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

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Mar 11, 2023
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Prepare for v0.8.0 release [skip vbump] #855

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4b8a9ce
Version bump/update NEWS [skip vbump]
edelarua Mar 10, 2023
4442474
Fix grammar
edelarua Mar 10, 2023
490d5f4
Add version requirements
edelarua Mar 10, 2023
dc2e632
empty commit
edelarua Mar 10, 2023
a341384
Merge branch 'main' into 849_prepare_release@main
shajoezhu Mar 11, 2023
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10 changes: 5 additions & 5 deletions DESCRIPTION
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@@ -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")),
Expand All @@ -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,
Expand All @@ -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,
Expand All @@ -50,7 +50,7 @@ Imports:
Suggests:
knitr,
lattice,
nestcolor (>= 0.1.0),
nestcolor (>= 0.1.1),
rmarkdown,
stringr,
testthat (>= 3.0)
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66 changes: 28 additions & 38 deletions NEWS.md
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# 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

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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -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.

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