diff --git a/main/pkgdown.yml b/main/pkgdown.yml
index 2b4e97b..6b51bd0 100644
--- a/main/pkgdown.yml
+++ b/main/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
articles:
admiraltemplate: admiraltemplate.html
adxx: adxx.html
-last_built: 2023-11-06T18:19Z
+last_built: 2023-11-13T19:26Z
urls:
reference: https://pharmaverse.github.io/admiraltemplate/main/reference
article: https://pharmaverse.github.io/admiraltemplate/main/articles
diff --git a/main/pull_request_template.html b/main/pull_request_template.html
index 112387e..91d3008 100644
--- a/main/pull_request_template.html
+++ b/main/pull_request_template.html
@@ -33,14 +33,6 @@
Changelog
-
- Versions
-
diff --git a/main/reference/admiraltemplate-package.html b/main/reference/admiraltemplate-package.html
index c783824..81a4fb2 100644
--- a/main/reference/admiraltemplate-package.html
+++ b/main/reference/admiraltemplate-package.html
@@ -35,14 +35,6 @@
Changelog
-
- Versions
-
diff --git a/main/reference/hello_admiral.html b/main/reference/hello_admiral.html
index 1a463ff..7414c62 100644
--- a/main/reference/hello_admiral.html
+++ b/main/reference/hello_admiral.html
@@ -33,14 +33,6 @@
Changelog
-
- Versions
-
diff --git a/main/reference/index.html b/main/reference/index.html
index a6b1158..3845681 100644
--- a/main/reference/index.html
+++ b/main/reference/index.html
@@ -33,14 +33,6 @@
Changelog
-
- Versions
-
diff --git a/main/search.json b/main/search.json
index d323b5b..ab11a39 100644
--- a/main/search.json
+++ b/main/search.json
@@ -1 +1 @@
-[{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004
","code":""},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. Grant of Copyright License","title":"Apache License","text":"Subject terms conditions License, Contributor hereby grants perpetual, worldwide, non-exclusive, -charge, royalty-free, irrevocable copyright license reproduce, prepare Derivative Works , publicly display, publicly perform, sublicense, distribute Work Derivative Works Source Object form.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"3-grant-of-patent-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"3. Grant of Patent License","title":"Apache License","text":"Subject terms conditions License, Contributor hereby grants perpetual, worldwide, non-exclusive, -charge, royalty-free, irrevocable (except stated section) patent license make, made, use, offer sell, sell, import, otherwise transfer Work, license applies patent claims licensable Contributor necessarily infringed Contribution(s) alone combination Contribution(s) Work Contribution(s) submitted. institute patent litigation entity (including cross-claim counterclaim lawsuit) alleging Work Contribution incorporated within Work constitutes direct contributory patent infringement, patent licenses granted License Work shall terminate date litigation filed.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"4-redistribution","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"4. Redistribution","title":"Apache License","text":"may reproduce distribute copies Work Derivative Works thereof medium, without modifications, Source Object form, provided meet following conditions: () must give recipients Work Derivative Works copy License; (b) must cause modified files carry prominent notices stating changed files; (c) must retain, Source form Derivative Works distribute, copyright, patent, trademark, attribution notices Source form Work, excluding notices pertain part Derivative Works; (d) Work includes “NOTICE” text file part distribution, Derivative Works distribute must include readable copy attribution notices contained within NOTICE file, excluding notices pertain part Derivative Works, least one following places: within NOTICE text file distributed part Derivative Works; within Source form documentation, provided along Derivative Works; , within display generated Derivative Works, wherever third-party notices normally appear. contents NOTICE file informational purposes modify License. may add attribution notices within Derivative Works distribute, alongside addendum NOTICE text Work, provided additional attribution notices construed modifying License. may add copyright statement modifications may provide additional different license terms conditions use, reproduction, distribution modifications, Derivative Works whole, provided use, reproduction, distribution Work otherwise complies conditions stated License.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"5-submission-of-contributions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"5. Submission of Contributions","title":"Apache License","text":"Unless explicitly state otherwise, Contribution intentionally submitted inclusion Work Licensor shall terms conditions License, without additional terms conditions. Notwithstanding , nothing herein shall supersede modify terms separate license agreement may executed Licensor regarding Contributions.