├── data ├── ae.rda ├── cm.rda ├── dm.rda ├── ds.rda ├── eg.rda ├── ex.rda ├── lb.rda ├── mh.rda ├── pc.rda ├── pp.rda ├── sv.rda ├── ts.rda ├── vs.rda ├── is_ada.rda ├── sdg_db.rda ├── smq_db.rda ├── suppae.rda ├── suppdm.rda ├── suppds.rda ├── ag_neuro.rda ├── dm_neuro.rda ├── dm_peds.rda ├── nv_neuro.rda ├── rs_onco.rda ├── tr_onco.rda ├── tu_onco.rda ├── vs_peds.rda ├── ae_ophtha.rda ├── ce_vaccine.rda ├── dm_vaccine.rda ├── ex_ophtha.rda ├── ex_vaccine.rda ├── is_vaccine.rda ├── oe_ophtha.rda ├── qs_ophtha.rda ├── sc_ophtha.rda ├── supptr_onco.rda ├── vs_vaccine.rda ├── dm_metabolic.rda ├── face_vaccine.rda ├── lb_metabolic.rda ├── qs_metabolic.rda ├── rs_onco_ca125.rda ├── rs_onco_imwg.rda ├── rs_onco_pcwg3.rda ├── suppnv_neuro.rda ├── vs_metabolic.rda ├── rs_onco_irecist.rda ├── rs_onco_recist.rda ├── suppce_vaccine.rda ├── suppdm_vaccine.rda ├── suppex_vaccine.rda ├── suppface_vaccine.rda ├── suppis_vaccine.rda ├── supprs_onco_imwg.rda ├── tr_onco_recist.rda ├── tu_onco_recist.rda └── supprs_onco_ca125.rda ├── NAMESPACE ├── R ├── pharmaversesdtm-package.R ├── smq_db.R ├── sdg_db.R ├── sv.R ├── ts.R ├── suppdm.R ├── suppce_vaccine.R ├── suppex_vaccine.R ├── suppdm_vaccine.R ├── suppface_vaccine.R ├── suppis_vaccine.R ├── suppds.R ├── suppnv_neuro.R ├── suppae.R ├── ag_neuro.R ├── supptr_onco.R ├── supprs_onco_ca125.R ├── ds.R ├── supprs_onco_imwg.R ├── ex_vaccine.R ├── sc_ophtha.R ├── ex.R ├── rs_onco_recist.R ├── ex_ophtha.R ├── rs_onco_imwg.R ├── tu_onco_recist.R ├── tu_onco.R ├── rs_onco_ca125.R ├── rs_onco_pcwg3.R ├── dm_metabolic.R ├── dm_peds.R ├── cm.R ├── dm_neuro.R ├── dm_vaccine.R ├── vs_vaccine.R ├── dm.R ├── tr_onco_recist.R ├── pc.R ├── nv_neuro.R ├── rs_onco.R ├── eg.R ├── ce_vaccine.R ├── rs_onco_irecist.R └── pp.R ├── man ├── figures │ ├── logo.png │ ├── gsk_logo.png │ ├── cytel_logo.png │ └── roche_logo.png ├── smq_db.Rd ├── get_terms.Rd ├── sdg_db.Rd ├── sv.Rd ├── suppdm.Rd ├── ts.Rd ├── suppce_vaccine.Rd ├── suppex_vaccine.Rd ├── suppdm_vaccine.Rd ├── suppface_vaccine.Rd ├── suppis_vaccine.Rd ├── suppds.Rd ├── suppnv_neuro.Rd ├── ag_neuro.Rd ├── suppae.Rd ├── supptr_onco.Rd ├── ds.Rd ├── supprs_onco_ca125.Rd ├── ex_vaccine.Rd ├── supprs_onco_imwg.Rd ├── sc_ophtha.Rd ├── ex.Rd ├── rs_onco_recist.Rd ├── ex_ophtha.Rd ├── tu_onco.Rd ├── rs_onco_imwg.Rd ├── tu_onco_recist.Rd ├── rs_onco_ca125.Rd ├── dm_peds.Rd ├── dm_metabolic.Rd ├── cm.Rd ├── dm_neuro.Rd ├── rs_onco_pcwg3.Rd ├── dm_vaccine.Rd ├── vs_vaccine.Rd ├── dm.Rd ├── pc.Rd ├── tr_onco_recist.Rd ├── nv_neuro.Rd ├── eg.Rd ├── rs_onco.Rd ├── pharmaversesdtm-package.Rd ├── ce_vaccine.Rd ├── is_vaccine.Rd ├── rs_onco_irecist.Rd ├── vs.Rd ├── tr_onco.Rd ├── pp.Rd ├── vs_peds.Rd ├── mh.Rd ├── is_ada.Rd ├── oe_ophtha.Rd ├── face_vaccine.Rd └── vs_metabolic.Rd ├── cran-comments.md ├── pkgdown └── favicon │ ├── favicon.ico │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon-96x96.png │ ├── apple-touch-icon.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── web-app-manifest-192x192.png │ ├── web-app-manifest-512x512.png │ └── site.webmanifest ├── data-raw ├── README.md ├── vs.R ├── ts.R ├── ex.R ├── cm.R ├── ae.R ├── sv.R ├── batch_run.sh ├── dm_metabolic.R ├── ae_ophtha.R ├── dm_peds.R ├── ex_ophtha.R ├── suppnv_neuro.R ├── suppdm_vaccine.R ├── suppce_vaccine.R ├── suppex_vaccine.R ├── suppface_vaccine.R ├── ex_vaccine.R ├── dm_neuro.R └── dm_vaccine.R ├── .devcontainer ├── rstudio-prefs.json └── postCreateCommand.sh ├── .lycheeignore ├── pharmaversesdtm.Rproj ├── .Rbuildignore ├── staged_dependencies.yaml ├── .lintr.R ├── .gitignore ├── .github ├── CODEOWNERS └── ISSUE_TEMPLATE │ ├── 03_docs_update.yml │ ├── 06_general_issue.yml │ ├── 01_bug_report.yml │ └── 02_feature_request.yml ├── DESCRIPTION └── _pkgdown.yml /data/ae.rda: 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https://raw.githubusercontent.com/pharmaverse/pharmaversesdtm/HEAD/pkgdown/favicon/web-app-manifest-512x512.png -------------------------------------------------------------------------------- /data-raw/README.md: -------------------------------------------------------------------------------- 1 | This folder is intended for scripts which create data frames in the `data` 2 | folder. They are excluded from the build as they should not be called by the 3 | user. 4 | 5 | For user facing scripts please create a separate folder. 6 | -------------------------------------------------------------------------------- /.devcontainer/rstudio-prefs.json: -------------------------------------------------------------------------------- 1 | { 2 | "save_workspace": "never", 3 | "always_save_history": false, 4 | "reuse_sessions_for_project_links": true, 5 | "posix_terminal_shell": "bash", 6 | "initial_working_directory": "/workspaces", 7 | "show_hidden_files": true 8 | } 9 | -------------------------------------------------------------------------------- /.lycheeignore: -------------------------------------------------------------------------------- 1 | # This is a list of urls to ignore in the link checking action Check URLS / 2 | # Validate Links 3 | 4 | https://packagemanager.rstudio.com/cran/linux/focal/latest 5 | https://github.com/pharmaverse/pharmaversesdtm/blob/main/ 6 | irongut/CodeCoverageSummary@v1.2.0 7 | insightsengineering/thevalidatoR@v1.2.1 8 | https://packagemanager.rstudio.com/cran/__linux__/focal/latest 9 | tj-actions/branch-names@v5.2 10 | -------------------------------------------------------------------------------- /.devcontainer/postCreateCommand.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$major, substr(R.version$minor, 1, 1), sep = "."), "renv.lock")); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);' 4 | 5 | jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json 6 | -------------------------------------------------------------------------------- /pharmaversesdtm.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: No 4 | SaveWorkspace: No 5 | AlwaysSaveHistory: Yes 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | LineEndingConversion: Posix 18 | 19 | BuildType: Package 20 | PackageUseDevtools: Yes 21 | PackageInstallArgs: --no-multiarch --with-keep.source 22 | -------------------------------------------------------------------------------- /pkgdown/favicon/site.webmanifest: -------------------------------------------------------------------------------- 1 | { 2 | "name": "", 3 | "short_name": "", 4 | "icons": [ 5 | { 6 | "src": "/web-app-manifest-192x192.png", 7 | "sizes": "192x192", 8 | "type": "image/png", 9 | "purpose": "maskable" 10 | }, 11 | { 12 | "src": "/web-app-manifest-512x512.png", 13 | "sizes": "512x512", 14 | "type": "image/png", 15 | "purpose": "maskable" 16 | } 17 | ], 18 | "theme_color": "#ffffff", 19 | "background_color": "#ffffff", 20 | "display": "standalone" 21 | } -------------------------------------------------------------------------------- /data-raw/vs.R: -------------------------------------------------------------------------------- 1 | # Dataset: vs 2 | # Description: Standard VS dataset from CDISC pilot study 3 | 4 | # Load libraries ----- 5 | library(haven) 6 | library(admiral) 7 | raw_vs <- read_xpt("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 8 | vs <- convert_blanks_to_na(raw_vs) 9 | 10 | # Label dataset ---- 11 | attr(vs, "label") <- "Vital Signs" 12 | 13 | # Save dataset ---- 14 | usethis::use_data(vs, overwrite = TRUE) 15 | -------------------------------------------------------------------------------- /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^.