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    pharmaversesdtm 0.1.0

    New Features

    -

    Updates of Existing Functions

    diff --git a/devel/pkgdown.yml b/devel/pkgdown.yml index 79c84e2..29005d7 100644 --- a/devel/pkgdown.yml +++ b/devel/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: adxx: adxx.html pharmaversesdtm: pharmaversesdtm.html -last_built: 2023-07-14T07:26Z +last_built: 2023-07-18T14:36Z 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 5c53474..e2cbc04 100644 --- a/devel/pull_request_template.html +++ b/devel/pull_request_template.html @@ -33,14 +33,6 @@
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    +
    +
    +

    Ophthalmology Exposure Dataset

    + Source: R/data.R +
    ex_ophtha.Rd
    +
    + +
    +

    An example Exposure SDTM dataset with ophthalmology-specific variables such as `EXLOC` and `EXLAT`

    +
    + +
    +

    Usage

    + 
    ex_ophtha
    +
    + +
    +

    Format

    +

    An object of class tbl_df (inherits from tbl, data.frame) with 591 rows and 19 columns.

    +
    +
    +

    Source

    +

    Constructed using `ex` from the `pharmaversesdtm` package # nolint

    +
    + +
    + + +
    +

    Developed by Edoardo Mancini.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + diff --git a/devel/reference/index.html b/devel/reference/index.html index e9e6479..7a58d80 100644 --- a/devel/reference/index.html +++ b/devel/reference/index.html @@ -33,14 +33,6 @@
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    • - @@ -294,6 +286,16 @@

    Example DatasetsVital Signs Dataset
    + ex_ophtha +
    +
    Ophthalmology Exposure Dataset
    +
    + + qs_ophtha +
    +
    Ophthalmology Questionnaire Dataset
    +
    + raw_ae
    Adverse Events Dataset-raw
    diff --git a/devel/reference/pharmaversesdtm-package.html b/devel/reference/pharmaversesdtm-package.html index 5bfa552..829195a 100644 --- a/devel/reference/pharmaversesdtm-package.html +++ b/devel/reference/pharmaversesdtm-package.html @@ -35,14 +35,6 @@
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    +
    +
    +

    Ophthalmology Questionnaire Dataset

    + Source: R/data.R +
    qs_ophtha.Rd
    +
    + +
    +

    An example Questionnaires SDTM dataset with ophthalmology-specific questionnaire of NEI VFQ-25

    +
    + +
    +

    Usage

    + 
    qs_ophtha
    +
    + +
    +

    Format

    +

    An object of class tbl_df (inherits from tbl, data.frame) with 197671 rows and 20 columns.

