From 859172d8a8f069d5ded46bd08fcb53064d95b50c Mon Sep 17 00:00:00 2001 From: cicdguy <26552821+cicdguy@users.noreply.github.com> Date: Mon, 6 Jan 2025 07:35:51 -0600 Subject: [PATCH] feat: Reintroduce multiversion docs --- .github/CONTRIBUTING.md | 6 +++--- .github/pull_request_template.md | 4 ++-- .github/workflows/common.yml | 9 ++++++++- DESCRIPTION | 2 +- NEWS.md | 26 ++++++++++++------------- README.md | 16 +++++++-------- _pkgdown.yml | 2 +- inst/templates/ad_adae.R | 2 +- inst/templates/ad_adcm.R | 4 ++-- inst/templates/ad_adeg.R | 6 +++--- inst/templates/ad_adex.R | 2 +- inst/templates/ad_adlb.R | 10 +++++----- inst/templates/ad_admh.R | 6 +++--- inst/templates/ad_adpc.R | 2 +- inst/templates/ad_adpp.R | 6 +++--- inst/templates/ad_adppk.R | 2 +- inst/templates/ad_adsl.R | 4 ++-- inst/templates/ad_advs.R | 6 +++--- man/admiral-package.Rd | 2 +- vignettes/articles/website-versions.Rmd | 2 +- vignettes/faq.Rmd | 2 +- 21 files changed, 64 insertions(+), 57 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index ac5d02c304..304bf4829d 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,6 +1,6 @@ # Contribution to {admiral} -This outlines how to propose a change to the admiral package. For more detailed info about contributing to {admiral}, and other [pharmaverse packages](https://pharmaverse.org/), please see the [Contribution Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) as well as other Developer Guides in the Articles section of the [{admiraldev} website](https://pharmaverse.github.io/admiraldev/). +This outlines how to propose a change to the admiral package. For more detailed info about contributing to {admiral}, and other [pharmaverse packages](https://pharmaverse.org/), please see the [Contribution Guide](https://pharmaverse.github.io/admiral/cran-release/CONTRIBUTING.html) as well as other Developer Guides in the Articles section of the [{admiraldev} website](https://pharmaverse.github.io/admiraldev/). Please note that we try to align to best practices used in other R packages' development processes - so veteran developers should be familiar with our processes. However, we do deviate slightly from some best practices and we advise all new contributors to review our package documentation accordingly. @@ -59,7 +59,7 @@ If you decide to contribute with code and you're ready to make your first code c If so, remember to run `devtools::document()` and include the updated `NAMESPACE` and `.Rd` files in `man/`. e. Does your code update have any impact on the [ADaM - template](https://pharmaverse.github.io/admiral/articles/admiral.html#starting-a-script) + template](https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#starting-a-script) R scripts stored in `inst/templates`? f. Does your code update have any impact on the vignettes stored in vignettes? @@ -67,7 +67,7 @@ If you decide to contribute with code and you're ready to make your first code c h. Did you build `{admiral}` 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/reference/)" page? + "[Reference](https://pharmaverse.github.io/admiral/cran-release/reference/)" page? 4. Once happy with all the updates, make a [pull request](https://pharmaverse.github.io/admiraldev/articles/git_usage.html#pull-request) to merge to the `main` branch and link the issue so that it closes after successful merging. diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 800e04452e..3b1c2972b0 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,4 +1,4 @@ -Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html#detailed-development-process) 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/admiral/cran-release/CONTRIBUTING.html#detailed-development-process) 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 `main` branch until you have checked off each task. @@ -11,7 +11,7 @@ Please check off each taskbox as an acknowledgment that you completed the task o - [ ] 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` under the header `# admiral (development version)` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers). A Developer Notes section is available in `NEWS.md` for tracking developer-facing issues. -- [ ] Build admiral 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/reference/index.html)" page. +- [ ] Build admiral 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. - [ ] 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 index 834ed5d6c7..ea31fdd071 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -81,7 +81,14 @@ jobs: needs: get_r_version with: r-version: "release" - skip-multiversion-docs: true + # 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$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$ secrets: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} linter: diff --git a/DESCRIPTION b/DESCRIPTION index 5869494f72..8523e299c8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,7 +36,7 @@ Description: A toolbox for programming Clinical Data Interchange Standards Analysis Data Model Team, 2021, ). License: Apache License (>= 2) -URL: https://pharmaverse.github.io/admiral/, +URL: https://pharmaverse.github.io/admiral/cran-release/, https://github.com/pharmaverse/admiral BugReports: https://github.com/pharmaverse/admiral/issues Depends: diff --git a/NEWS.md b/NEWS.md index 6b68c49c1b..75b12bd971 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1092,7 +1092,7 @@ updated to process additional parameter (#1125). imputation functions themselves (#1299). I.e., if a derivation like last known alive date is based on dates, DTC variables have to be converted to numeric date or datetime variables in a preprocessing step. For examples see the [ADSL -vignette](https://pharmaverse.github.io/admiral/articles/adsl.html). +vignette](https://pharmaverse.github.io/admiral/cran-release/articles/adsl.html). The following arguments were deprecated: - `date_imputation`, `time_imputation`, and `preserve` in `date_source()` @@ -1191,7 +1191,7 @@ empty (#1309) - `create_query_data()` is provided to create the [queries -dataset](https://pharmaverse.github.io/admiral/articles/queries_dataset.html) required as input for `derive_vars_query()` (#606) +dataset](https://pharmaverse.github.io/admiral/cran-release/articles/queries_dataset.html) required as input for `derive_vars_query()` (#606) - `create_single_dose_dataset()` - Derives dataset of single dose from aggregate dose information (#660) @@ -1224,7 +1224,7 @@ first disease progression. (#1023) ### ADLB - New ADLB template script available `ad_adlb.R`, specific ADLB functions developed and - [BDS Finding vignette](https://pharmaverse.github.io/admiral/articles/bds_finding.html) has examples enhanced with ADLB functions. (#1122) + [BDS Finding vignette](https://pharmaverse.github.io/admiral/cran-release/articles/bds_finding.html) has examples enhanced with ADLB functions. (#1122) - `derive_var_shift()` - Derives a character shift variable containing concatenated shift in values based on user-defined pairing (#944) - `derive_var_analysis_ratio()` - Derives a ratio variable based on user-supplied variables from a BDS dataset, e.g. ADLB. (#943) @@ -1306,7 +1306,7 @@ specific for admiral. Derivations like this can be implemented calling - Updated `derive_var_worst_flag()` and `derive_var_extreme_flag()` vignettes to clarify their purpose (#691) - Added example of ASEQ derivation in ADCM to -[OCCDS vignette](https://pharmaverse.github.io/admiral/articles/occds.html#aseq) +[OCCDS vignette](https://pharmaverse.github.io/admiral/cran-release/articles/occds.html#aseq) (#720) - Examples have been added for `format_reason_default()`, `format_eoxxstt_default()`, `extend_source_datasets()` and `filter_date_sources()` (#745) @@ -1392,7 +1392,7 @@ this case the day is imputed as `15` (#592) - README and site homepage has been updated with important new section around expectations of {admiral}, as well as other useful references such as links to conference talks (#868 & #802) -- New vignette [Development Process](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) and improvements made to contribution vignettes (#765 & #758) +- New vignette [Development Process](https://pharmaverse.github.io/admiral/cran-release/CONTRIBUTING.html) and improvements made to contribution vignettes (#765 & #758) - Updated [Pull Request Review Guidance](https://pharmaverse.github.io/admiraldev/articles/pr_review_guidance.html) on using `task-list-completed` workflow (#817) @@ -1406,7 +1406,7 @@ this case the day is imputed as `15` (#592) - The first truly open source release licensed under Apache 2.0 (#680) -- New vignette [Contributing to admiral](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) (#679) +- New vignette [Contributing to admiral](https://pharmaverse.github.io/admiral/cran-release/CONTRIBUTING.html) (#679) - New vignette [Unit Test Guidance](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html) (#679) @@ -1428,7 +1428,7 @@ age in different units (#569) - `derive_param_tte()` derives time-to-event-parameters (#546) - For common