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"6-trademarks","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"6. Trademarks","title":"Apache License","text":"License grant permission use trade names, trademarks, service marks, product names Licensor, except required reasonable customary use describing origin Work reproducing content NOTICE file.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"7-disclaimer-of-warranty","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"7. Disclaimer of Warranty","title":"Apache License","text":"Unless required applicable law agreed writing, Licensor provides Work (Contributor provides Contributions) “” BASIS, WITHOUT WARRANTIES CONDITIONS KIND, either express implied, including, without limitation, warranties conditions TITLE, NON-INFRINGEMENT, MERCHANTABILITY, FITNESS PARTICULAR PURPOSE. solely responsible determining appropriateness using redistributing Work assume risks associated exercise permissions License.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"8-limitation-of-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"8. Limitation of Liability","title":"Apache License","text":"event legal theory, whether tort (including negligence), contract, otherwise, unless required applicable law (deliberate grossly negligent acts) agreed writing, shall Contributor liable damages, including direct, indirect, special, incidental, consequential damages character arising result License use inability use Work (including limited damages loss goodwill, work stoppage, computer failure malfunction, commercial damages losses), even Contributor advised possibility damages.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"9-accepting-warranty-or-additional-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"9. Accepting Warranty or Additional Liability","title":"Apache License","text":"redistributing Work Derivative Works thereof, may choose offer, charge fee , acceptance support, warranty, indemnity, liability obligations /rights consistent License. However, accepting obligations, may act behalf sole responsibility, behalf Contributor, agree indemnify, defend, hold Contributor harmless liability incurred , claims asserted , Contributor reason accepting warranty additional liability. END TERMS CONDITIONS","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"appendix-how-to-apply-the-apache-license-to-your-work","dir":"","previous_headings":"","what":"APPENDIX: How to apply the Apache License to your work","title":"Apache License","text":"apply Apache License work, attach following boilerplate notice, fields enclosed brackets [] replaced identifying information. (Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright 2021 F. Hoffmann-La Roche AG and GlaxoSmithKline LLC Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://pharmaverse.github.io/admiraltemplate/main/articles/adxx.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Creating ADXX","text":"article describes creating ADXX ADaM.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Open Source. Author, maintainer.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Source O (2023). admiraltemplate: ADaM R Asset Library - Extension. https://pharmaverse.github.io/admiraltemplate/main, https://github.com/pharmaverse/admiraltemplate.","code":"@Manual{, title = {admiraltemplate: ADaM in R Asset Library - Extension}, author = {Open Source}, year = {2023}, note = {https://pharmaverse.github.io/admiraltemplate/main, https://github.com/pharmaverse/admiraltemplate}, }"},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of Contents","title":"ADaM in R Asset Library - Extension","text":"Extension Expectations included template Package Extension Guidance Quick Start Guide Template","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"extension-expectations","dir":"","previous_headings":"","what":"Extension Expectations","title":"ADaM in R Asset Library - Extension","text":"included admiral package extension expect developers adhere following standards: Code Conduct Manifesto Programming Strategy Development Process Follow consistent workflow checks CRAN Release means 90% greater test coverage developed repository template order reduce burden developers follow standards. template also help harmonize admiral family R packages, ensure consistent user experience ease installing adopting packages. mind, expect core package dependencies versions used admiral.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"what-is-included-in-the-template","dir":"","previous_headings":"","what":"What is included in the template","title":"ADaM in R Asset Library - Extension","text":"repository template includes following: License file (Apache 2.0 - company co-developers need added copyright section) Required folders (R; test; templates; vignettes; renv; etc) Set-files (DESCRIPTION; NAMESPACE; renv.lock; etc) Issue Templates (Bug Template; Feature Request; Documentation Request/Update; Onboarding) Pull Request Template Workflow actions (selection generic specific CI/CD auto-checks) Package badges (Test coverage; etc) Branch protection rules","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"package-extension-guidance","dir":"","previous_headings":"","what":"Package