Closes #10 add function create_iso8601() (#21)

* clean up dummy test

* add `dtc_formats` data set

* update .Rbuildignore

* add tibble support for automatic pretty printing of tibbles

* add `create_iso8601()` (closes #10)

* clean up `lintr::lint_package()` issues

* Automatic renv profile update.

* Automatic renv profile update.

* Fix typos in R/dtc_utils.R

Co-authored-by: edgar-manukyan <[email protected]>

* remove `dummy()` function

* remove `.onLoad()` function

This function was likely added as part of an automatic setup of the R package as a whole but I guess we should add the `.onLoad()` if really needed.

* Remove the `is_dtc_fmt()` function

Initially I thought of calling this function from within `assert_dtc_fmt()` but I think now that the current usage of `rlang::arg_match()` leads to more concise code, so this is preferred.

* Import `.data` from rlang globally

Import `.data` from rlang globally by using the R package level documentation (https://roxygen2.r-lib.org/articles/rd-other.html?q=_PACKAGE#packages).

* Update WORDLIST

* Update `assert_capture_matrix()` and `complete_capture_matrix()` docs

* Add `coalesce_capture_matrices()` doc

* Fix typo in `assert_dtc_fmt()` doc

* Add `regex_or()` doc

* Add `fmt_rg()` doc

* Add `fmt_c()` doc

* Add `parse_dttm_fmt()` doc

* Fix doc of `parse_dttm_fmt()`

* Add `dttm_fmt_to_regex()` doc

* Bump development version to 0.0.0.9001

* Style updates

Style updates on R/dtc_create_iso8601.R, R/dtc_parse_dttm.R, R/dtc_utils.R. Mostly indentation corrections, wrapping single line body if-conditions in braces, white space removal.

* Style update to tests/testthat/test-yy_to_yyyy.R

* Style update

Style updates on tests/testthat/test-iso8601.R and tests/testthat/test-reg_matches.R

* Blank lines removal

* Style update

* Update docs after style update

* Refactor code about parsing dttm formats

Made `dttm_fmt_to_regex()` interface more intitutive by accepting directly the argument `fmt` instead of `tbl_fmt_c` which was an intermediate R object returned by `parse_dttm_fmt()`. Also, introduced unit tests for `parse_dttm_fmt_()`.

* Make `parse_dttm_fmt()` handle the case of no matching format components

* Use `fmt_dttmc()` in unit tests

* Small clarification on unit test description

* Remove futile assertion from `assert_dtc_fmt()`

* Add staged_dependencies for admiraldev (#26)

* Add staged_dependencies for admiraldev

* Add new line

* Fix admiraldev links.

* Fix admiraldev articles links.

* Remove R 4.1 a it causing dependencies issues. We want to use purrr >= 1.0.0

* Test latest lintr

* Test lintr with install package locally

* Add install pacakge variable for lintr

* Skip multi version pkgdown workflow.

* R build ignore staged_dependencies.yaml

* Automatic renv profile update.

* Automatic renv profile update.

* Cleaned up lintr issues

* Export `fmt_cmp()` and add early draft of `create_iso8601()` article

* Update `create_iso8601()` article

* Link `create_iso8601()` doc to article "iso_8601"

* Add RM as author to DESCRIPTION

* Fix author role of RM

* Fix indentation at `fmt_cmp()` source

* Remove `.check_format` from examples and add an example with `fmt_cmp()`

* Add an example to `create_iso8601()` with involving alternative formats and unk values

* Add example to `create_iso8601()` about the interplay of `.format` and `.fmt_c`

* Update common.yml

* Update style

* Change "oak" to "sdtm.oak" in DESCRIPTION

* Change "oak" to "sdtm.oak" in README

---------

Co-authored-by: ramiromagno <[email protected]>
Co-authored-by: edgar-manukyan <[email protected]>
Co-authored-by: Adam Foryś <[email protected]>

