diff --git a/devel/404.html b/devel/404.html index d660af5..c80cfbf 100644 --- a/devel/404.html +++ b/devel/404.html @@ -46,14 +46,6 @@ - - diff --git a/devel/authors.html b/devel/authors.html index 221e549..5bdd02f 100644 --- a/devel/authors.html +++ b/devel/authors.html @@ -24,14 +24,6 @@ - - diff --git a/devel/index.html b/devel/index.html index dbf1b32..f45c5c2 100644 --- a/devel/index.html +++ b/devel/index.html @@ -54,14 +54,6 @@ - - diff --git a/devel/pkgdown.yml b/devel/pkgdown.yml index 5e19f5c..b534a20 100644 --- a/devel/pkgdown.yml +++ b/devel/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.17.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-08-09T14:09Z +last_built: 2023-08-15T13:36Z urls: reference: https://pharmaverse.github.io/pharmaversesdtm/devel/reference article: https://pharmaverse.github.io/pharmaversesdtm/devel/articles diff --git a/devel/pull_request_template.html b/devel/pull_request_template.html index 652f6f7..9b8f75c 100644 --- a/devel/pull_request_template.html +++ b/devel/pull_request_template.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/admiral_eg.html b/devel/reference/admiral_eg.html index 0a50f23..e5074ce 100644 --- a/devel/reference/admiral_eg.html +++ b/devel/reference/admiral_eg.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/ae.html b/devel/reference/ae.html index 5aa8b25..c082026 100644 --- a/devel/reference/ae.html +++ b/devel/reference/ae.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/ae_ophtha.html b/devel/reference/ae_ophtha.html index ca24d4c..dbf0994 100644 --- a/devel/reference/ae_ophtha.html +++ b/devel/reference/ae_ophtha.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/cm.html b/devel/reference/cm.html index 513cd37..ff965e6 100644 --- a/devel/reference/cm.html +++ b/devel/reference/cm.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/dm.html b/devel/reference/dm.html index 3ca101d..a22d733 100644 --- a/devel/reference/dm.html +++ b/devel/reference/dm.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/ds.html b/devel/reference/ds.html index 846e4bc..aaabf43 100644 --- a/devel/reference/ds.html +++ b/devel/reference/ds.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/ex.html b/devel/reference/ex.html index e496ec4..5c65ec5 100644 --- a/devel/reference/ex.html +++ b/devel/reference/ex.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/ex_ophtha.html b/devel/reference/ex_ophtha.html index 72877ac..155e6a0 100644 --- a/devel/reference/ex_ophtha.html +++ b/devel/reference/ex_ophtha.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/get_terms.html b/devel/reference/get_terms.html new file mode 100644 index 0000000..d59a0ee --- /dev/null +++ b/devel/reference/get_terms.html @@ -0,0 +1,101 @@ + +An example function as expected by the `get_terms_fun` parameter of +`admiral::create_query_data()` — get_terms • pharmaversesdtm + Skip to contents + + +
+
+
+ +
+

An example function as expected by the `get_terms_fun` parameter of +`admiral::create_query_data()`

+
+ +
+

Usage

+
get_terms(basket_select, version, keep_id, temp_env)
+
+ +
+

Arguments

+
basket_select
+

A basket_select object defining the terms

+ + +
version
+

MedDRA version

+ + +
keep_id
+

Should `GRPID` be included in the output?

+ + +
temp_env
+

Temporary environment

+ +
+ +
+ + +
+ + + + + + + diff --git a/devel/reference/index.html b/devel/reference/index.html index 0b17d31..9fc5683 100644 --- a/devel/reference/index.html +++ b/devel/reference/index.html @@ -24,14 +24,6 @@ - - @@ -104,6 +96,12 @@