Extension Guidance","title":"ADaM in R Asset Library - Extension","text":"admiral made family packages foresee growing time cover specific areas TA (Therapeutic Area) package extensions, wider range companies individuals getting board join development efforts. step--step guidance talks recommendations new development teams go creating package extensions. critical guidance followed, users need feel consistent experience working across admiral packages. admiral package extension doesn’t follow conventions wouldn’t include pharmaverse part admiral family. Note: ordering numbers suggested don’t need strictly followed sequence. Raise need new admiral package extension sponsors (Ross Farrugia ross.farrugia@roche.com & Ben Arancibia benjamin.c.arancibia@gsk.com). naming convention needs {admiralxxx} request scope targeted overly narrow, example instead package extension HIV ’d prefer one across virology. Otherwise number packages may become unmanageable. agreed, reach company contacts working similar areas see collaborative development can achieved. recommendation always target least 2 companies start implementation remains robust protect going company-specific route. However, consider 4 5 companies get involved early may slow decision-making. companies agree co-develop, identify lead . One company act driver overall package extension put forward product owner technical lead ultimately final say contentious decisions. product owner cover project decisions (e.g. around scope priorities), whereas technical lead cover technical decisions (e.g. around design implementation). Ideally, technical lead earlier involvement admiral part core development team contributor, key role order keep design true manifesto. Agree charter expectations company, e.g. usually ask least 3 developers least 25% capacity mix R, GitHub TA experience. Within charter make sure scope timelines clear. important try boil ocean. Focus first common endpoints required foundation package can build via contributions co-development companies also wider across-industry admiral community. useful, admiralonco charter shared guide. company start identify required developer resources. need attend one monthly admiral onboarding sessions (advertised via Slack channel - join using link). read admiral site, especially developer guides need followed package extensions. Optionally can useful host kick-meeting decide team work, recommend agile/scrum practices. Set “admiralxxx_dev” channel Slack add team members informal team chat, agree way share working documents across co-development team. useful starter development activity look {admiral.test} check test data sufficient TA needs, e.g. admiralonco generate new test data SDTM domains RS TU. Note personal data used (even anonymized) important keep data generated -line CDISC pilot data use , .e. use USUBJIDs DM etc. Optionally draft, agree sign collaboration agreement collaborating companies wish, useful protecting secondary IP company standard specifications may shared within team. example stored , work Legal teams required. Share company-specific implementations specifications able harmonize design strategy package extension. important remain pragmatic consider higher perspective one company. Engage company standards representatives find discrepancies across company approaches question really need things differently (health authorities patients benefit ?). Also consider always expect level company-specifics covered internal company package extensions. Set new public GitHub repo pharmaverse org using admiraltemplate - includes set-pieces (CI/CD checks issue/PR templates) enable package stay consistent others admiral family, well core package dependencies versions. See Quick Start Guide Template section instructions. Note step requires org member access granted pharmaverse council reps, admins org. Also free add additional package dependencies needed assuming reliable packages used, must depend newer versions packages (always reply “” updates suggested installation). repo available technical lead granted admin access repo set GitHub team name package extension assign required access co-development team members. require write access, may choose give leads admin access well never bottle-neck waiting one person. Update template license file repo adding co-development company names place Roche & GSK - admiral package extensions use Apache 2.0, preferred permissive license. Agree co-development companies required extra wording copyright/IP section. Set project board, , help manage backlog. Assuming work agile/scrum, create product backlog, prioritize make sprint plan. intention always re-use much possible admiral core package. find anything additional needed package extension, first question whether might common need TAs consider instead raising issue admiral core. designing new functions always try stay aligned programming strategy.. Start development foundational first release 0.1.0. Follow consistent development process admiral. Line testers companies