    +
    +
    +

    Source

    +

    Constructed using `qs` from the `pharmaversesdtm` package # nolint

    +
    + +
    + + +
    +

    Developed by Edoardo Mancini.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + diff --git a/devel/reference/raw_ae.html b/devel/reference/raw_ae.html index 813bc49..2f8dcfc 100644 --- a/devel/reference/raw_ae.html +++ b/devel/reference/raw_ae.html @@ -33,14 +33,6 @@
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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/devel/articles/adxx.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Creating ADXX","text":"article describes creating SDTM datasets.","code":""},{"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 Github repository detailed information regarding source specific datasets.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"naming-conventions","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: prefix domain name TA (e.g., onco_rs, ophtha_oe). Note: SDTM domain used multiple TAs, pharmaversesdtm may provide multiple versions corresponding test dataset. instance, package contains ex ophtha_ex 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 repo 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 dev/ 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 ggplot2, currently specified renv.lock file. feel need install packages addition just mentioned, please tag @pharmaverse/admiral discuss development core team. created program dev/ 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: example, dataset dm renamed raw_dm saving raw_dm.rda; save dm raw_dm.rda subsequently load .rda file, dm (raw_dm) loaded global environment. programs dev/ stored within pharmaversesdtm GitHub repository, part pharmaversesdtm package–dev/ folder specified .Rbuildignore. run program dev/ folder, generate dataset written data/ folder, become part pharmaversesdtm package. names 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":"Create program dev/ folder, named .R, SDTM domain name, (e.g. rs.R), generate test data output .rda data/ folder. Use CDISC pilot data dm input program order create realistic synthetic data remains consistent domains. 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/.","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":"Rename source dataset raw_, SDTM domain name (e.g. rename ds raw_ds), save data/ folder raw_.rda (e.g. save(raw_ds, file = \"data/raw_ds.rda\")). Create program dev/ folder, named update_.R, load raw_.rda, make updates, output .rda data/ folder. Run program. Reflect update, specifying raw_ R/data.R. Run devtools::document() order update NAMESPACE update .Rd files man/.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ae.html","id":null,"dir":"Reference","previous_headings":"","what":"Adverse Events Dataset-updated — admiral_ae","title":"Adverse Events Dataset-updated — admiral_ae","text":"updated SDTM AE dataset uses CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ae.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adverse Events Dataset-updated — admiral_ae","text":"","code":"admiral_ae"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ae.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Adverse Events Dataset-updated — admiral_ae","text":"object class tbl_df (inherits tbl, data.frame) 1191 rows 36 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ae.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Adverse Events Dataset-updated — admiral_ae","text":"https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ae.rda","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_cm.html","id":null,"dir":"Reference","previous_headings":"","what":"Concomitant Medication Dataset — admiral_cm","title":"Concomitant Medication Dataset — admiral_cm","text":"SDTM CM dataset CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_cm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concomitant Medication Dataset — admiral_cm","text":"","code":"admiral_cm"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_cm.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Concomitant Medication Dataset — admiral_cm","text":"object class tbl_df (inherits tbl, data.frame) 7510 rows 21 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_cm.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Concomitant Medication Dataset — admiral_cm","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/cm.xpt?raw=true # nolint","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_dm.html","id":null,"dir":"Reference","previous_headings":"","what":"Demography Dataset — admiral_dm","title":"Demography Dataset — admiral_dm","text":"SDTM DM dataset CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_dm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Demography Dataset — admiral_dm","text":"","code":"admiral_dm"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_dm.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Demography Dataset — admiral_dm","text":"object class tbl_df (inherits tbl, data.frame) 306 rows 25 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_dm.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Demography Dataset — admiral_dm","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/dm.xpt?raw=true # nolint","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":null,"dir":"Reference","previous_headings":"","what":"Disposition Dataset-updated — admiral_ds","title":"Disposition Dataset-updated — admiral_ds","text":"updated SDTM DS dataset uses CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Disposition Dataset-updated — admiral_ds","text":"","code":"admiral_ds"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Disposition Dataset-updated — admiral_ds","text":"object class tbl_df (inherits tbl, data.frame) 850 rows 13 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Disposition Dataset-updated — admiral_ds","text":"https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ds.rda","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Disposition Dataset-updated — admiral_ds","text":"Gopi Vegesna","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/admiral_ex.html","id":null,"dir":"Reference","previous_headings":"","what":"Exposure Dataset — admiral_ex","title":"Exposure Dataset — admiral_ex","text":"SDTM EX dataset CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Exposure Dataset — admiral_ex","text":"","code":"admiral_ex"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ex.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Exposure Dataset — admiral_ex","text":"object class tbl_df (inherits tbl, data.frame) 591 rows 17 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ex.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Exposure Dataset — admiral_ex","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true # nolint","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_lb.html","id":null,"dir":"Reference","previous_headings":"","what":"Laboratory Measurements Dataset — admiral_lb","title":"Laboratory Measurements Dataset — admiral_lb","text":"updated SDTM LB dataset uses data CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_lb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Laboratory Measurements Dataset — admiral_lb","text":"","code":"admiral_lb"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_lb.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Laboratory Measurements Dataset — admiral_lb","text":"object class tbl_df (inherits tbl, data.frame) 59580 rows 23 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_lb.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Laboratory Measurements Dataset — admiral_lb","text":"https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_lb.rda","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_lb.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Laboratory Measurements Dataset — admiral_lb","text":"Annie Yang","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_mh.html","id":null,"dir":"Reference","previous_headings":"","what":"Medical History Dataset-updated — admiral_mh","title":"Medical History Dataset-updated — admiral_mh","text":"updated SDTM MH dataset uses data CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_mh.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Medical History Dataset-updated — admiral_mh","text":"","code":"admiral_mh"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_mh.