All functionsget_terms() + +
An example function as expected by the `get_terms_fun` parameter of +`admiral::create_query_data()`
+
+ lb
Laboratory Measurements Dataset
diff --git a/devel/reference/lb.html b/devel/reference/lb.html index ab2555b..8a2c2f7 100644 --- a/devel/reference/lb.html +++ b/devel/reference/lb.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/mh.html b/devel/reference/mh.html index a5c2471..f8d481d 100644 --- a/devel/reference/mh.html +++ b/devel/reference/mh.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/oe_ophtha.html b/devel/reference/oe_ophtha.html index 25c7554..6dd0ee0 100644 --- a/devel/reference/oe_ophtha.html +++ b/devel/reference/oe_ophtha.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/pc.html b/devel/reference/pc.html index b61872c..b322e48 100644 --- a/devel/reference/pc.html +++ b/devel/reference/pc.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/pharmaversesdtm-package.html b/devel/reference/pharmaversesdtm-package.html index f5fb5ef..6f04646 100644 --- a/devel/reference/pharmaversesdtm-package.html +++ b/devel/reference/pharmaversesdtm-package.html @@ -26,14 +26,6 @@ - - diff --git a/devel/reference/pp.html b/devel/reference/pp.html index 9ac2297..b45b929 100644 --- a/devel/reference/pp.html +++ b/devel/reference/pp.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/qs_ophtha.html b/devel/reference/qs_ophtha.html index a85f0f9..b75b8ca 100644 --- a/devel/reference/qs_ophtha.html +++ b/devel/reference/qs_ophtha.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/rs_onco.html b/devel/reference/rs_onco.html index 2f2a74a..1ecc5e8 100644 --- a/devel/reference/rs_onco.html +++ b/devel/reference/rs_onco.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/sc_ophtha.html b/devel/reference/sc_ophtha.html index 1f5ce66..b9e58ca 100644 --- a/devel/reference/sc_ophtha.html +++ b/devel/reference/sc_ophtha.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/sdg_db.html b/devel/reference/sdg_db.html index 4a1871c..73dce9a 100644 --- a/devel/reference/sdg_db.html +++ b/devel/reference/sdg_db.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/smq_db.html b/devel/reference/smq_db.html index 68b3585..96dbe56 100644 --- a/devel/reference/smq_db.html +++ b/devel/reference/smq_db.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/suppae.html b/devel/reference/suppae.html index 7d96cf5..477d914 100644 --- a/devel/reference/suppae.html +++ b/devel/reference/suppae.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/suppdm.html b/devel/reference/suppdm.html index 38ba09d..26373ef 100644 --- a/devel/reference/suppdm.html +++ b/devel/reference/suppdm.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/suppds.html b/devel/reference/suppds.html index 764dc0c..5a638b1 100644 --- a/devel/reference/suppds.html +++ b/devel/reference/suppds.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/supptr_onco.html b/devel/reference/supptr_onco.html index 3935467..3860c85 100644 --- a/devel/reference/supptr_onco.html +++ b/devel/reference/supptr_onco.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/sv.html b/devel/reference/sv.html index b2bfb7e..b8044d5 100644 --- a/devel/reference/sv.html +++ b/devel/reference/sv.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/tr_onco.html b/devel/reference/tr_onco.html index 57c5700..5f3a755 100644 --- a/devel/reference/tr_onco.html +++ b/devel/reference/tr_onco.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/ts.html b/devel/reference/ts.html index d3b9934..495be78 100644 --- a/devel/reference/ts.html +++ b/devel/reference/ts.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/tu_onco.html b/devel/reference/tu_onco.html index a81d68f..2819dd8 100644 --- a/devel/reference/tu_onco.html +++ b/devel/reference/tu_onco.html @@ -24,14 +24,6 @@ - - diff --git a/devel/reference/vs.html b/devel/reference/vs.html index 77fc95c..9aa2b9d 100644 --- a/devel/reference/vs.html +++ b/devel/reference/vs.html @@ -24,14 +24,6 @@ - - diff --git a/devel/search.json b/devel/search.json index e6bf9b6..478a89f 100644 --- a/devel/search.json +++ b/devel/search.json @@ -1 +1 @@ -[{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/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/pharmaversesdtm/devel/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/pharmaversesdtm/devel/LICENSE.html","id":"2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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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/pharmaversesdtm/devel/LICENSE.html","id":"5-submission-of-contributions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"5. 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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/pharmaversesdtm/devel/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/pharmaversesdtm/devel/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/pharmaversesdtm/devel/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edoardo Mancini. Author, maintainer.