others set expectations around believe stable version available user testing. can use admiral Slack community raise interest get involved. Add pharmaverse badge README: https://pharmaverse.org/contribute/badges/ - needs support pharmaverse council rep. Raise admiral repo issue ensure package extension site linked core admiral site . important admiral family packages keep similar release schedule cadence, order ease adoption users give clear expectations. admiral core package cadence releases one every quarter fixed schedule (every first Monday last month quarter - March, June, September, December). core package set release schedule package extensions follow, .e. admiral releases ’d expect package extension releases targeted within 2 week window. releases communicated via Slack channel well quarterly user community meetings. happy package extension well tested sufficient state make submission CRAN. technical lead named maintainer. CRAN release, advertise via Slack & LinkedIn. Plan future enhancements make issues. team feels ready can open development contributions wider community - see page.. Please use “good first issue” (ideal new starters) & “help wanted” (ideal experienced contributors) issue labels.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"quick-start-guide-for-template","dir":"","previous_headings":"","what":"Quick Start Guide for Template","title":"ADaM in R Asset Library - Extension","text":"Please thoroughly read Package Extension Guidance . intention Quick Start just get template code new repo check package works environment. Please contact us via slack issues arise. Click Green Use Template Button. Change owner pharmaverse enter repository name Create devel patch branches. important later workflows! repo created click Green Code button download repo using https ssh ensure development environment extension package synced admiral packages DESCRIPTION File - Name, Authors admiraltemplate.Rproj testthat.R News.md Run devtools::load_all() resolve issues Run devtools::document() resolve issues Reach slack help creating hex sticker/logo replace pharmaverse logo Recommended: Review documentation CI/CD workflows information reuse workflows template. Pay special attention section creating badges orphan branch section. Test dummy branch Pull Request ensure CI/CD works. clearly dummy files like R/my_first_fcn.R inst/templates/ad_adxx.R can updated removed. Set branch protections rules main, devel, optionally pre-release test depending branching strategy. Set assign admin write rights Settings/Collaborators members repository - using GitHub team developers. Change badges hex image README.Rmd package.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/admiraltemplate-package.html","id":null,"dir":"Reference","previous_headings":"","what":"admiraltemplate: ADaM in R Asset Library - Extension — admiraltemplate-package","title":"admiraltemplate: ADaM in R Asset Library - Extension — admiraltemplate-package","text":"toolbox programming Clinical Data Standards Interchange Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets R. ADaM datasets mandatory part New Drug Biologics License Application submitted United States Food Drug Administration (FDA). Analysis derivations implemented accordance \"Analysis Data Model Implementation Guide\" (CDISC Analysis Data Model Team, 2021, https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package).","code":""},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/admiraltemplate-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"admiraltemplate: ADaM in R Asset Library - Extension — admiraltemplate-package","text":"Maintainer: Open Source admiraltemplate@pharmaverse.com","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":null,"dir":"Reference","previous_headings":"","what":"Derive Extension Example — hello_admiral","title":"Derive Extension Example — hello_admiral","text":"Says hello admiral","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derive Extension Example — hello_admiral","text":"","code":"hello_admiral(hw = TRUE)"},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derive Extension Example — hello_admiral","text":"hw TRUE FALSE","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derive Extension Example — hello_admiral","text":"Happy Message","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Derive Extension Example — hello_admiral","text":"roxygen documentation find tags family keywords. create organized sections Reference tab pkgdown website. can modify _pkgdown.yml necessary create appropriate sections necessary. ./man/roxygen/meta.R, find store family/keywords.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Derive Extension Example — hello_admiral","text":"","code":"hello_admiral(hw = FALSE) #> Welcome to the admiral family!"