.Rbuildignore

@@ -11,3 +11,6 @@
 ^pkgdown$
 ^LICENSE\.md$
 ^\.lintr$
+^data-raw$
+^staged_dependencies.yaml$
+^vignettes/articles$

.Rprofile

@@ -27,7 +27,7 @@ Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE)
 if (!Sys.getenv("RENV_AUTOLOADER_ENABLED") %in% c("false", "FALSE")) {
   .renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
   if (!file.exists("./renv/profile")) {
-    if (.renv_profile %in% c("4.1", "4.2", "4.3")) {
+    if (.renv_profile %in% c("4.2", "4.3")) {
       message("Set renv profile to `", .renv_profile, "`")
       Sys.setenv("RENV_PROFILE" = .renv_profile)
     } else {

.github/workflows/common.yml

@@ -71,17 +71,15 @@ jobs:
       # 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
-      skip-multiversion-docs: false
-      latest-tag-alt-name: cran-release
-      multiversion-docs-landing-page: cran-release
-      branches-or-tags-to-list: >-
-        ^cran-release$|^main$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$
+      skip-multiversion-docs: true
   linter:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
     if: github.event_name == 'pull_request'
     with:
       r-version: "4.3"
+      latest-lintr: "true"
+      install-package: "true"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main

.github/workflows/r-renv-lock.yml

@@ -22,7 +22,6 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04, r: '4.1', repos: 'https://packagemanager.posit.co/cran/2022-03-10/'}
           - {os: ubuntu-20.04, r: '4.2', repos: 'https://packagemanager.posit.co/cran/2023-03-15/'}
           - {os: ubuntu-20.04, r: '4.3', repos: 'https://packagemanager.posit.co/cran/2023-04-20/'}
 

DESCRIPTION

@@ -1,10 +1,13 @@
 Package: sdtm.oak
 Type: Package
 Title: SDTM Data Transformation Engine
-Version: 0.0.0.9000
+Version: 0.0.0.9001
 Authors@R: c(
     person("Omar", "Garcia", email = "[email protected]", role = c("aut", "cre")),
     person("Rammprasad", "Ganapathy", role = "aut"),
+    person("Ramiro", "Magno", email = "[email protected]",
+    role = "aut", comment = c(ORCID = "0000-0001-5226-3441")),
+    person("Pattern Institute", role = c("cph", "fnd")),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")),
     person("Pfizer Inc", role = c("cph", "fnd"))
     )
@@ -13,21 +16,25 @@ Description: An EDC and Data Standard agnostic SDTM data transformation engine
     based on standard mapping algorithms.
 Language: en-US
 License: Apache License (>= 2)
-BugReports: https://github.com/pharmaverse/oak/issues
-URL: https://pharmaverse.github.io/oak/, https://github.com/pharmaverse/oak
+BugReports: https://github.com/pharmaverse/sdtm.oak/issues
+URL: https://pharmaverse.github.io/sdtm.oak/, https://github.com/pharmaverse/sdtm.oak
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Depends: R (>= 4.1)
+Depends: R (>= 4.2)
 Imports: 
-    rlang (>= 1.0.0)
+    admiraldev,
+    dplyr (>= 1.0.0),
+    purrr (>= 1.0.0),
+    rlang (>= 1.0.0),
+    stringr,
+    tibble
 Suggests:
     knitr,
     rmarkdown,
     spelling,
-    testthat (>= 3.1.7),
-    tibble
+    testthat (>= 3.1.7)
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Config/testthat/parallel: true

NAMESPACE

@@ -1,3 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-import(rlang)
+export(create_iso8601)
+export(fmt_cmp)
+importFrom(rlang,.data)
+importFrom(tibble,tibble)

NEWS.md

@@ -1,3 +1,5 @@
-# sdtm.oak (development version)
+# sdtm.oak 0.0.0.9001 (development version)
 
-* Initial CRAN submission.
+## New Features
+
+* New function `create_iso8601()` for conversion of vectors of dates, times or date-times to ISO8601 format.