pharmaverse · barnett11 · Oct 30, 2024 · Jun 2, 2023 · Jun 2, 2023 · Jun 27, 2023
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,7 +5,6 @@
 ^.github$
 ^docs$
 ^.lintr$
-^codecov\.yml$
 ^datacutr\.Rcheck$
 ^datacutr.*\.tar\.gz$
 ^datacutr.*\.tgz$

diff --git a/.Rprofile b/.Rprofile
diff --git a/.github/ISSUE_TEMPLATE/05_onboard.yml b/.github/ISSUE_TEMPLATE/05_onboard.yml
@@ -18,7 +18,7 @@ body:
         - label: Given a tour of Github from a Core member
         - label: Understand how to Create Issues and do a Pull Request
         - label: Understand the Programming Strategy
-        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/cran-release/index.html)
+        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/CONTRIBUTING.html)
         - label: Invited to all relevant meetings - Stand Ups, Retrospective, Sprint Planning, Question/Comments, Backlog, Community Meeting
         - label: Given access to Box and relevant documents
         - label: Given write access to Github Repository
@@ -33,7 +33,7 @@ body:
         - label: Given a tour of Github from a Core member
         - label: Understand how to Create Issues and do a Pull Request
         - label: Understand the Programming Strategy
-        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/cran-release/index.html)
+        - label: Read and understand [Developer Guides Articles](https://pharmaverse.github.io/admiral/CONTRIBUTING.html)
         - label: Invited to all relevant meetings - Question/Comments, Community Meeting
         - label: Given write access to Github Repository
         - label: Slack channel invites to admiral

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,16 +1,16 @@
-Thank you for your Pull Request! [admiraldev](https://pharmaverse.github.io/admiraldev/devel/index.html) have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the datacutr codebase remains robust and consistent.   
+Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the datacutr codebase remains robust and consistent.   
 
 Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `devel` branch until you have checked off each task.
 
 - [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
 - [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files
-- [ ] Updated relevant unit tests or have written new unit tests - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html#writing-unit-tests-in-admiral-)
-- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html#deprecation-1)?
-- [ ] Update to all relevant roxygen headers and examples 
+- [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios)
+- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)?
+- [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
 - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately
 - [ ] Address any updates needed for vignettes and/or templates
 - [ ] Update `NEWS.md` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
-- [ ] Build datacutr site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiral/cran-release/reference/index.html)" page. 
+- [ ] Build datacutr site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/datacutr/main/reference/index.html)" page. 
 - [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`
 - [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`
 - [ ] Link the issue in the Development Section on the right hand side.

diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml
@@ -2,7 +2,7 @@
 # Source: https://github.com/pharmaverse/admiralci
 # Common workflows designed for Admiral
 # but can be easily used by any other R package
-name: Admiral Workflows
+name: admiral CI/CD Workflows
 
