From 4b8a9cef138a801a199f3c84631e8d68ede10877 Mon Sep 17 00:00:00 2001 From: Emily de la Rua Date: Fri, 10 Mar 2023 14:29:51 -0500 Subject: [PATCH 1/4] Version bump/update NEWS [skip vbump] --- DESCRIPTION | 6 ++--- NEWS.md | 63 ++++++++++++++++++++++------------------------------- README.md | 6 ++--- 3 files changed, 32 insertions(+), 43 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8722202a4a..06c59a465e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: tern Title: Create Common TLGs Used in Clinical Trials -Version: 0.7.10.9056 +Version: 0.8.0 Date: 2023-03-09 Authors@R: c( person("Joe", "Zhu", , "joe.zhu@roche.com", role = c("aut", "cre")), @@ -21,7 +21,7 @@ URL: https://github.com/insightsengineering/tern BugReports: https://github.com/insightsengineering/tern/issues Depends: R (>= 3.6), - rtables (>= 0.5.3.5) + rtables (>= 0.6.0) Imports: broom, car, @@ -30,7 +30,7 @@ Imports: dplyr, emmeans (>= 1.4.5), forcats (>= 1.0.0), - formatters (>= 0.3.4.21), + formatters (>= 0.4.0), ggplot2, grid, gridExtra, diff --git a/NEWS.md b/NEWS.md index dbb84eeef4..2384b1f26d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,62 +1,51 @@ -# tern 0.7.10.9056 +# tern 0.8.0 ### Enhancements -* Added `summarize_glm_count` function to tern. -* Replaced `synthetic_cdisc_data` with re-factored `synthetic_cdisc_dataset` - function to speed up data set loading in tests/examples. -* Updated all tests to use `rcd_2022_06_27` version of cached data. -* Added more tests to increase code coverage. +* 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 `format_count_fraction_fixed_dp` with fixed single decimal place in percentages. -* Removed `summary_in_cols` helper functions because redundant. -* Added `na_level` and `labelstr` to `summarize_vars_in_cols`. -* Added tests for `pkct01`, `adat03`, `pdt01`, and `pdt02`. -* Added `analyze_num_patients` to have total summary at the beginning that does not +* Added `na_level` and `labelstr` arguments to `summarize_vars_in_cols`. +* Added `analyze_num_patients` to include summary at the beginning that does not repeat when paginating. * Added `h_row_first_values` function as a more general helper function to retrieve first values from specific rows. -* Replaced table template tests with snapshot testing. * Added option to remove `"(n)"` suffix from `unique_count` labels for `s_num_patients`. -* Updated `summarize_ancova` examples to use `iris` dataset in examples instead of `scda` data. -* Created vignette which saves cached synthetic CDISC dataset files to the `data/` folder. -* Added cached synthetic datasets to `data/` folder to use in tests/examples instead of `scda` data. -* Updated examples to use datasets from the `tern` package instead of `scda` datasets. -* Replaced all applicable tests with snapshot testing. -* Updated all tests to use `tern` data. * 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 grades are present in `s_count_occurrences_by_grade`. -* Changed `summarize_vars_in_cols` to work with pagination machinery. -* Fixed bug passing `conf_level` to `emmeans::contrast()` in `s_ancova` to make - it works. Tests are also updated. -* Fixed table tests (`aet02`, `aet02_smq`, `aet_03`, `aet_06_smq`, `aet_09`, - `aet_09_smq`, `mth01`, `cmt01`, `aet07`, `aet06`) that used - `summarize_num_patients` to generate an initial summary so there is no repetition - when paginating. -* Removed deprecated `ggplot2` functions/arguments to resolve warnings. -* Fixed bugs in `rtables_access.R` that did not check for specific combination - (also the standard values, that where never used) of column indices and names. +* 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`. +* Fixed bugs in `rtables_access.R` caused by not checking for specific combinations + (also the standard values that were never used) of column indices and names. * Fixed single applicable record bug in `count_abnormal_by_grade`. * Fixed bug in `add_rowcounts` that caused all row count row values to be counted as zero. * Fixed bug in `h_col_indices` causing an error when pruning with an overall column added. -### Miscellaneous -* Renamed `test_pkc01.R` and `summarize_variables_in_cols.R` into `test_pkct01.R` - and `summarize_vars_in_cols.R`, respectively. -* Renamed `summarize_vars_in_cols` into `analyze_vars_in_cols` to reflect the - appropriate `analyze` logic. -* Exported function `format_xx`. -* Updated tests to use `testthat` 3rd edition. +### Documentation and Tests +* 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. -* Removed