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Mancini E (2023). pharmaversesdtm: Test Data Pharmaverse Family Packages. https://pharmaverse.github.io/pharmaversesdtm, https://github.com/pharmaverse/pharmaversesdtm.","code":"@Manual{, title = {pharmaversesdtm: Test Data for the Pharmaverse Family of Packages}, author = {Edoardo Mancini}, year = {2023}, note = {https://pharmaverse.github.io/pharmaversesdtm, https://github.com/pharmaverse/pharmaversesdtm}, }"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"pharmaversesdtm-","dir":"","previous_headings":"","what":"Test Data for the Pharmaverse Family of Packages","title":"Test Data for the Pharmaverse Family of Packages","text":"Test data (SDTM) pharmaverse family packages","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"purpose","dir":"","previous_headings":"","what":"Purpose","title":"Test Data for the Pharmaverse Family of Packages","text":"provide one-stop-shop SDTM test data pharmaverse family packages. includes datasets therapeutic area (TA)-agnostic (DM, VS, EG, etc.) well TA-specific ones (RS, TR, OE, etc.).","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Test Data for the Pharmaverse Family of Packages","text":"package available CRAN can installed running install.packages(\"pharmaversesdtm\"). install latest development version package directly GitHub use following code:","code":"if (!requireNamespace(\"remotes\", quietly = TRUE)) { install.packages(\"remotes\") } remotes::install_github(\"pharmaverse/pharmaversesdtm\", ref = \"devel\")"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"data-sources","dir":"","previous_headings":"","what":"Data Sources","title":"Test Data for the Pharmaverse Family of Packages","text":"test datasets sourced CDISC pilot project, datasets constructed ad-hoc admiral team. Please check Reference page detailed information regarding source specific datasets.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"naming","dir":"","previous_headings":"","what":"Naming Conventions","title":"Test Data for the Pharmaverse Family of Packages","text":"Datasets TA-agnostic: SDTM domain name (e.g., dm, rs). Datasets TA-specific: domain_TA_others, others go broader categories specific ones (e.g., oe_ophtha, rs_onco, rs_onco_irecist). Note: SDTM domain used multiple TAs, pharmaversesdtm may provide multiple versions corresponding test dataset. instance, package contains ex ex_ophtha latter contains ophthalmology-specific variables EXLAT EXLOC, EXROUTE exchanged plausible ophthalmology value.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"how-to-update","dir":"","previous_headings":"","what":"How To Update","title":"Test Data for the Pharmaverse Family of Packages","text":"Firstly, make GitHub issue {pharmaversesdtm} planned updates tag @pharmaverse/admiral one development core team can sanity check request. two main ways extend test data: either adding new datasets extending existing datasets new records/variables. Whichever method choose, worth noting following: Programs generate test data stored data-raw/ folder. programs written standalone R script: packages need loaded given program, call library() start program (please call library(pharmaversesdtm)). packages likely need already specified renv.lock file, already installed keeping sync–can check entering renv::status() Console. However, may also wish install metatools, currently specified renv.lock file. feel need install packages addition just mentioned, please tag @pharmaverse/admiral discuss development core team. created program data-raw/ folder, need run standalone R script, order generate test dataset become part pharmaversesdtm package, need build package. Following best practice, dataset stored .rda file whose name consistent name dataset, e.g., dataset xx stored xx.rda. easiest way achieve use usethis::use_data(xx) programs data-raw/ stored within pharmaversesdtm GitHub repository, part pharmaversesdtm package–data-raw/ folder specified .Rbuildignore. run program data-raw/ folder, generate dataset written data/ folder, become part pharmaversesdtm package. names sources test datasets specified R/data.R, purpose generating documentation man/ folder.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"adding-new-sdtm-datasets","dir":"","previous_headings":"","what":"Adding New SDTM Datasets","title":"Test Data for the Pharmaverse Family of Packages","text":"Use CDISC pilot data dm input program order create realistic synthetic data remains consistent domains (mandatory). Note personal data used part package, even anonymized. Run program. Reflect update, specifying R/data.R. Run devtools::document() order update NAMESPACE update .Rd files man/. Add GitHub handle .github/CODEOWNERS. Update NEWS.md.