*\.Rproj$ 2 | ^.*\.lycheeignore$ 3 | ^\.Rproj\.user$ 4 | ^pkgdown$ 5 | ^_pkgdown\.yml$ 6 | ^.github$ 7 | ^.lintr.R$ 8 | ^docs$ 9 | ^Meta$ 10 | ^codecov\.yml$ 11 | ^man/dev_util_.+\.Rd$ 12 | ^LICENSE\.md$ 13 | ^\.github$ 14 | ^pharmaversesdtm\.Rcheck$ 15 | ^pharmaversesdtm.*\.tar\.gz$ 16 | ^pharmaversesdtm.*\.tgz$ 17 | ^staged_dependencies.yaml$ 18 | ^README.Rmd$ 19 | ^dev$ 20 | ^vignettes/adxx\.Rmd$ 21 | ^vignettes/pharmaversesdtm\.Rmd$ 22 | ^data-raw$ 23 | ^CRAN-SUBMISSION$ 24 | ^cran-comments\.md$ 25 | ^.devcontainer$ 26 | ^revdep 27 | -------------------------------------------------------------------------------- /data-raw/ts.R: -------------------------------------------------------------------------------- 1 | # Datasets: ts 2 | # Description: Standard TS dataset from CDISC pilot study 3 | 4 | # Load libraries ----- 5 | library(haven) 6 | library(admiral) 7 | raw_ts <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ts.xpt?raw=true") # nolint 8 | ts <- convert_blanks_to_na(raw_ts) 9 | 10 | # Label dataset ---- 11 | attr(ts, "label") <- "Trial Summary Information" 12 | 13 | # Save dataset ----- 14 | usethis::use_data(ts, overwrite = TRUE) 15 | -------------------------------------------------------------------------------- /data-raw/ex.R: -------------------------------------------------------------------------------- 1 | # Dataset: ex 2 | # Description: Standard EX dataset from CDISC pilot study 3 | 4 | # Load libraries ----- 5 | library(haven) 6 | library(admiral) 7 | 8 | # Create ex ---- 9 | raw_ex <- read_xpt("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 10 | ex <- convert_blanks_to_na(raw_ex) 11 | 12 | # Label dataset ---- 13 | attr(ex, "label") <- "Exposure" 14 | 15 | # Save dataset ---- 16 | usethis::use_data(ex, overwrite = TRUE) 17 | -------------------------------------------------------------------------------- /staged_dependencies.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | current_repo: 3 | repo: pharmaverse/pharmaversesdtm 4 | host: https://github.com 5 | upstream_repos: 6 | - repo: pharmaverse/admiraldev 7 | host: https://github.com 8 | downstream_repos: 9 | - repo: pharmaverse/admiral 10 | host: https://github.com 11 | - repo: pharmaverse/admiralonco 12 | host: https://github.com 13 | - repo: pharmaverse/admiralvaccine 14 | host: https://github.com 15 | - repo: pharmaverse/admiralophtha 16 | host: https://github.com 17 | - repo: pharmaverse/admiralpeds 18 | host: https://github.com 19 | 20 | 21 | -------------------------------------------------------------------------------- /.lintr.R: -------------------------------------------------------------------------------- 1 | # source in temporary environment to avoid changing the global environment 2 | temp_env <- new.env(parent = globalenv()) 3 | 4 | source(system.file("lintr/linters.R", package = "admiraldev"), local = temp_env) 5 | 6 | linters <- temp_env$admiral_linters() 7 | 8 | # remove temporary environment to avoid lintr warning regarding "unused settings" 9 | rm(temp_env) 10 | 11 | exclusions <- list( 12 | "R/" = Inf, 13 | "inst" = list(undesirable_function_linter = Inf), 14 | "vignettes" = list(undesirable_function_linter = Inf), 15 | "data-raw" = list( 16 | undesirable_function_linter = Inf, 17 | line_length_linter = Inf 18 | ) 19 | ) 20 | -------------------------------------------------------------------------------- /man/smq_db.