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Medical History Dataset-updated — admiral_mh","text":"object class tbl_df (inherits tbl, data.frame) 1818 rows 28 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_mh.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Medical History Dataset-updated — admiral_mh","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true # 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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/articles/adxx.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Creating ADXX","text":"article describes creating SDTM datasets.","code":""},{"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 Github repository detailed information regarding source specific datasets.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/index.html","id":"naming-conventions","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: prefix domain name TA (e.g., onco_rs, ophtha_oe). Note: SDTM domain used multiple TAs, pharmaversesdtm may provide multiple versions corresponding test dataset. instance, package contains ex ophtha_ex 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 repo 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 dev/ 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 ggplot2, currently specified renv.lock file. feel need install packages addition just mentioned, please tag @pharmaverse/admiral discuss development core team. created program dev/ 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: example, dataset dm renamed raw_dm saving raw_dm.rda; save dm raw_dm.rda subsequently load .rda file, dm (raw_dm) loaded global environment. programs dev/ stored within pharmaversesdtm GitHub repository, part pharmaversesdtm package–dev/ folder specified .Rbuildignore. run program dev/ folder, generate dataset written data/ folder, become part pharmaversesdtm package. names 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":"Create program dev/ folder, named .R, SDTM domain name, (e.g. rs.R), generate test data output .rda data/ folder. Use CDISC pilot data dm input program order create realistic synthetic data remains consistent domains. 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/.","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":"Rename source dataset raw_, SDTM domain name (e.g. rename ds raw_ds), save data/ folder raw_.rda (e.g. save(raw_ds, file = \"data/raw_ds.rda\")). Create program dev/ folder, named update_.R, load raw_.rda, make updates, output .rda data/ folder. Run program. Reflect update, specifying raw_ R/data.R. Run devtools::document() order update NAMESPACE update .Rd files man/.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ae.html","id":null,"dir":"Reference","previous_headings":"","what":"Adverse Events Dataset-updated — admiral_ae","title":"Adverse Events Dataset-updated — admiral_ae","text":"updated SDTM AE dataset uses CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ae.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adverse Events Dataset-updated — admiral_ae","text":"","code":"admiral_ae"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ae.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Adverse Events Dataset-updated — admiral_ae","text":"object class tbl_df (inherits tbl, data.frame) 1191 rows 36 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ae.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Adverse Events Dataset-updated — admiral_ae","text":"https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ae.rda","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_cm.html","id":null,"dir":"Reference","previous_headings":"","what":"Concomitant Medication Dataset — admiral_cm","title":"Concomitant Medication Dataset — admiral_cm","text":"SDTM CM dataset CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_cm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concomitant Medication Dataset — admiral_cm","text":"","code":"admiral_cm"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_cm.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Concomitant Medication Dataset — admiral_cm","text":"object class tbl_df (inherits tbl, data.frame) 7510 rows 21 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_cm.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Concomitant Medication Dataset — admiral_cm","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/cm.xpt?raw=true # nolint","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_dm.html","id":null,"dir":"Reference","previous_headings":"","what":"Demography Dataset — admiral_dm","title":"Demography Dataset — admiral_dm","text":"SDTM DM dataset CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_dm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Demography Dataset — admiral_dm","text":"","code":"admiral_dm"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_dm.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Demography Dataset — admiral_dm","text":"object class tbl_df (inherits tbl, data.frame) 306 rows 25 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_dm.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Demography Dataset — admiral_dm","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/dm.xpt?raw=true # nolint","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":null,"dir":"Reference","previous_headings":"","what":"Disposition Dataset-updated — admiral_ds","title":"Disposition Dataset-updated — admiral_ds","text":"updated SDTM DS dataset uses CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Disposition Dataset-updated — admiral_ds","text":"","code":"admiral_ds"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Disposition Dataset-updated — admiral_ds","text":"object class tbl_df (inherits tbl, data.frame) 850 rows 13 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Disposition Dataset-updated — admiral_ds","text":"https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ds.rda","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ds.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Disposition Dataset-updated — admiral_ds","text":"Gopi Vegesna","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/admiral_ex.html","id":null,"dir":"Reference","previous_headings":"","what":"Exposure Dataset — admiral_ex","title":"Exposure Dataset — admiral_ex","text":"SDTM EX dataset CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Exposure Dataset — admiral_ex","text":"","code":"admiral_ex"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ex.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Exposure Dataset — admiral_ex","text":"object class tbl_df (inherits tbl, data.frame) 591 rows 17 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_ex.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Exposure Dataset — admiral_ex","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true # nolint","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_lb.html","id":null,"dir":"Reference","previous_headings":"","what":"Laboratory Measurements Dataset — admiral_lb","title":"Laboratory Measurements Dataset — admiral_lb","text":"updated SDTM LB dataset uses data CDISC pilot project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_lb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Laboratory Measurements Dataset — admiral_lb","text":"","code":"admiral_lb"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_lb.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Laboratory Measurements Dataset — admiral_lb","text":"object class tbl_df (inherits tbl, data.frame) 59580 rows 23 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project","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_mh.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Medical History Dataset-updated — admiral_mh","text":"","code":"admiral_mh"},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_mh.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Medical History Dataset-updated — admiral_mh","text":"object class tbl_df (inherits tbl, data.frame) 1818 rows 28 columns.","code":""},{"path":"https://pharmaverse.github.io/pharmaversesdtm/devel/reference/admiral_mh.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Medical History Dataset-updated — admiral_mh","text":"https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true # 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