= 1.34), + knitr (>= 1.42), lattice (>= 0.18-4), lubridate (>= 1.7.9), nestcolor (>= 0.1.1), - rmarkdown (>= 2.19), stringr (>= 1.4.1), testthat (>= 3.1.5), vdiffr (>= 1.0.0) @@ -84,7 +83,6 @@ Config/Needs/verdepcheck: deepayan/lattice, tidyverse/lubridate, insightsengineering/nestcolor, - rstudio/rmarkdown, tidyverse/stringr, r-lib/testthat, r-lib/vdiffr From 10f1edc033f7d14203f10e7cb20c2be0a8bedefc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 5 Sep 2023 13:32:49 +0200 Subject: [PATCH 06/15] docs: typo on NEWS.md --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 68dcb33766..dbfeb5c7e0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -41,7 +41,7 @@ ## Miscellaneous -* Specify minimal version of dependent packages. +* Specified minimal version of package dependencies. # tern 0.9.0 From c258274dea304c33972d7fe1111f386dacb2604a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Wed, 20 Sep 2023 14:38:00 +0200 Subject: [PATCH 07/15] docs: updates news --- .github/workflows/scheduled.yaml | 6 ------ NEWS.md | 3 --- 2 files changed, 9 deletions(-) diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index e696caac63..df66705fe6 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -5,12 +5,6 @@ on: schedule: - cron: '45 3 * * 0' workflow_dispatch: - # Section to be removed before action is merged - # note: branch below needs to point to main instead of new-verdepcheck-strategy - push: - branches: - - verdepcheck_action - # end of section to be removed jobs: dependency-test: diff --git a/NEWS.md b/NEWS.md index dbfeb5c7e0..06b7e1fa7b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -38,9 +38,6 @@ * Started deprecation of `summary_custom()` and `a_summary()` as a `S3` method. * Renamed statistical method for `p-value` in the discrete case to `pval_counts`. * Removed `a_summary_internal()` in favor of only one main `a_summary()`. - -## Miscellaneous - * Specified minimal version of package dependencies. # tern 0.9.0 From 8c9672b3e682a4ba805012238be6ff18ea3e3eaf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 26 Sep 2023 00:36:46 +0200 Subject: [PATCH 08/15] docs: bumps minimum broom version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index f459f1c27c..cd32183f3a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,7 +23,7 @@ Depends: R (>= 3.6), rtables (>= 0.6.5) Imports: - broom (>= 0.5.4), + broom (>= 0.7.4), car (>= 3.0-13), checkmate (>= 2.1.0), cowplot (>= 0.7.0), From 660fa28d33b4280e55247d598933e3b38cf0584f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 26 Sep 2023 02:24:21 +0200 Subject: [PATCH 09/15] docs: revert broom and bump emmeans --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cd32183f3a..5d0b2f4020 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,12 +23,12 @@ Depends: R (>= 3.6), rtables (>= 0.6.5) Imports: - broom (>= 0.7.4), + broom (>= 0.5.4), car (>= 3.0-13), checkmate (>= 2.1.0), cowplot (>= 0.7.0), dplyr (>= 1.0.0), - emmeans (>= 1.4.5), + emmeans (>= 1.8.0), forcats (>= 1.0.0), formatters (>= 0.5.4), ggplot2 (>= 3.4.0), From e5eb0500f07f1457b7636cfa6a3b23c6b30e7b2b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 26 Sep 2023 11:43:47 +0200 Subject: [PATCH 10/15] docs: bump testthat to include expect_contains --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5d0b2f4020..89704d82da 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -53,7 +53,7 @@ Suggests: lubridate (>= 1.7.9), nestcolor (>= 0.1.1), stringr (>= 1.4.1), - testthat (>= 3.1.5), + testthat (>= 3.1.9), vdiffr (>= 1.0.0) VignetteBuilder: knitr From 75b69dc62f3fb1f634e0380a65525e5e3e65bfd6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 26 Sep 2023 13:06:11 +0200 