Merge pull request #1631 from pharmaverse/pre-release

Pre release

.github/pull_request_template.md

@@ -1,13 +1,12 @@
-
-Thank you for your Pull Request! We 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 admiral 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/admiraldev/devel/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 admiral 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/devel/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/devel/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/devel/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)

.github/workflows/common.yml

@@ -29,10 +29,6 @@ on:
   release:
     types: [published]
 
-env:
-  # R version to use for the workflows
-  R_VERSION: "3.6"
-
 # Docs on concurrency:
 # https://docs.github.com/en/actions/using-jobs/using-concurrency
 concurrency:
@@ -45,25 +41,25 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: $R_VERSION
+      r-version: "4.0"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: $R_VERSION
+      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: $R_VERSION
+      r-version: "4.0"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
     with:
-      r-version: $R_VERSION
+      r-version: "4.0"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
@@ -75,7 +71,7 @@ jobs:
     # Change this after the next release to remove the ref condition
     if: github.event_name == 'push' && github.ref == 'refs/heads/main'
     with:
-      r-version: $R_VERSION
+      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
@@ -85,7 +81,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: $R_VERSION
+      r-version: "4.0"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -97,7 +93,7 @@ jobs:
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
     with:
-      r-version: $R_VERSION
+      r-version: "4.0"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
@@ -107,4 +103,4 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: $R_VERSION
+      r-version: "4.0"

.github/workflows/cran-status.yml

@@ -0,0 +1,24 @@
+---
+# Source: https://github.com/pharmaverse/admiralci
+name: CRAN Status Monitor
+
+on:
+  # 'workflow_dispatch' gives you the ability
+  # to run this workflow on demand, anytime
+  workflow_dispatch:
+  # 'schedule' events are triggered on a schedule
+  schedule:
+    - cron: '1 0 * * 1,3,5'
+
+jobs:
+  cran-status:
+    name: Check & Report
+    uses: pharmaverse/admiralci/.github/workflows/cran-status.yml@main
+    with:
+      # Whom should the issue be assigned to if errors are encountered
+      # in the CRAN status checks?
+      issue-assignees: "bundfussr,esimms999-gsk,thomas-neitmann,bms63,rossfarrugia"
+      # Create an issue if one or more of the following
+      # statuses are reported on the check report.
+      status-types: "WARNING,ERROR,NOTE"
+

.github/workflows/templates.yml

@@ -6,14 +6,10 @@ on:
   pull_request_review:
     types: [submitted]
 
-env:
-  # R version to use for the workflows
-  R_VERSION: "3.6"
-
 jobs:
   templates:
     name: Check Templates
     uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
     if: github.event.review.state == 'approved'
     with:
-      r-version: $R_VERSION
+      r-version: "4.0"

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: admiral
 Type: Package
 Title: ADaM in R Asset Library
-Version: 0.8.4
+Version: 0.9.0
 Authors@R: c(
     person("Thomas", "Neitmann", email = "thomas.neitmann@roche.com", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),
@@ -25,9 +25,17 @@ Authors@R: c(
     person("Pooja", "Kumari", role = "aut"),
     person("Claudia", "Carlucci", role = "aut"),
     person("Daniil", "Stefonishin", role = "aut"), 
+    person("Sadchla", "Mascary", role = "aut"),
+    person("Zelos", "Zhu", role = "aut"),
+    person("Jeffrey", "Dickinson", role = "aut"),
+    person("Ania", "Golab", role = "aut"),
     person("Michael", "Thorpe", role = "ctb"),
+    person("Declan", "Hodges", role = "ctb"),
+    person("Jaxon", "Abercrombie", role = "ctb"),
+    person("Nick", "Ramirez", role = "ctb"),
     person("Pavan", "Kumar", role = "ctb"),
     person("Hamza", "Rahal", role = "ctb"),
+    person("Yohann", "Omnes", role = "ctb"),
     person("Alice", "Ehmann", role = "ctb"),
     person("Tom", "Ratford", role = "ctb"),
     person("Vignesh", "Thanikachalam", role = "ctb"),
@@ -39,6 +47,7 @@ Authors@R: c(
     person("Syed", "Mubasheer", role = "ctb"),
     person("Wenyi", "Liu", role = "ctb"),
     person("Dinakar", "Kulkarni", role = "ctb"),
+    person("Franciszek", "Walkowiak", role = "ctb"),
     person("Tamara", "Senior", role = "ctb"),
     person("Jordanna", "Morrish", role = "ctb"),
     person("Anthony", "Howard", role = "ctb"),
@@ -61,11 +70,10 @@ URL: https://pharmaverse.github.io/admiral/, https://github.com/pharmaverse/admi
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 Depends: R (>= 3.5)
 Imports:
-    admiraldev,
-    assertthat (>= 0.2.1),
+    admiraldev (>= 0.2.0),
     dplyr (>= 0.8.4),
     hms (>= 0.5.3),
     lifecycle (>= 0.1.0),
@@ -75,9 +83,9 @@ Imports:
     rlang (>= 0.4.4),
     stringr (>= 1.4.0),
     tidyr (>= 1.0.2),
-    tidyselect (>= 1.0.0)
+    tidyselect (>= 1.1.0)
 Suggests:
-    admiral.test,
+    admiral.test (>= 0.4.0),
     covr,
     devtools,
     DT,

