[skip vbump] Prepare for v0.8.0 release (#855)

Closes #849

---------

Signed-off-by: Joe Zhu <[email protected]>
Co-authored-by: Joe Zhu <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.7.10.9057
+Version: 0.8.0
 Date: 2023-03-10
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", 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,
@@ -30,8 +30,8 @@ Imports:
     dplyr,
     emmeans (>= 1.4.5),
     forcats (>= 1.0.0),
-    formatters (>= 0.3.4.21),
-    ggplot2,
+    formatters (>= 0.4.0),
+    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)

NEWS.md

@@ -1,62 +1,52 @@
-# tern 0.7.10.9057
+# 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.
+* 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.
+* Fixed bug in `test_proportion_diff` missing argument for `var_labels`.
 
-### 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.
+* 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 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
 

README.md

@@ -41,19 +41,19 @@ The package provides a large range of functionality, for example:
 
 <!-- markdownlint-enable MD007 MD030 -->
 
-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")
 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.