Subject: [PATCH 11/15] docs: bumps vdiffr as 1.0.6 had compilation issues --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 89704d82da..9d04aae3a8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,7 +54,7 @@ Suggests: nestcolor (>= 0.1.1), stringr (>= 1.4.1), testthat (>= 3.1.9), - vdiffr (>= 1.0.0) + vdiffr (>= 1.0.7) VignetteBuilder: knitr RdMacros: From 5388ac7b29b32c5a808a748bdeb80f54b5f8b47a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Mon, 16 Oct 2023 14:12:26 +0200 Subject: [PATCH 12/15] specify version for rmarkdown --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index 9d04aae3a8..856daab66b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -49,6 +49,7 @@ Imports: utils Suggests: knitr (>= 1.42), + rmarkdown (>= 2.19), lattice (>= 0.18-4), lubridate (>= 1.7.9), nestcolor (>= 0.1.1), From d0add23909816af579b2576f20117b1568476f05 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Wed, 18 Oct 2023 14:15:27 +0200 Subject: [PATCH 13/15] correct news after rebase --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 06b7e1fa7b..cd66cc9cc6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -15,6 +15,7 @@ ### Miscellaneous * Began deprecation of `na_level` argument in `s_count_abnormal_by_baseline`, `a_summary`, `analyze_vars`, `analyze_vars_in_cols`, `compare_vars`, `h_map_for_count_abnormal`, `h_stack_by_baskets`, `summarize_colvars`, `a_coxreg`, and `summarize_coxreg` and replaced it with the `na_str` argument. +* Specified minimal version of package dependencies. # tern 0.9.1 @@ -38,7 +39,6 @@ * Started deprecation of `summary_custom()` and `a_summary()` as a `S3` method. * Renamed statistical method for `p-value` in the discrete case to `pval_counts`. * Removed `a_summary_internal()` in favor of only one main `a_summary()`. -* Specified minimal version of package dependencies. # tern 0.9.0 From c01069c04d3da48a4cba3ec088a9180b518d1425 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 20 Oct 2023 13:53:20 +0200 Subject: [PATCH 14/15] Update DESCRIPTION MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Signed-off-by: AndrĂ© VerĂ­ssimo <211358+averissimo@users.noreply.github.com> --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index 856daab66b..8b48cf4d9a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -84,6 +84,7 @@ Config/Needs/verdepcheck: deepayan/lattice, tidyverse/lubridate, insightsengineering/nestcolor, + rstudio/rmarkdown, tidyverse/stringr, r-lib/testthat, r-lib/vdiffr From 93cae1d5448c94b8875c6061a092c52f1193410a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Fri, 20 Oct 2023 13:55:22 +0200 Subject: [PATCH 15/15] rebase after release --- DESCRIPTION | 2 +- NEWS.md | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8b48cf4d9a..0924da27ff 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -49,10 +49,10 @@ Imports: utils Suggests: knitr (>= 1.42), - rmarkdown (>= 2.19), lattice (>= 0.18-4), lubridate (>= 1.7.9), nestcolor (>= 0.1.1), + rmarkdown (>= 2.19), stringr (>= 1.4.1), testthat (>= 3.1.9), vdiffr (>= 1.0.7) diff --git a/NEWS.md b/NEWS.md index cd66cc9cc6..192e14cb29 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # tern 0.9.2.9000 +### Miscellaneous +* Specified minimal version of package dependencies. + # tern 0.9.2 ### New Features @@ -15,7 +18,6 @@ ### Miscellaneous * Began deprecation of `na_level` argument in `s_count_abnormal_by_baseline`, `a_summary`, `analyze_vars`, `analyze_vars_in_cols`, `compare_vars`, `h_map_for_count_abnormal`, `h_stack_by_baskets`, `summarize_colvars`, `a_coxreg`, and `summarize_coxreg` and replaced it with the `na_str` argument. -* Specified minimal version of package dependencies. # tern 0.9.1