},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"new-features-0-0-2","dir":"Changelog","previous_headings":"","what":"New Features","title":"admiraltemplate 0.0.2","text":"New renv lock files setup (#48)","code":""},{"path":[]},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"documentation-0-0-2","dir":"Changelog","previous_headings":"","what":"Documentation","title":"admiraltemplate 0.0.2","text":"Many updates across documentation made match v0.10.0 admiral PR #51, including: Links fixed website Templates aligned current admiral standards Package dependencies updated Explanation use family/keywords provided","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"various-0-0-2","dir":"Changelog","previous_headings":"","what":"Various","title":"admiraltemplate 0.0.2","text":"Renamed admiralext admiraltemplate","code":""},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"new-features-0-0-1","dir":"Changelog","previous_headings":"","what":"New Features","title":"admiraltemplate 0.0.1","text":"can link GitHub Issue Changelog using (#ISSUE-NUMBER)","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"updates-of-existing-functions-0-0-1","dir":"Changelog","previous_headings":"","what":"Updates of Existing Functions","title":"admiraltemplate 0.0.1","text":"Updates made version (#ISSUE-NUMBER)","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"breaking-changes-0-0-1","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"admiraltemplate 0.0.1","text":"Deprecated functions. (#ISSUE-NUMBER) Bug Fixes (#ISSUE-NUMBER)","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"documentation-0-0-1","dir":"Changelog","previous_headings":"","what":"Documentation","title":"admiraltemplate 0.0.1","text":"Stuff (#ISSUE-NUMBER)","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"various-0-0-1","dir":"Changelog","previous_headings":"","what":"Various","title":"admiraltemplate 0.0.1","text":"Stuff (#ISSUE-NUMBER)","code":""}]
+[{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004
","code":""},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. Grant of Copyright License","title":"Apache License","text":"Subject terms conditions License, Contributor hereby grants perpetual, worldwide, non-exclusive, -charge, royalty-free, irrevocable copyright license reproduce, prepare Derivative Works , publicly display, publicly perform, sublicense, distribute Work Derivative Works Source Object form.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"3-grant-of-patent-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"3. Grant of Patent License","title":"Apache License","text":"Subject terms conditions License, Contributor hereby grants perpetual, worldwide, non-exclusive, -charge, royalty-free, irrevocable (except stated section) patent license make, made, use, offer sell, sell, import, otherwise transfer Work, license applies patent claims licensable Contributor necessarily infringed Contribution(s) alone combination Contribution(s) Work Contribution(s) submitted. institute patent litigation entity (including cross-claim counterclaim lawsuit) alleging Work Contribution incorporated within Work constitutes direct contributory patent infringement, patent licenses granted License Work shall terminate date litigation filed.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"4-redistribution","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"4. Redistribution","title":"Apache License","text":"may reproduce distribute copies Work Derivative Works thereof medium, without modifications, Source Object form, provided meet following conditions: () must give recipients Work Derivative Works copy License; (b) must cause modified files carry prominent notices stating changed files; (c) must retain, Source form Derivative Works distribute, copyright, patent, trademark, attribution notices Source form Work, excluding notices pertain part Derivative Works; (d) Work includes “NOTICE” text file part distribution, Derivative Works distribute must include readable copy attribution notices contained within NOTICE file, excluding notices pertain part Derivative Works, least one following places: within NOTICE text file distributed part Derivative Works; within Source form documentation, provided along Derivative Works; , within display generated Derivative Works, wherever third-party notices normally appear. contents NOTICE file informational purposes modify License. may add attribution notices within Derivative Works distribute, alongside addendum NOTICE text Work, provided additional attribution notices construed modifying License. may add copyright statement modifications may provide additional different license terms conditions use, reproduction, distribution modifications, Derivative Works whole, provided use, reproduction, distribution Work otherwise complies conditions stated License.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"5-submission-of-contributions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"5. Submission of Contributions","title":"Apache License","text":"Unless explicitly state otherwise, Contribution intentionally submitted inclusion Work Licensor shall terms conditions License, without additional terms conditions. Notwithstanding , nothing herein shall supersede modify terms separate license agreement may executed Licensor regarding Contributions.