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"updating-existing-sdtm-datasets","dir":"","previous_headings":"","what":"Updating Existing SDTM Datasets","title":"Test Data for the Pharmaverse Family of Packages","text":"Locate existing program .R data-raw/ folder, update accordingly. Run program, output updated .rda data/ folder. Run devtools::document() order update NAMESPACE update .Rd files man/. Add GitHub handle .github/CODEOWNERS. Update NEWS.md.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_eg.html","id":null,"dir":"Reference","previous_headings":"","what":"Electrocardiogram Dataset — admiral_eg","title":"Electrocardiogram Dataset — admiral_eg","text":"example standard SDTM EG dataset used deriving ADEG dataset","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_eg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Electrocardiogram Dataset — admiral_eg","text":"","code":"admiral_eg"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_eg.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Electrocardiogram Dataset — admiral_eg","text":"object class tbl_df (inherits tbl, data.frame) 26669 rows 24 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/ae.html","id":null,"dir":"Reference","previous_headings":"","what":"Adverse Events Dataset-updated — ae","title":"Adverse Events Dataset-updated — ae","text":"updated SDTM AE dataset uses CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/ae.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adverse Events Dataset-updated — ae","text":"","code":"ae"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/ae.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Adverse Events Dataset-updated — ae","text":"object class tbl_df (inherits tbl, data.frame) 1191 rows 35 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/ae.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Adverse Events 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(#15)","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]}] +[{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/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/pharmaversesdtm/devel/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/pharmaversesdtm/devel/LICENSE.html","id":"2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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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/pharmaversesdtm/devel/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/pharmaversesdtm/devel/LICENSE.html","id":"6-trademarks","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"6. 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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/pharmaversesdtm/devel/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/pharmaversesdtm/devel/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/pharmaversesdtm/devel/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/pharmaversesdtm/devel/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edoardo Mancini. Author, maintainer.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Mancini E (2023). pharmaversesdtm: Test Data Pharmaverse Family Packages. https://pharmaverse.github.io/pharmaversesdtm, https://github.com/pharmaverse/pharmaversesdtm.","code":"@Manual{, title = {pharmaversesdtm: Test Data for the Pharmaverse Family of Packages}, author = {Edoardo Mancini}, year = {2023}, note = {https://pharmaverse.github.io/pharmaversesdtm, https://github.com/pharmaverse/pharmaversesdtm}, }"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"pharmaversesdtm-","dir":"","previous_headings":"","what":"Test Data for the Pharmaverse Family of Packages","title":"Test Data for the Pharmaverse Family of Packages","text":"Test data (SDTM) pharmaverse family packages","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"purpose","dir":"","previous_headings":"","what":"Purpose","title":"Test Data for the Pharmaverse Family of Packages","text":"provide one-stop-shop SDTM test data pharmaverse family packages. includes datasets therapeutic area (TA)-agnostic (DM, VS, EG, etc.) well TA-specific ones (RS, TR, OE, etc.).","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Test Data for the Pharmaverse Family of Packages","text":"package available CRAN can installed running install.packages(\"pharmaversesdtm\"). install latest development version package directly GitHub use following code:","code":"if (!requireNamespace(\"remotes\", quietly = TRUE)) { install.packages(\"remotes\") } remotes::install_github(\"pharmaverse/pharmaversesdtm\", ref = \"devel\")"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"data-sources","dir":"","previous_headings":"","what":"Data Sources","title":"Test Data for the Pharmaverse Family of Packages","text":"test datasets sourced CDISC pilot project, datasets constructed ad-hoc admiral team. Please check Reference page detailed information regarding source specific datasets.