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/smq_db.R 3 | \docType{data} 4 | \name{smq_db} 5 | \alias{smq_db} 6 | \title{Standardized MedDRA Queries} 7 | \format{ 8 | A data frame with 6 columns: 9 | \describe{ 10 | \item{termchar}{Reported Term} 11 | \item{scope}{Scope} 12 | \item{smq_name}{Name} 13 | \item{smq_id}{Name ID} 14 | \item{version}{Version} 15 | \item{termvar}{Variable} 16 | } 17 | } 18 | \source{ 19 | Generated dataset. 20 | } 21 | \usage{ 22 | smq_db 23 | } 24 | \description{ 25 | An example SMQ dataset 26 | } 27 | \details{ 28 | Standardized MedDRA Queries 29 | 30 | An example SMQ dataset 31 | } 32 | \keyword{dataset} 33 | \keyword{generic} 34 | -------------------------------------------------------------------------------- /man/get_terms.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/get_terms.R 3 | \name{get_terms} 4 | \alias{get_terms} 5 | \title{An example function as expected by the \code{get_terms_fun} parameter of 6 | \code{admiral::create_query_data()}} 7 | \usage{ 8 | get_terms(basket_select, version, keep_id, temp_env) 9 | } 10 | \arguments{ 11 | \item{basket_select}{A basket_select object defining the terms} 12 | 13 | \item{version}{MedDRA version} 14 | 15 | \item{keep_id}{Should \code{GRPID} be included in the output?} 16 | 17 | \item{temp_env}{Temporary environment} 18 | } 19 | \description{ 20 | An example function as expected by the \code{get_terms_fun} parameter of 21 | \code{admiral::create_query_data()} 22 | } 23 | -------------------------------------------------------------------------------- /man/sdg_db.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/sdg_db.R 3 | \docType{data} 4 | \name{sdg_db} 5 | \alias{sdg_db} 6 | \title{SDG} 7 | \format{ 8 | A data frame with 5 columns: 9 | \describe{ 10 | \item{termchar}{Reported Term} 11 | \item{sdg_name}{Name} 12 | \item{sdg_id}{Name ID} 13 | \item{termvar}{Variable} 14 | \item{version}{Version} 15 | } 16 | } 17 | \source{ 18 | \href{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/sv.xpt?raw=true}{Access the source of the SDG dataset.} 19 | } 20 | \usage{ 21 | sdg_db 22 | } 23 | \description{ 24 | An example SDG dataset 25 | } 26 | \details{ 27 | SDG 28 | 29 | An example SDG dataset 30 | } 31 | \keyword{dataset} 32 | \keyword{generic} 33 | -------------------------------------------------------------------------------- /R/smq_db.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Standardized MedDRA Queries 5 | #' 6 | #' An example SMQ dataset 7 | #' 8 | #' @name smq_db 9 | #' @title Standardized MedDRA Queries 10 | #' @keywords dataset generic 11 | #' @description An example SMQ dataset 12 | #' @docType data 13 | #' @format A data frame with 6 columns: 14 | #' \describe{ 15 | #' \item{termchar}{Reported Term} 16 | #' \item{scope}{Scope} 17 | #' \item{smq_name}{Name} 18 | #' \item{smq_id}{Name ID} 19 | #' \item{version}{Version} 20 | #' \item{termvar}{Variable} 21 | #' } 22 | #' 23 | #' @source Generated dataset. 