all template tests from `tern`. These tests are in internal repo `scda.test`. +* 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 + 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 kept in internal repo `scda.test`. + +### Miscellaneous +* Renamed `summarize_vars_in_cols` to `analyze_vars_in_cols` to reflect the appropriate `analyze` logic. +* Removed redundant `summary_in_cols` helper functions. +* Exported function `format_xx`. +* Replaced deprecated `ggplot2` functions/arguments to fix warnings. * Replaced deprecated function `forcats::fct_explicit_na` with `forcats::fct_na_value_to_level`. -* Removal of deprecated `wrap_text` and related files. -* Deprecation cycle started for `footnotes` functions. +* Removed deprecated `wrap_text` function and related files. +* Started deprecation cycle for `footnotes` functions. # tern 0.7.10 diff --git a/README.md b/README.md index e6529011e1..2c1139963d 100644 --- a/README.md +++ b/README.md @@ -41,11 +41,11 @@ The package provides a large range of functionality, for example: -Many of these outputs are available to be added into `teal` applications for interactive exploration of data. These `teal` modules are available in the [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical) package. +Many of these outputs are available to be added into [`teal`](https://insightsengineering.github.io/teal) applications for interactive exploration of data. These [`teal`](https://insightsengineering.github.io/teal) modules are available in the [`teal.modules.clinical`](https://insightsengineering.github.io/teal.modules.clinical) package. ## Installation -For releases from August 2022 it is recommended that you [create and use a Github PAT](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following: +It is recommended that you [create and use a Github PAT](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following: ```r Sys.setenv(GITHUB_PAT = "your_access_token_here") @@ -53,7 +53,7 @@ if (!require("remotes")) install.packages("remotes") remotes::install_github("insightsengineering/tern@*release") ``` -A stable release of all `NEST` packages from June 2022 is also available [here](https://github.com/insightsengineering/depository#readme). +A stable release of all `NEST` packages from October 2022 is also available [here](https://github.com/insightsengineering/depository#readme). See package vignettes `browseVignettes(package = "tern")` for usage of this package. From 4442474cc4c0fb713d2c10f08d8225fdf9db8a45 Mon Sep 17 00:00:00 2001 From: Emily de la Rua Date: Fri, 10 Mar 2023 15:02:20 -0500 Subject: [PATCH 2/4] Fix grammar --- NEWS.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 2384b1f26d..f3a3be058d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -22,8 +22,8 @@ * Fixed bugs in `rtables_access.R` caused by not checking for specific combinations (also the standard values that were never used) of column indices and names. * Fixed single applicable record bug in `count_abnormal_by_grade`. -* Fixed bug in `add_rowcounts` that caused all row count row values to be counted as zero. -* Fixed bug in `h_col_indices` causing an error when pruning with an overall column added. +* Fixed bug in `add_rowcounts` that caused all row count row values to count as zero. +* Fixed bug in `h_col_indices` causing an error when pruning with combination columns. ### Documentation and Tests * Added more tests to increase code coverage. @@ -36,7 +36,7 @@ * 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 kept in internal repo `scda.test`. +* Removed all template tests from `tern`. These tests are in internal repo `scda.test`. ### Miscellaneous * Renamed `summarize_vars_in_cols` to `analyze_vars_in_cols` to reflect the appropriate `analyze` logic. From 490d5f48384008d5142b804aa64560da7a9418be Mon Sep 17 00:00:00 2001 From: Emily de la Rua Date: Fri, 10 Mar 2023 15:26:10 -0500 Subject: [PATCH 3/4] Add version requirements --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 06c59a465e..d5d9226232 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -31,7 +31,7 @@ Imports: emmeans (>= 1.4.5), forcats (>= 1.0.0), formatters (>= 0.4.0), - ggplot2, + ggplot2 (>= 3.4.0), grid, gridExtra, gtable, @@ -50,7 +50,7 @@ Imports: Suggests: knitr, lattice, - nestcolor (>= 0.1.0), + nestcolor (>= 0.1.1), rmarkdown, stringr, testthat (>= 3.0) From dc2e632d18918fce52c5bef8842ad5f707681bdf Mon Sep 17 00:00:00 2001 From: Emily de la Rua Date: Fri, 10 Mar 2023 15:36:27 -0500 Subject: [PATCH 4/4] empty commit