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"naming","dir":"","previous_headings":"","what":"Naming Conventions","title":"Test Data for the Pharmaverse Family of Packages","text":"Datasets TA-agnostic: SDTM domain name (e.g., dm, rs). Datasets TA-specific: domain_TA_others, others go broader categories specific ones (e.g., oe_ophtha, rs_onco, rs_onco_irecist). Note: SDTM domain used multiple TAs, pharmaversesdtm may provide multiple versions corresponding test dataset. instance, package contains ex ex_ophtha latter contains ophthalmology-specific variables EXLAT EXLOC, EXROUTE exchanged plausible ophthalmology value.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"how-to-update","dir":"","previous_headings":"","what":"How To Update","title":"Test Data for the Pharmaverse Family of Packages","text":"Firstly, make GitHub issue {pharmaversesdtm} planned updates tag @pharmaverse/admiral one development core team can sanity check request. two main ways extend test data: either adding new datasets extending existing datasets new records/variables. Whichever method choose, worth noting following: Programs generate test data stored data-raw/ folder. programs written standalone R script: packages need loaded given program, call library() start program (please call library(pharmaversesdtm)). packages likely need already specified renv.lock file, already installed keeping sync–can check entering renv::status() Console. However, may also wish install metatools, currently specified renv.lock file. feel need install packages addition just mentioned, please tag @pharmaverse/admiral discuss development core team. created program data-raw/ folder, need run standalone R script, order generate test dataset become part pharmaversesdtm package, need build package. Following best practice, dataset stored .rda file whose name consistent name dataset, e.g., dataset xx stored xx.rda. easiest way achieve use usethis::use_data(xx) programs data-raw/ stored within pharmaversesdtm GitHub repository, part pharmaversesdtm package–data-raw/ folder specified .Rbuildignore. run program data-raw/ folder, generate dataset written data/ folder, become part pharmaversesdtm package. names sources test datasets specified R/data.R, purpose generating documentation man/ folder.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"adding-new-sdtm-datasets","dir":"","previous_headings":"","what":"Adding New SDTM Datasets","title":"Test Data for the Pharmaverse Family of Packages","text":"Use CDISC pilot data dm input program order create realistic synthetic data remains consistent domains (mandatory). Note personal data used part package, even anonymized. Run program. Reflect update, specifying R/data.R. Run devtools::document() order update NAMESPACE update .Rd files man/. Add GitHub handle .github/CODEOWNERS. Update NEWS.md.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"updating-existing-sdtm-datasets","dir":"","previous_headings":"","what":"Updating Existing SDTM Datasets","title":"Test Data for the Pharmaverse Family of Packages","text":"Locate existing program .R data-raw/ folder, update accordingly. Run program, output updated .rda data/ folder. Run devtools::document() order update NAMESPACE update .Rd files man/. Add GitHub handle .github/CODEOWNERS. Update NEWS.md.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_eg.html","id":null,"dir":"Reference","previous_headings":"","what":"Electrocardiogram Dataset — admiral_eg","title":"Electrocardiogram Dataset — admiral_eg","text":"example standard SDTM EG dataset used deriving ADEG dataset","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_eg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Electrocardiogram Dataset — admiral_eg","text":"","code":"admiral_eg"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_eg.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Electrocardiogram Dataset — admiral_eg","text":"object class tbl_df (inherits tbl, data.frame) 26669 rows 24 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/ae.html","id":null,"dir":"Reference","previous_headings":"","what":"Adverse Events Dataset-updated — ae","title":"Adverse Events Dataset-updated — ae","text":"updated SDTM AE dataset uses CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/ae.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adverse Events Dataset-updated — ae","text":"","code":"ae"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/ae.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Adverse Events Dataset-updated — ae","text":"object class tbl_df (inherits tbl, data.frame) 1191 rows 35 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/ae.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Adverse Events 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