24 | "smq_db" 25 | -------------------------------------------------------------------------------- /data-raw/cm.R: -------------------------------------------------------------------------------- 1 | # Dataset: cm 2 | # Description: Standard CM dataset from CDISC pilot study 3 | 4 | # Load libraries ----- 5 | library(haven) 6 | library(admiral) 7 | library(dplyr) 8 | library(metatools) 9 | 10 | # Create cm ---- 11 | raw_cm <- read_xpt("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 12 | cm <- convert_blanks_to_na(raw_cm) %>% 13 | mutate(CMENRTPT = if_else(is.na(CMENDTC), "ONGOING", NA_character_)) 14 | 15 | # Label variables ---- 16 | cm <- cm %>% 17 | add_labels( 18 | CMENRTPT = "End Relative to Reference Time Point" 19 | ) 20 | 21 | # Label dataset ---- 22 | attr(cm, "label") <- "Concomitant Medications" 23 | 24 | # Save dataset ---- 25 | usethis::use_data(cm, overwrite = TRUE) 26 | -------------------------------------------------------------------------------- /R/sdg_db.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' SDG 5 | #' 6 | #' An example SDG dataset 7 | #' 8 | #' @name sdg_db 9 | #' @title SDG 10 | #' @keywords dataset generic 11 | #' @description An example SDG dataset 12 | #' @docType data 13 | #' @format A data frame with 5 columns: 14 | #' \describe{ 15 | #' \item{termchar}{Reported Term} 16 | #' \item{sdg_name}{Name} 17 | #' \item{sdg_id}{Name ID} 18 | #' \item{termvar}{Variable} 19 | #' \item{version}{Version} 20 | #' } 21 | #' 22 | #' @source [Access the source of the SDG dataset.](https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/sv.xpt?raw=true) 23 | "sdg_db" 24 | -------------------------------------------------------------------------------- /man/sv.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/sv.R 3 | \docType{data} 4 | \name{sv} 5 | \alias{sv} 6 | \title{Subject Visits} 7 | \format{ 8 | A data frame with 8 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{VISITNUM}{Visit Number} 14 | \item{VISIT}{Visit Name} 15 | \item{VISITDY}{Planned Study Day of Visit} 16 | \item{SVSTDTC}{Start Date/Time of Visit} 17 | \item{SVENDTC}{End Date/Time of Visit} 18 | } 19 | } 20 | \source{ 21 | Constructed by {admiralvaccine} developers 22 | } 23 | \usage{ 24 | sv 25 | } 26 | \description{ 27 | A SDTM SV dataset from the CDISC pilot project with corrected duplicate observation 28 | } 29 | \details{ 30 | Subject Visits 31 | 32 | A SDTM SV dataset from the CDISC pilot project with corrected duplicate observation 33 | } 34 | \keyword{dataset} 35 | \keyword{generic} 36 | -------------------------------------------------------------------------------- /man/suppdm.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppdm.R 3 | \docType{data} 4 | \name{suppdm} 5 | \alias{suppdm} 6 | \title{Supplemental Demography} 7 | \format{ 8 | A data frame with 10 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{RDOMAIN}{Related Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QLABEL}{Qualifier Variable Label} 17 | \item{QVAL}{Data Value} 18 | \item{QORIG}{Origin} 19 | \item{QEVAL}{Evaluator} 20 | } 21 | } 22 | \source{ 23 | Generated dataset. 24 | } 25 | \usage{ 26 | suppdm 27 | } 28 | \description{ 29 | A SDTM SUPPDM dataset from the CDISC pilot project 30 | } 31 | \details{ 32 | Supplemental Demography 33 | 34 | A SDTM SUPPDM dataset from the CDISC pilot project 35 | } 36 | \keyword{dataset} 37 | \keyword{generic} 38 | -------------------------------------------------------------------------------- /man/ts.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ts.R 3 | \docType{data} 4 | \name{ts} 5 | \alias{ts} 6 | \title{Trial Design} 7 | \format{ 8 | A data frame with 6 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{TSSEQ}{Sequence Number} 13 | \item{TSPARMCD}{Trial Summary Parameter Short Name} 14 | \item{TSPARM}{Trial Summary Parameter} 15 | \item{TSVAL}{Parameter Value} 16 | } 17 | } 18 | \source{ 19 | \href{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}{Access the source of the Trial Design dataset.