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"6-trademarks","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"6. Trademarks","title":"Apache License","text":"License grant permission use trade names, trademarks, service marks, product names Licensor, except required reasonable customary use describing origin Work reproducing content NOTICE file.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"7-disclaimer-of-warranty","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"7. Disclaimer of Warranty","title":"Apache License","text":"Unless required applicable law agreed writing, Licensor provides Work (Contributor provides Contributions) “” BASIS, WITHOUT WARRANTIES CONDITIONS KIND, either express implied, including, without limitation, warranties conditions TITLE, NON-INFRINGEMENT, MERCHANTABILITY, FITNESS PARTICULAR PURPOSE. solely responsible determining appropriateness using redistributing Work assume risks associated exercise permissions License.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"8-limitation-of-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"8. Limitation of Liability","title":"Apache License","text":"event legal theory, whether tort (including negligence), contract, otherwise, unless required applicable law (deliberate grossly negligent acts) agreed writing, shall Contributor liable damages, including direct, indirect, special, incidental, consequential damages character arising result License use inability use Work (including limited damages loss goodwill, work stoppage, computer failure malfunction, commercial damages losses), even Contributor advised possibility damages.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"9-accepting-warranty-or-additional-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"9. Accepting Warranty or Additional Liability","title":"Apache License","text":"redistributing Work Derivative Works thereof, may choose offer, charge fee , acceptance support, warranty, indemnity, liability obligations /rights consistent License. However, accepting obligations, may act behalf sole responsibility, behalf Contributor, agree indemnify, defend, hold Contributor harmless liability incurred , claims asserted , Contributor reason accepting warranty additional liability. END TERMS CONDITIONS","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/LICENSE.html","id":"appendix-how-to-apply-the-apache-license-to-your-work","dir":"","previous_headings":"","what":"APPENDIX: How to apply the Apache License to your work","title":"Apache License","text":"apply Apache License work, attach following boilerplate notice, fields enclosed brackets [] replaced identifying information. (Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright 2021 F. Hoffmann-La Roche AG and GlaxoSmithKline LLC Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://pharmaverse.github.io/admiraltemplate/main/articles/adxx.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Creating ADXX","text":"article describes creating ADXX ADaM.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Open Source. Author, maintainer.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Source O (2023). admiraltemplate: ADaM R Asset Library - Extension. https://pharmaverse.github.io/admiraltemplate, https://github.com/pharmaverse/admiraltemplate.","code":"@Manual{, title = {admiraltemplate: ADaM in R Asset Library - Extension}, author = {Open Source}, year = {2023}, note = {https://pharmaverse.github.io/admiraltemplate, https://github.com/pharmaverse/admiraltemplate}, }"},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of Contents","title":"ADaM in R Asset Library - Extension","text":"Extension Expectations included template Package Extension Guidance Quick Start Guide Template","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"extension-expectations","dir":"","previous_headings":"","what":"Extension Expectations","title":"ADaM in R Asset Library - Extension","text":"included admiral package extension expect developers adhere following standards: Code Conduct Manifesto Programming Strategy Development Process Follow consistent workflow checks CRAN Release means 90% greater test coverage developed repository template order reduce burden developers follow standards. template also help harmonize admiral family R packages, ensure consistent user experience ease installing adopting packages. mind, expect core package dependencies versions used admiral.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"what-is-included-in-the-template","dir":"","previous_headings":"","what":"What is included in the template","title":"ADaM in R Asset Library - Extension","text":"repository template includes following: License file (Apache 2.0 - company co-developers need added copyright section) Required folders (R; test; templates; vignettes; renv; etc) Set-files (DESCRIPTION; NAMESPACE; renv.lock; etc) Issue Templates (Bug Template; Feature Request; Documentation Request/Update; Onboarding) Pull Request Template Workflow actions (selection generic specific CI/CD auto-checks) Package badges (Test coverage; etc) Branch protection rules","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/index.html","id":"package-extension-guidance","dir":"","previous_headings":"","what":"Package Extension Guidance","title":"ADaM in R Asset Library - Extension","text":"detailed information regarding ethos admiral package extensions decide set one , please see Package Extension Guidance. also find details team setup, suggested workflow lessons learned past package extensions.