time-to-event endpoints [event and censoring source -objects](https://pharmaverse.github.io/admiral/reference/index.html#section-pre-defined-time-to-event-sources) are +objects](https://pharmaverse.github.io/admiral/cran-release/reference/index.html#section-pre-defined-time-to-event-sources) are provided (#612) ### Developer @@ -1463,9 +1463,9 @@ to specify the unit of the input age (#569) ## Documentation -- New vignette [Creating a BDS Time-to-Event ADaM](https://pharmaverse.github.io/admiral/articles/bds_tte.html) (#549) +- New vignette [Creating a BDS Time-to-Event ADaM](https://pharmaverse.github.io/admiral/cran-release/articles/bds_tte.html) (#549) -- New vignette [Queries Dataset Documentation](https://pharmaverse.github.io/admiral/articles/queries_dataset.html) (#561) +- New vignette [Queries Dataset Documentation](https://pharmaverse.github.io/admiral/cran-release/articles/queries_dataset.html) (#561) - New vignette [Writing Vignettes](https://pharmaverse.github.io/admiraldev/articles/writing_vignettes.html) (#334) @@ -1660,10 +1660,10 @@ to specify the unit of the input age (#569) ## Documentation -- [Frequently Asked Questions](https://pharmaverse.github.io/admiral/articles/faq.html) +- [Frequently Asked Questions](https://pharmaverse.github.io/admiral/cran-release/articles/faq.html) -- [Creating ADSL](https://pharmaverse.github.io/admiral/articles/adsl.html) +- [Creating ADSL](https://pharmaverse.github.io/admiral/cran-release/articles/adsl.html) -- [Creating a BDS Finding ADaM](https://pharmaverse.github.io/admiral/articles/bds_finding.html) +- [Creating a BDS Finding ADaM](https://pharmaverse.github.io/admiral/cran-release/articles/bds_finding.html) -- [Creating an OCCDS ADaM](https://pharmaverse.github.io/admiral/articles/occds.html) +- [Creating an OCCDS ADaM](https://pharmaverse.github.io/admiral/cran-release/articles/occds.html) diff --git a/README.md b/README.md index 4cc7f5946b..4d75760821 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ devtools::install_github("pharmaverse/admiral") The `{admiral}` family has several downstream and upstream dependencies and so releases are done in two Phases: -* Phase 1 release is for [{admiraldev}](https://pharmaverse.github.io/admiraldev/), [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/), and [{admiral}](https://pharmaverse.github.io/admiral/) core +* Phase 1 release is for [{admiraldev}](https://pharmaverse.github.io/admiraldev/), [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/), and [{admiral}](https://pharmaverse.github.io/admiral/cran-release/) core * Phase 2 release is extension packages, e.g. [{admiralonco}](https://pharmaverse.github.io/admiralonco/), [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/), [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/) and [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/). | Release Schedule | Phase 1- Date and Packages | Phase 2- Date and Packages | @@ -47,12 +47,12 @@ The `{admiral}` family has several downstream and upstream dependencies and so r | Q4-2024 | December 2nd | December 9th | | | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/) | [{admiralonco}](https://pharmaverse.github.io/admiralonco/) | | | [{admiraldev}](https://pharmaverse.github.io/admiraldev/) | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/) | -| | [{admiral}](https://pharmaverse.github.io/admiral/) | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/) | | | | [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/) | +| | [{admiral}](https://pharmaverse.github.io/admiral/cran-release/) | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/) | | | | [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/) | | | | | | Q2-2025 | June 2nd | June 10th | | | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/) | [{admiralonco}](https://pharmaverse.github.io/admiralonco/) | | | [{admiraldev}](https://pharmaverse.github.io/admiraldev/) | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/) | -| | [{admiral}](https://pharmaverse.github.io/admiral/) | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/) | | | | [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/) | +| | [{admiral}](https://pharmaverse.github.io/admiral/cran-release/) | [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/) | | | | [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/) | ## Main Goal @@ -79,7 +79,7 @@ We will provide: * Pharmaceutical communities and companies are encouraged to contribute to `{admiral}` following the