 on:
   # 'workflow_dispatch' gives you the ability
@@ -11,19 +11,19 @@ on:
   # 'push' events are triggered when commits
   # are pushed to one of these branches
   push:
+    tags:
+      - "v*"
     branches:
       - main
+      - patch
       - devel
-      - pre-release
-      - test
   # 'pull_request' events are triggered when PRs are
   # created against one of these target branches.
   pull_request:
     branches:
       - main
+      - patch
       - devel
-      - pre-release
-      - test
   # 'release' events are triggered when...
   # you guessed it - when releases are made.
   release:
@@ -35,77 +35,100 @@ concurrency:
   group: admiral-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+env:
+  R_VERSION: "release"
+
 jobs:
+  get_r_version:
+    name: Get R version
+    runs-on: ubuntu-latest
+    outputs:
+      r-version: ${{ steps.get_r_version.outputs.R_VERSION }}
+    steps:
+      - name: Get R Version for Downstream Container Jobs
+        id: get_r_version
+        run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
+        shell: bash
   style:
     name: Code Style
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.0"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.0"
-  readme:
-    name: Render README
-    uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
-    if: github.event_name == 'push'
-    with:
-      r-version: "4.0"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
+    needs: get_r_version
     with:
-      r-version: "4.0"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
+    with:
+      error-on: warning # TODO: find a way to ignore specific notes
     if: github.event_name == 'pull_request'
   docs:
     name: Documentation
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
-    if: github.event_name == 'push'
+    if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/v')
+    needs: get_r_version
     with:
-      r-version: "4.0"
-      # Whether to skip multiversion docs
-      # Note that if you have multiple versions of docs,
-      # your URL links are likely to break due to path changes
+      r-version: "release"
       skip-multiversion-docs: false
+      insert-tweak-page-hook: false
+      multiversion-docs-landing-page: main
+    secrets:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
   linter:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
+    needs: get_r_version
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
-    if: >
-      github.event_name == 'push' || github.event_name == 'pull_request'
+    if: github.event_name == 'pull_request'
   coverage:
     name: Code Coverage
     uses: pharmaverse/admiralci/.github/workflows/code-coverage.yml@main
     if: >
-      github.event_name == 'push' || github.event_name == 'pull_request'
+      github.event_name != 'release'
+    needs: get_r_version
     with:
-      r-version: "4.0"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
       skip-coverage-badges: false
-  templates:
-    name: Check Templates
-    uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
-    if: >
-      github.event_name == 'push' || github.event_name == 'pull_request'
-    with:
-      r-version: "4.0"
   man-pages:
     name: Man Pages
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  templates:
+    name: Check Templates
+    uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
+    secrets: inherit
+    if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
+    needs: get_r_version
     with:
-      r-version: "4.0"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  vbump:
+    name: Version Bump 🤜🤛
+    if: github.event_name == 'push'
+    uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.PHARMAVERSE_BOT }}
diff --git a/.lintr b/.lintr
@@ -1,2 +1,10 @@
-linters: with_defaults(line_length_linter(100), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20))
-exclusions: list("R/data.R")
+linters: linters_with_defaults(
+    line_length_linter(100),
+    object_usage_linter=NULL,
+    infix_spaces_linter=NULL,
+    indentation_linter=NULL,
+    cyclocomp_linter(complexity_limit = 22)
+  )
+exclusions: list(
+    "R/data.R",
+    "tests/testthat")
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,32 +1,36 @@
 Package: datacutr
 Type: Package
 Title: SDTM Datacut
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
     person("Tim", "Barnett", email = "[email protected]", role = c("cph","aut", "cre")), 
     person("Nathan", "Rees", email = "[email protected]", role = c("aut")), 
-    person("Alana", "Harris", email = "[email protected]", role = c("aut")))
+    person("Alana", "Harris", email = "[email protected]", role = c("aut")),
+    person("Cara", "Andrews", email = "[email protected]", role = c("aut")))
 Description: Supports the process of applying a cut to Standard Data Tabulation Model (SDTM),
     as part of the analysis of specific points in time of the data, normally as part of 
     investigation into clinical trials. The functions support different approaches of
     cutting to the different domains of SDTM normally observed.
 License: Apache License (>= 2)
+BugReports: https://github.com/pharmaverse/datacutr/issues
+URL: https://pharmaverse.github.io/datacutr/, https://github.com/pharmaverse/datacutr
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
-Depends: R (>= 3.5)
+RoxygenNote: 7.3.2
+Depends: R (>= 4.1)
 Imports:
-    admiraldev,
+    admiraldev (>= 0.3.0),
     assertthat (>= 0.2.1),
     dplyr (>= 1.0.5),
     lubridate (>= 1.7.4),
     magrittr (>= 1.5),
     purrr (>= 0.3.3),
-    stringr,
+    stringr (>= 1.4.0),
     rlang (>= 0.4.4),
-    tibble
+    tibble (>= 3.0.0),
+    reactable (>= 0.4.4)
 Suggests:
     devtools,
     lintr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -8,6 +8,7 @@ export(impute_dcutdtc)
 export(impute_sdtm)
 export(process_cut)
 export(pt_cut)
+export(read_out)
 export(special_dm_cut)
 importFrom(admiraldev,assert_character_scalar)
 importFrom(admiraldev,assert_data_frame)
@@ -36,12 +37,14 @@ importFrom(magrittr,"%>%")
 importFrom(purrr,map)
 importFrom(purrr,map_lgl)
 importFrom(purrr,pmap)
+importFrom(reactable,reactable)
 importFrom(rlang,"!!")
 importFrom(rlang,":=")
 importFrom(rlang,as_quosures)
 importFrom(rlang,enexpr)
 importFrom(rlang,expr_name)
 importFrom(rlang,exprs)
+importFrom(rlang,is_named)
 importFrom(rlang,is_quosure)
 importFrom(rlang,quo_is_null)
 importFrom(rlang,quo_name)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,36 @@
+# datacutr 0.2.0
+
+## New Features
+- Added a "Report a bug" link to `{datacutr}` website (#182)
+- Added a `read_out` function that enables the generation of a read-out file (.html), to summarize changes applied to data during a datacut. (#107)
+
+## Updates of Existing Functions
+- Update to `impute_dcutdtc()`, `date_cut()` and `special_dm_cut()` functions to allow for 
+datacut date to be null. In this case, all records for this patient 
+will be kept/left unchanged. (#179, #189, #190)
+- Warning added to `process_cut` if expected dataset `dm` is missing (#172)
+- Warning added to `create_dcut` if cut date being passed as `NULL`, 
+and not valid date or `NA`/`""` (#181)
+- `process_cut` updated so that the `patient_cut_v`, `date_cut_m` and `no_cut_v`
+arguments have a default value of `NULL` (#188)
+- `process_cut` updated to have more detailed error messages when incorrect datasets 
+are fed in (#180)
+- `process_cut` updated to have arguments `read_out` and `out_path` to integrate the `read_out` function into the wrapper function; enabling auto-generation of the datacutr read-out file (#107)
+
+## Breaking Changes
+- Added dependency on `admiraldev` >= 0.3.0 (#173)
+- Added dependency on R version >= 4.1 due to an update in `admiraldev` to use R native pipe
+
+## Documentation
+- Added notes on SDTM compatibility (#171)
+- Cleaned install packages code format (#177)
+- Fixed broken link to source (#184)
+- Added report a bug link to site (#182)
+
+## Various
+- Added CRAN badge to site (#174)
+- Pull Request template updated (#192)
+
 # datacutr 0.1.0
 