NAMESPACE

@@ -4,11 +4,14 @@ S3method(convert_blanks_to_na,character)
 S3method(convert_blanks_to_na,data.frame)
 S3method(convert_blanks_to_na,default)
 S3method(convert_blanks_to_na,list)
-S3method(format,sdg_select)
-S3method(format,smq_select)
+S3method(convert_na_to_blanks,character)
+S3method(convert_na_to_blanks,data.frame)
+S3method(convert_na_to_blanks,default)
+S3method(convert_na_to_blanks,list)
+S3method(format,basket_select)
 S3method(print,adam_templates)
-S3method(print,derivation_slice)
-S3method(print,tte_source)
+S3method(print,source)
+export("%>%")
 export(ae_event)
 export(ae_gr1_event)
 export(ae_gr2_event)
@@ -21,9 +24,11 @@ export(ae_sev_event)
 export(ae_wd_event)
 export(assert_terms)
 export(assert_valid_queries)
+export(basket_select)
 export(call_derivation)
 export(call_user_fun)
 export(censor_source)
+export(chr2vars)
 export(compute_bmi)
 export(compute_bsa)
 export(compute_dtf)
@@ -39,7 +44,9 @@ export(convert_blanks_to_na)
 export(convert_date_to_dtm)
 export(convert_dtc_to_dt)
 export(convert_dtc_to_dtm)
+export(convert_na_to_blanks)
 export(count_vals)
+export(create_period_dataset)
 export(create_query_data)
 export(create_single_dose_dataset)
 export(date_source)
@@ -48,12 +55,14 @@ export(default_qtc_paramcd)
 export(derivation_slice)
 export(derive_derived_param)
 export(derive_extreme_records)
+export(derive_locf_records)
 export(derive_param_bmi)
 export(derive_param_bsa)
 export(derive_param_computed)
 export(derive_param_doseint)
 export(derive_param_exist_flag)
 export(derive_param_exposure)
+export(derive_param_extreme_event)
 export(derive_param_first_event)
 export(derive_param_framingham)
 export(derive_param_map)
@@ -88,11 +97,14 @@ export(derive_var_last_dose_grp)
 export(derive_var_merged_cat)
 export(derive_var_merged_character)
 export(derive_var_merged_exist_flag)
+export(derive_var_merged_summary)
 export(derive_var_obs_number)
 export(derive_var_ontrtfl)
 export(derive_var_pchg)
+export(derive_var_relative_flag)
 export(derive_var_shift)
 export(derive_var_trtdurd)
+export(derive_var_trtemfl)
 export(derive_var_worst_flag)
 export(derive_vars_aage)
 export(derive_vars_atc)
@@ -103,11 +115,13 @@ export(derive_vars_dtm_to_dt)
 export(derive_vars_dtm_to_tm)
 export(derive_vars_duration)
 export(derive_vars_dy)
+export(derive_vars_joined)
 export(derive_vars_last_dose)
 export(derive_vars_merged)
 export(derive_vars_merged_dt)
 export(derive_vars_merged_dtm)
 export(derive_vars_merged_lookup)
+export(derive_vars_period)
 export(derive_vars_query)
 export(derive_vars_suppqual)
 export(derive_vars_transposed)
@@ -121,10 +135,10 @@ export(extract_unit)
 export(filter_confirmation)
 export(filter_date_sources)
 export(filter_extreme)
-export(filter_if)
 export(filter_relative)
 export(format_eoxxstt_default)
 export(format_reason_default)
+export(get_admiral_option)
 export(get_duplicates_dataset)
 export(get_many_to_one_dataset)
 export(get_not_mapped)
@@ -139,21 +153,21 @@ export(max_cond)
 export(min_cond)
 export(negate_vars)
 export(params)
+export(print_named_list)
 export(query)
 export(restrict_derivation)
 export(sdg_select)
+export(set_admiral_options)
 export(signal_duplicate_records)
 export(slice_derivation)
 export(smq_select)
 export(use_ad_template)
+export(validate_basket_select)
 export(validate_query)
-export(validate_sdg_select)
-export(validate_smq_select)
 export(vars)
-export(vars2chr)
 export(yn_to_numeric)
 import(admiraldev)
-importFrom(assertthat,assert_that)
+importFrom(dplyr,across)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
@@ -162,6 +176,7 @@ importFrom(dplyr,coalesce)
 importFrom(dplyr,desc)
 importFrom(dplyr,distinct)
 importFrom(dplyr,ends_with)
+importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
@@ -241,6 +256,7 @@ importFrom(rlang,eval_tidy)
 importFrom(rlang,expr)
 importFrom(rlang,expr_interp)
 importFrom(rlang,expr_label)
+importFrom(rlang,exprs)
 importFrom(rlang,f_lhs)
 importFrom(rlang,f_rhs)
 importFrom(rlang,inform)
@@ -282,19 +298,23 @@ importFrom(stringr,str_match)
 importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace)
+importFrom(stringr,str_replace_all)
 importFrom(stringr,str_sub)
 importFrom(stringr,str_subset)
 importFrom(stringr,str_to_lower)
 importFrom(stringr,str_to_title)
 importFrom(stringr,str_to_upper)
 importFrom(stringr,str_trim)
+importFrom(tidyr,crossing)
 importFrom(tidyr,drop_na)
+importFrom(tidyr,fill)
 importFrom(tidyr,nest)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,all_of)
 importFrom(tidyselect,contains)
+importFrom(tidyselect,matches)
 importFrom(tidyselect,vars_select)
 importFrom(utils,capture.output)
 importFrom(utils,str)