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pkgdown: 2.0.7
pkgdown_sha: ~
articles: {}
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+last_built: 2023-09-04T08:39Z
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reference: https://pharmaverse.github.io/pharmaversesdtm/main/reference
article: https://pharmaverse.github.io/pharmaversesdtm/main/articles
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(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/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edoardo Mancini. Author, maintainer. Gayatri G. Author. Kangjie Zhang. Author. Pooja Kumari. Author. Stefan Bundfuss. Author. Zelos Zhu. Author.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Mancini E, G G, Zhang K, Kumari P, Bundfuss S, Zhu Z (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 and Gayatri G and Kangjie Zhang and Pooja Kumari and Stefan Bundfuss and Zelos Zhu}, year = {2023}, note = {https://pharmaverse.github.io/pharmaversesdtm, https://github.com/pharmaverse/pharmaversesdtm}, }"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/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/main/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/main/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/main/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. 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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/main/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/main/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/main/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/main/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/main/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/main/reference/ae.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Adverse Events 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Vegesna","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/sv.html","id":null,"dir":"Reference","previous_headings":"","what":"Subject Visits Dataset — sv","title":"Subject Visits Dataset — sv","text":"SDTM SV dataset CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/sv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subject Visits Dataset — sv","text":"","code":"sv"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/sv.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subject Visits Dataset — sv","text":"object class tbl_df (inherits tbl, data.frame) 3559 rows 8 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/sv.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subject Visits Dataset — 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nolint","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/tu_onco.html","id":null,"dir":"Reference","previous_headings":"","what":"Tumor Identification Dataset — tu_onco","title":"Tumor Identification Dataset — tu_onco","text":"SDTM TU dataset simulated Gopi Vegesna","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/tu_onco.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tumor Identification Dataset — tu_onco","text":"","code":"tu_onco"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/tu_onco.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Tumor Identification Dataset — tu_onco","text":"object class tbl_df (inherits tbl, data.frame) 7734 rows 18 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project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/vs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vital Signs Dataset — vs","text":"","code":"vs"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/vs.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Vital Signs Dataset — vs","text":"object class tbl_df (inherits tbl, data.frame) 29643 rows 24 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/reference/vs.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Vital Signs Dataset — vs","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/vs.xpt?raw=true # nolint","code":""},{"path":[]},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"pharmaversesdtm 0.1.0","text":"Ophthalmology variants ex qs SDTM datasets added. (#15) Migrate data function get_terms() admiral.test. (#1, #49) Oncology datasets tu_onco_recist, tr_onco_recist, rs_onco_recist using RECIST 1.1 response criteria. datasets contain just patients. intended vignettes examples ADaM datasets creation. (#33)","code":""}]
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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/main/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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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/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/pharmaversesdtm/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/pharmaversesdtm/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edoardo Mancini. Author, maintainer. Gayatri G. Author. Kangjie Zhang. Author. Pooja Kumari. Author. Stefan Bundfuss. Author. Zelos Zhu. Author.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Mancini E, G G, Zhang K, Kumari P, Bundfuss S, Zhu Z (2023). pharmaversesdtm: Test Data Pharmaverse Family Packages. https://pharmaverse.github.io/pharmaversesdtm/cran-release/, https://github.com/pharmaverse/pharmaversesdtm.","code":"@Manual{, title = {pharmaversesdtm: Test Data for the Pharmaverse Family of Packages}, author = {Edoardo Mancini and Gayatri G and Kangjie Zhang and Pooja Kumari and Stefan Bundfuss and Zelos Zhu}, year = {2023}, note = {https://pharmaverse.github.io/pharmaversesdtm/cran-release/, https://github.com/pharmaverse/pharmaversesdtm}, }"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/main/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/main/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/main/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/main/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/main/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/main/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/main/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. 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