provided programming strategy and modular approach * Functions that are comprehensively documented and tested, including example calls---these are - all listed in the [Reference section](https://pharmaverse.github.io/admiral/reference/index.html). + all listed in the [Reference section](https://pharmaverse.github.io/admiral/cran-release/reference/index.html). * Vignettes on how to create ADSL, BDS and OCCDS datasets, including example scripts. * Vignettes for ADaM dataset specific functionality (i.e. dictionary coding, date imputation, SMQs ...). @@ -161,12 +161,12 @@ that all our developers and contributors must follow, so that all our code has a ## References and Documentation -* Please go to [Get Started](https://pharmaverse.github.io/admiral/articles/admiral.html) section to start using `{admiral}`. +* Please go to [Get Started](https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html) section to start using `{admiral}`. * Please see the [pharmaverse YouTube channel](https://www.youtube.com/channel/UCxQFEv8HNqM01DXzdQLCy6Q) for videos related to `{admiral}`. * Please see the [Programming Strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html) to understand how functions are created. -* Please see the [FAQ](https://pharmaverse.github.io/admiral/articles/faq.html) for the most frequent questions. -* Please see the [Contribution Model](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) for how to get involved with making contributions. -* Please see [FAQ: R and Package Versions](https://pharmaverse.github.io/admiral/articles/faq.html#why-do-we-use-a-certain-r-version-and-package-versions-for-development) for why we develop with certain R and package versions. +* Please see the [FAQ](https://pharmaverse.github.io/admiral/cran-release/articles/faq.html) for the most frequent questions. +* Please see the [Contribution Model](https://pharmaverse.github.io/admiral/cran-release/CONTRIBUTING.html) for how to get involved with making contributions. +* Please see [FAQ: R and Package Versions](https://pharmaverse.github.io/admiral/cran-release/articles/faq.html#why-do-we-use-a-certain-r-version-and-package-versions-for-development) for why we develop with certain R and package versions. ## Pharmaverse Blog diff --git a/_pkgdown.yml b/_pkgdown.yml index f8ff939087..7d379918a7 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -24,7 +24,7 @@ development: version_label: default authors: - before: "We define *authors* as those who are actively maintaining the code base, and *contributors* as those who made a significant contribution in the past. For all acknowledgements, see the eponymous section in the [Home Page](https://pharmaverse.github.io/admiral/)." + before: "We define *authors* as those who are actively maintaining the code base, and *contributors* as those who made a significant contribution in the past. For all acknowledgements, see the eponymous section in the [Home Page](https://pharmaverse.github.io/admiral/cran-release/)." footer: roles: [aut, ctb, cre, fnd] text: "Developed by" diff --git a/inst/templates/ad_adae.R b/inst/templates/ad_adae.R index f4db91f1cb..7ef19660db 100644 --- a/inst/templates/ad_adae.R +++ b/inst/templates/ad_adae.R @@ -22,7 +22,7 @@ ex_single <- admiral::ex_single # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint ae <- convert_blanks_to_na(ae) ex <- convert_blanks_to_na(ex_single) diff --git a/inst/templates/ad_adcm.R b/inst/templates/ad_adcm.R index 41b0541f8c..013455c477 100644 --- a/inst/templates/ad_adcm.R +++ b/inst/templates/ad_adcm.R @@ -20,7 +20,7 @@ adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint cm <- convert_blanks_to_na(cm) @@ -106,7 +106,7 @@ adcm <- adcm %>% ## Derive APHASE and APHASEN Variable ---- # Other timing variable can be derived similarly. # See also the "Visit and Period Variables" vignette -# (https://pharmaverse.github.io/admiral/articles/visits_periods.html) +# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html) adcm <- adcm %>% mutate( APHASE = case_when( diff --git a/inst/templates/ad_adeg.R b/inst/templates/ad_adeg.R index e490f8d93c..abcc2bb7a2 100644 --- a/inst/templates/ad_adeg.R +++ b/inst/templates/ad_adeg.R @@ -23,7 +23,7 @@ adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint eg <- convert_blanks_to_na(eg) @@ -151,7 +151,7 @@ adeg <- adeg %>% ## Get visit info ---- # See also the "Visit and Period Variables" vignette -# (https://pharmaverse.github.io/admiral/articles/visits_periods.html#visits) +# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#visits) adeg <- adeg %>% # Derive Timing mutate( @@ -276,7 +276,7 @@ adeg <- adeg %>% ## Get treatment information ---- # See also the "Visit and Period Variables" vignette -# (https://pharmaverse.github.io/admiral/articles/visits_periods.html#treatment_bds) +# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#treatment_bds) adeg <- adeg %>% # Assign TRTA, TRTP mutate(TRTP = TRT01P, TRTA = TRT01A) diff --git a/inst/templates/ad_adex.R b/inst/templates/ad_adex.R index ac0f980cac..8d496d669b 100644 --- a/inst/templates/ad_adex.R +++ b/inst/templates/ad_adex.R @@ -22,7 +22,7 @@ adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint ex <- convert_blanks_to_na(ex) diff --git a/inst/templates/ad_adlb.R b/inst/templates/ad_adlb.R index d6ad0f5ec3..31d7e49088 100644 --- a/inst/templates/ad_adlb.R +++ b/inst/templates/ad_adlb.R @@ -21,7 +21,7 @@ adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint lb <- convert_blanks_to_na(lb) @@ -156,7 +156,7 @@ adlb <- adlb %>% ## Get Visit Info ---- # See also the "Visit and Period Variables" vignette -# (https://pharmaverse.github.io/admiral/articles/visits_periods.html#visits) +# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#visits) adlb <- adlb %>% # Derive Timing mutate( @@ -239,7 +239,7 @@ adlb <- adlb %>% # Assign ATOXDSCL and ATOXDSCH to hold lab grading terms # ATOXDSCL and ATOXDSCH hold terms defined by NCI-CTCAEv4. -# See (https://pharmaverse.github.io/admiral/articles/lab_grading.html#implement_ctcv4) +# See (https://pharmaverse.github.io/admiral/cran-release/articles/lab_grading.html#implement_ctcv4) grade_lookup <- tibble::tribble( ~PARAMCD, ~ATOXDSCL, ~ATOXDSCH, "ALB", "Hypoalbuminemia", NA_character_, @@ -267,7 +267,7 @@ grade_lookup <- tibble::tribble( # user could change to atoxgr_criteria_ctcv5 to implement NCI-CTCAEv5 # Note: Hyperglycemia and Hypophosphatemia not defined in NCI-CTCAEv5 so # user would need to amend look-up table grade_lookup -# See (https://pharmaverse.github.io/admiral/articles/lab_grading.html#implement_ctcv5) +# See (https://pharmaverse.github.io/admiral/cran-release/articles/lab_grading.html#implement_ctcv5) grade_crit <- atoxgr_criteria_ctcv4 @@ -378,7 +378,7 @@ adlb <- adlb %>% ## Get treatment information ---- # See also the "Visit and Period Variables" vignette -# (https://pharmaverse.github.io/admiral/articles/visits_periods.html#treatment_bds) +# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#treatment_bds) adlb <- adlb %>% # Assign TRTA, TRTP mutate( diff --git a/inst/templates/ad_admh.R b/inst/templates/ad_admh.R index 6130271a7b..4a8998d22d 100644 --- a/inst/templates/ad_admh.R +++ b/inst/templates/ad_admh.R @@ -21,7 +21,7 @@ adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint mh <- convert_blanks_to_na(mh) @@ -125,14 +125,14 @@ admh <- mh %>% mutate(ANL01FL = ifelse(MHOCCUR != "N", "Y", NA_character_)) %>% ## Assign TRTA, TRTP (company specific variables derivation) ---- # See also the "Visit and Period Variables" vignette - # (https://pharmaverse.github.io/admiral/articles/visits_periods.html#treatment_bds) + # (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#treatment_bds) mutate( TRTP = TRT01P, TRTA = TRT01A ) %>% ## Assign APHASE and APHASEN Variable (company specific variable derivation) ---- # See also the "Visit and Period Variables" vignette - # (https://pharmaverse.github.io/admiral/articles/visits_periods.html#periods_bds) + # (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#periods_bds) mutate( APHASE = case_when( ADT < TRTSDT ~ "Screening", diff --git a/inst/templates/ad_adpc.R b/inst/templates/ad_adpc.R index 0678b7e302..fe7ec96f1d 100644 --- a/inst/templates/ad_adpc.R +++ b/inst/templates/ad_adpc.R @@ -28,7 +28,7 @@ adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint ex <- convert_blanks_to_na(ex) pc <- convert_blanks_to_na(pc) diff --git a/inst/templates/ad_adpp.R b/inst/templates/ad_adpp.R index a95f7e5242..436182231e 100644 --- a/inst/templates/ad_adpp.R +++ b/inst/templates/ad_adpp.R @@ -25,7 +25,7 @@ admiral_adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint pp <- convert_blanks_to_na(pp) @@ -108,7 +108,7 @@ adpp_aval <- adpp_pp %>% ## Get visit info ---- # See also the "Visit and Period Variables" vignette -# (https://pharmaverse.github.io/admiral/articles/visits_periods.html#visit_bds) +# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#visit_bds) adpp_avisit <- adpp_aval %>% # Derive Timing mutate( @@ -119,7 +119,7 @@ adpp_avisit <- adpp_aval %>% ) %>% ## Assign TRTA, TRTP ---- # See also the "Visit and Period Variables" vignette - # (https://pharmaverse.github.io/admiral/articles/visits_periods.html#treatment_bds) + # (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#treatment_bds) mutate( TRTP = TRT01P, TRTA = TRT01A diff --git a/inst/templates/ad_adppk.R b/inst/templates/ad_adppk.R index 9db9c4457a..ba87e16f4a 100644 --- a/inst/templates/ad_adppk.R +++ b/inst/templates/ad_adppk.R @@ -27,7 +27,7 @@ adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint ex <- convert_blanks_to_na(ex) pc <- convert_blanks_to_na(pc) diff --git a/inst/templates/ad_adsl.R b/inst/templates/ad_adsl.R index cb625db74f..39e73c1187 100644 --- a/inst/templates/ad_adsl.R +++ b/inst/templates/ad_adsl.R @@ -24,7 +24,7 @@ lb <- pharmaversesdtm::lb # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint dm <- convert_blanks_to_na(dm) @@ -98,7 +98,7 @@ ex_ext <- ex %>% adsl <- dm %>% ## derive treatment variables (TRT01P, TRT01A) ---- # See also the "Visit and Period Variables" vignette - # (https://pharmaverse.github.io/admiral/articles/visits_periods.html#treatment_adsl) + # (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#treatment_adsl) mutate(TRT01P = ARM, TRT01A = ACTARM) %>% ## derive treatment start date (TRTSDTM) ---- derive_vars_merged( diff --git a/inst/templates/ad_advs.R b/inst/templates/ad_advs.R index 5a6151ee13..434e121da1 100644 --- a/inst/templates/ad_advs.R +++ b/inst/templates/ad_advs.R @@ -21,7 +21,7 @@ adsl <- admiral::admiral_adsl # When SAS datasets are imported into R using haven::read_sas(), missing # character values from SAS appear as "" characters in R, instead of appearing # as NA values. Further details can be obtained via the following link: -# https://pharmaverse.github.io/admiral/articles/admiral.html#handling-of-missing-values # nolint +# https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#handling-of-missing-values # nolint vs <- convert_blanks_to_na(vs) @@ -124,7 +124,7 @@ advs <- advs %>% ## Get visit info ---- # See also the "Visit and Period Variables" vignette -# (https://pharmaverse.github.io/admiral/articles/visits_periods.html#visits) +# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#visits) advs <- advs %>% # Derive Timing mutate( @@ -243,7 +243,7 @@ advs <- advs %>% ## Get treatment information ---- # See also the "Visit and Period Variables" vignette -# (https://pharmaverse.github.io/admiral/articles/visits_periods.html#treatment_bds) +# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#treatment_bds) advs <- advs %>% # Assign TRTA, TRTP # Create End of Treatment Record diff --git a/man/admiral-package.Rd b/man/admiral-package.Rd index 940cbc960f..9ba487424f 100644 --- a/man/admiral-package.Rd +++ b/man/admiral-package.Rd @@ -13,7 +13,7 @@ A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) \seealso{ Useful links: \itemize{ - \item \url{https://pharmaverse.github.io/admiral/} + \item \url{https://pharmaverse.github.io/admiral/cran-release/} \item \url{https://github.com/pharmaverse/admiral} \item Report bugs at \url{https://github.com/pharmaverse/admiral/issues} } diff --git a/vignettes/articles/website-versions.Rmd b/vignettes/articles/website-versions.Rmd index fdb51e2805..dcb561f73f 100644 --- a/vignettes/articles/website-versions.Rmd +++ b/vignettes/articles/website-versions.Rmd @@ -15,7 +15,7 @@ knitr::opts_chunk$set( ```{r setup, include=FALSE} base_url <- - "https://pharmaverse.github.io/admiral/" # include the trailing backslash! + "https://pharmaverse.github.io/admiral/cran-release/" # include the trailing backslash! # get list of all files in the `gh-pages` branch df_all_files <- tryCatch(gert::git_ls(ref = "gh-pages"), error = function(x) FALSE) diff --git a/vignettes/faq.Rmd b/vignettes/faq.Rmd index 724abe3101..d2e90d9a5c 100644 --- a/vignettes/faq.Rmd +++ b/vignettes/faq.Rmd @@ -64,7 +64,7 @@ knitr::opts_chunk$set( ##### Where a user can quickly find some **references or advice** to use a function? * A [Cheat Sheet](https://github.com/pharmaverse/admiral/blob/main/inst/cheatsheet/admiral_cheatsheet.pdf) is available, providing some examples of the many `{admiral}` functions. -* For more detailed description, please refer to the [Reference section](https://pharmaverse.github.io/admiral/reference/index.html). +* For more detailed description, please refer to the [Reference section](https://pharmaverse.github.io/admiral/cran-release/reference/index.html). ##### Would `{admiral}` **create a whole** ADaM dataset?