} 20 | } 21 | \usage{ 22 | ts 23 | } 24 | \description{ 25 | A SDTM TS dataset from the CDISC pilot project 26 | } 27 | \details{ 28 | Trial Design 29 | 30 | A SDTM TS dataset from the CDISC pilot project 31 | } 32 | \keyword{dataset} 33 | \keyword{generic} 34 | -------------------------------------------------------------------------------- /data-raw/ae.R: -------------------------------------------------------------------------------- 1 | # Datasets: ae, suppae 2 | # Description: Standard AE, SUPPAE datasets from CDISC pilot study 3 | 4 | # Load libraries ----- 5 | library(dplyr) 6 | library(metatools) 7 | library(haven) 8 | library(admiral) 9 | 10 | # Create ae, suppae ---- 11 | raw_ae <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ae.xpt?raw=true") # nolint 12 | raw_suppae <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true") # nolint 13 | ae <- convert_blanks_to_na(raw_ae) 14 | suppae <- convert_blanks_to_na(raw_suppae) 15 | 16 | # Label dataset ---- 17 | attr(ae, "label") <- "Adverse Events" 18 | attr(suppae, "label") <- "Supplemental Qualifiers for AE" 19 | 20 | # Save datasets ---- 21 | usethis::use_data(ae, overwrite = TRUE) 22 | usethis::use_data(suppae, overwrite = TRUE) 23 | -------------------------------------------------------------------------------- /man/suppce_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppce_vaccine.R 3 | \docType{data} 4 | \name{suppce_vaccine} 5 | \alias{suppce_vaccine} 6 | \title{Supplemental Qualifiers for Clinical Events for Vaccine} 7 | \format{ 8 | A data frame with 9 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{USUBJID}{Unique Subject Identifier} 12 | \item{RDOMAIN}{Related Domain Abbreviation} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QVAL}{Data Value} 17 | \item{QLABEL}{Qualifier Variable Label} 18 | \item{QORIG}{Origin} 19 | } 20 | } 21 | \source{ 22 | Constructed by {admiralvaccine} developers 23 | } 24 | \usage{ 25 | suppce_vaccine 26 | } 27 | \description{ 28 | An example SDTM SUPPCE for vaccine studies 29 | } 30 | \details{ 31 | Supplemental Qualifiers for Clinical Events for Vaccine 32 | 33 | An example SDTM SUPPCE for vaccine studies 34 | } 35 | \keyword{dataset} 36 | \keyword{vaccine} 37 | -------------------------------------------------------------------------------- /man/suppex_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppex_vaccine.R 3 | \docType{data} 4 | \name{suppex_vaccine} 5 | \alias{suppex_vaccine} 6 | \title{Supplemental Qualifiers for Exposures for Vaccine} 7 | \format{ 8 | A data frame with 9 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{USUBJID}{Unique Subject Identifier} 12 | \item{RDOMAIN}{Related Domain Abbreviation} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QVAL}{Data Value} 17 | \item{QLABEL}{Qualifier Variable Label} 18 | \item{QORIG}{Origin} 19 | } 20 | } 21 | \source{ 22 | Constructed by {admiralvaccine} developers 23 | } 24 | \usage{ 25 | suppex_vaccine 26 | } 27 | \description{ 28 | An example SDTM SUPPEX dataset for vaccine studies 29 | } 30 | \details{ 31 | Supplemental Qualifiers for Exposures for Vaccine 32 | 33 | An example SDTM SUPPEX dataset for vaccine studies 34 | } 35 | \keyword{dataset} 36 | \keyword{vaccine} 37 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # History files 2 | .Rhistory 3 | .Rapp.history 4 | 5 | # Session Data files 6 | .RData 7 | 8 | # User-specific files 9 | .Ruserdata 10 | 11 | # Example code in package build process 12 | *-Ex.R 13 | 14 | # Output files from R CMD build 15 | /*.tar.gz 16 | 17 | # Output files from R CMD check 18 | /*.Rcheck/ 19 | 20 | # RStudio files 21 | .Rproj.user/ 22 | 23 | # helper files for interchange data between scripts 24 | data-raw/tu_help_data.rds 25 | 26 | # produced vignettes 27 | vignettes/*.html 28 | vignettes/*.pdf 29 | 30 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 31 | .httr-oauth 32 | 33 | # knitr and R markdown default cache directories 34 | *_cache/ 35 | /cache/ 36 | 37 | # Temporary files created by R markdown 38 | *.utf8.md 39 | *.knit.md 40 | 41 | # Web Documentation files 42 | /docs/* 43 | !/docs/pkgdown.yml 44 | 45 | # R Environment Variables 46 | .Renviron 47 | pharmaversesdtm.Rcheck/ 48 | pharmaversesdtm*.tar.gz 49 | pharmaversesdtm*.tgz 50 | 51 | # MacOS 52 | .DS_Store 53 | 54 | # Docs 55 | docs/ 56 | -------------------------------------------------------------------------------- /man/suppdm_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppdm_vaccine.R 3 | \docType{data} 4 | \name{suppdm_vaccine} 5 | \alias{suppdm_vaccine} 6 | \title{Supplemental Qualifiers for Demographics for Vaccine} 7 | \format{ 8 | A data frame with 9 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{USUBJID}{Unique Subject Identifier} 12 | \item{RDOMAIN}{Related Domain Abbreviation} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QVAL}{Data Value} 17 | \item{QLABEL}{Qualifier Variable Label} 18 | \item{QORIG}{Origin} 19 | } 20 | } 21 | \source{ 22 | Constructed by {admiralvaccine} developers 23 | } 24 | \usage{ 25 | suppdm_vaccine 26 | } 27 | \description{ 28 | An example SDTM SUPPDM dataset for vaccine studies 29 | } 30 | \details{ 31 | Supplemental Qualifiers for Demographics for Vaccine 32 | 33 | An example SDTM SUPPDM dataset for vaccine studies 34 | } 35 | \keyword{dataset} 36 | \keyword{vaccine} 37 | -------------------------------------------------------------------------------- /data-raw/sv.R: -------------------------------------------------------------------------------- 1 | # Dataset: sv 2 | # Description: StandardSV dataset from CDISC pilot study 3 | 4 | # Load libraries ----- 5 | library(haven) 6 | library(admiral) 7 | library(dplyr) 8 | library(metatools) 9 | raw_sv <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/sv.xpt?raw=true") # nolint 10 | sv <- convert_blanks_to_na(raw_sv) 11 | 12 | sv <- sv %>% 13 | group_by(USUBJID, VISITNUM) %>% 14 | mutate( 15 | ASEQ = row_number(), 16 | n = n() 17 | ) %>% 18 | mutate( 19 | VISIT = ifelse(n > 1, paste0("UNSCHEDULED ", floor(VISITNUM), ".", ASEQ), VISIT), 20 | VISITNUM = ifelse(n > 1, as.numeric(paste0(floor(VISITNUM), ".", ASEQ)), VISITNUM) 21 | ) %>% 22 | ungroup() %>% 23 | select(-ASEQ, -n) %>% 24 | add_labels( 25 | VISIT = "Visit Name", 26 | VISITNUM = "Visit Number" 27 | ) 28 | 29 | 30 | # Label dataset ---- 31 | attr(sv, "label") <- "Subject Visits" 32 | 33 | # Save dataset ---- 34 | usethis::use_data(sv, overwrite = TRUE) 35 | -------------------------------------------------------------------------------- /R/sv.