 ## New Features
@@ -16,4 +49,3 @@
 ## Various
 - N/A
 
-
diff --git a/R/create_dcut.R b/R/create_dcut.R
@@ -10,7 +10,7 @@
 #' @param ds_date_var Character date/time variable in the DS SDTMv to be compared against the
 #' datacut date
 #' @param filter Condition to filter patients in DS, should give 1 row per patient
-#' @param cut_date Datacut date/time, e.g. "2022-10-22"
+#' @param cut_date Datacut date/time, e.g. "2022-10-22", or NA if no date cut is to be applied
 #' @param cut_description Datacut date/time description, e.g. "Clinical Cut Off Date"
 #'
 #' @author Alana Harris
@@ -62,6 +62,11 @@ create_dcut <- function(dataset_ds,
    must be stored in ISO 8601 format."
   )
 
+  # Check that cut date is not NULL
+  assert_that(!is.null(cut_date),
+    msg = "Cut date is NULL, please populate as NA or valid ISO8601 date format"
+  )
+
   # Check that cut_date is in ISO 8601 format
   valid_dtc <- is_valid_dtc(cut_date)
   assert_that(valid_dtc,
@@ -74,13 +79,18 @@ create_dcut <- function(dataset_ds,
     mutate(DCUTDTC = cut_date) %>%
     mutate(DCUTDESC = cut_description) %>%
     impute_dcutdtc(dsin = ., varin = DCUTDTC, varout = DCUTDTM) %>%
-    filter(., DCUTDTM >= DCUT_TEMP_DATE) %>%
+    filter(., (!is.na(DCUTDTM) & DCUTDTM >= DCUT_TEMP_DATE) | is.na(DCUTDTM)) %>%
     filter_if(filter) %>%
     subset(select = c(USUBJID, DCUTDTC, DCUTDTM, DCUTDESC))
 
   assert_that(
     (length(get_duplicates(dataset$USUBJID)) == 0),
     msg = "Duplicate patients in the final returned dataset, please update."
   )
+
+  # Print message if cut date is null
+  ifelse(any(is.na(mutate(dataset, DCUTDTM))) == TRUE,
+    print("At least 1 patient with missing datacut date."), NA
+  )
   dataset
 }
diff --git a/R/datcutr-package.R b/R/datcutr-package.R
@@ -3,11 +3,13 @@
 #' syms pull if_else
 #' @importFrom magrittr %>%
 #' @importFrom rlang := quo_name !! is_quosure quo_is_null as_quosures exprs enexpr expr_name
+#' is_named
 #' @importFrom purrr map_lgl pmap map
 #' @importFrom lubridate ymd_hms is.POSIXt
 #' @importFrom admiraldev assert_symbol assert_data_frame assert_character_scalar assert_filter_cond
 #' filter_if is_valid_dtc warn_if_invalid_dtc get_duplicates
 #' @importFrom assertthat assert_that
 #' @importFrom tibble tribble
+#' @importFrom reactable reactable
 #' @importFrom stringr str_match str_detect
 "_PACKAGE"