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/admiraltemplate-package.html","id":null,"dir":"Reference","previous_headings":"","what":"admiraltemplate: ADaM in R Asset Library - Extension — admiraltemplate-package","title":"admiraltemplate: ADaM in R Asset Library - Extension — admiraltemplate-package","text":"toolbox programming Clinical Data Standards Interchange Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets R. ADaM datasets mandatory part New Drug Biologics License Application submitted United States Food Drug Administration (FDA). Analysis derivations implemented accordance \"Analysis Data Model Implementation Guide\" (CDISC Analysis Data Model Team, 2021, https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package).","code":""},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/admiraltemplate-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"admiraltemplate: ADaM in R Asset Library - Extension — admiraltemplate-package","text":"Maintainer: Open Source admiraltemplate@pharmaverse.com","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":null,"dir":"Reference","previous_headings":"","what":"Derive Extension Example — hello_admiral","title":"Derive Extension Example — hello_admiral","text":"Says hello admiral","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derive Extension Example — hello_admiral","text":"","code":"hello_admiral(hw = TRUE)"},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derive Extension Example — hello_admiral","text":"hw TRUE FALSE","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derive Extension Example — hello_admiral","text":"Happy Message","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Derive Extension Example — hello_admiral","text":"roxygen documentation find tags family keywords. create organized sections Reference tab pkgdown website. can modify _pkgdown.yml necessary create appropriate sections necessary. ./man/roxygen/meta.R, find store family/keywords.","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/reference/hello_admiral.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Derive Extension Example — hello_admiral","text":"","code":"hello_admiral(hw = FALSE) #> Welcome to the admiral family!"},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"updates-to-site-0-0-3","dir":"Changelog","previous_headings":"","what":"Updates to site","title":"admiraltemplate 0.0.3","text":"Package Extension guidance front page updated moved location admiraldev, link added point new location (#61).","code":""},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"new-features-0-0-2","dir":"Changelog","previous_headings":"","what":"New Features","title":"admiraltemplate 0.0.2","text":"New renv lock files setup (#48)","code":""},{"path":[]},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"documentation-0-0-2","dir":"Changelog","previous_headings":"","what":"Documentation","title":"admiraltemplate 0.0.2","text":"Many updates across documentation made match v0.10.0 admiral PR #51, including: Links fixed website Templates aligned current admiral standards Package dependencies updated Explanation use family/keywords provided","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"various-0-0-2","dir":"Changelog","previous_headings":"","what":"Various","title":"admiraltemplate 0.0.2","text":"Renamed admiralext admiraltemplate","code":""},{"path":[]},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"new-features-0-0-1","dir":"Changelog","previous_headings":"","what":"New Features","title":"admiraltemplate 0.0.1","text":"can link GitHub Issue Changelog using (#ISSUE-NUMBER)","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"updates-of-existing-functions-0-0-1","dir":"Changelog","previous_headings":"","what":"Updates of Existing Functions","title":"admiraltemplate 0.0.1","text":"Updates made version (#ISSUE-NUMBER)","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"breaking-changes-0-0-1","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"admiraltemplate 0.0.1","text":"Deprecated functions. (#ISSUE-NUMBER) Bug Fixes (#ISSUE-NUMBER)","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"documentation-0-0-1","dir":"Changelog","previous_headings":"","what":"Documentation","title":"admiraltemplate 0.0.1","text":"Stuff (#ISSUE-NUMBER)","code":""},{"path":"https://pharmaverse.github.io/admiraltemplate/main/news/index.html","id":"various-0-0-1","dir":"Changelog","previous_headings":"","what":"Various","title":"admiraltemplate 0.0.1","text":"Stuff (#ISSUE-NUMBER)","code":""}]