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Subject Visits 5 | #' 6 | #' A SDTM SV dataset from the CDISC pilot project with corrected duplicate observation 7 | #' 8 | #' @name sv 9 | #' @title Subject Visits 10 | #' @keywords dataset generic 11 | #' @description A SDTM SV dataset from the CDISC pilot project with corrected duplicate observation 12 | #' @docType data 13 | #' @format A data frame with 8 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{VISITNUM}{Visit Number} 19 | #' \item{VISIT}{Visit Name} 20 | #' \item{VISITDY}{Planned Study Day of Visit} 21 | #' \item{SVSTDTC}{Start Date/Time of Visit} 22 | #' \item{SVENDTC}{End Date/Time of Visit} 23 | #' } 24 | #' 25 | #' @source Constructed by {admiralvaccine} developers 26 | "sv" 27 | -------------------------------------------------------------------------------- /R/ts.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Trial Design 5 | #' 6 | #' A SDTM TS dataset from the CDISC pilot project 7 | #' 8 | #' @name ts 9 | #' @title Trial Design 10 | #' @keywords dataset generic 11 | #' @description A SDTM TS dataset from the CDISC pilot project 12 | #' @docType data 13 | #' @format A data frame with 6 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{TSSEQ}{Sequence Number} 18 | #' \item{TSPARMCD}{Trial Summary Parameter Short Name} 19 | #' \item{TSPARM}{Trial Summary Parameter} 20 | #' \item{TSVAL}{Parameter Value} 21 | #' } 22 | #' 23 | #' @source [Access the source of the Trial Design dataset.](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) 24 | "ts" 25 | -------------------------------------------------------------------------------- /man/suppface_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppface_vaccine.R 3 | \docType{data} 4 | \name{suppface_vaccine} 5 | \alias{suppface_vaccine} 6 | \title{Supplemental Qualifiers for Findings About for Clinical Events for Vaccine} 7 | \format{ 8 | A data frame with 9 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{USUBJID}{Unique Subject Identifier} 12 | \item{RDOMAIN}{Related Domain Abbreviation} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QVAL}{Data Value} 17 | \item{QLABEL}{Qualifier Variable Label} 18 | \item{QORIG}{Origin} 19 | } 20 | } 21 | \source{ 22 | Constructed by {admiralvaccine} developers 23 | } 24 | \usage{ 25 | suppface_vaccine 26 | } 27 | \description{ 28 | An example SDTM SUPPFACE dataset for vaccine studies 29 | } 30 | \details{ 31 | Supplemental Qualifiers for Findings About for Clinical Events for Vaccine 32 | 33 | An example SDTM SUPPFACE dataset for vaccine studies 34 | } 35 | \keyword{dataset} 36 | \keyword{vaccine} 37 | -------------------------------------------------------------------------------- /R/suppdm.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Demography 5 | #' 6 | #' A SDTM SUPPDM dataset from the CDISC pilot project 7 | #' 8 | #' @name suppdm 9 | #' @title Supplemental Demography 10 | #' @keywords dataset generic 11 | #' @description A SDTM SUPPDM dataset from the CDISC pilot project 12 | #' @docType data 13 | #' @format A data frame with 10 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{RDOMAIN}{Related Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QLABEL}{Qualifier Variable Label} 22 | #' \item{QVAL}{Data Value} 23 | #' \item{QORIG}{Origin} 24 | #' \item{QEVAL}{Evaluator} 25 | #' } 26 | #' 27 | #' @source Generated dataset. 28 | "suppdm" 29 | -------------------------------------------------------------------------------- /man/suppis_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppis_vaccine.R 3 | \docType{data} 4 | \name{suppis_vaccine} 5 | \alias{suppis_vaccine} 6 | \title{Supplemental Qualifiers for Immunogenicity Specimen Assessments for Vaccine} 7 | \format{ 8 | A data frame with 10 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{RDOMAIN}{Related Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QLABEL}{Qualifier Variable Label} 17 | \item{QVAL}{Data Value} 18 | \item{QORIG}{Origin} 19 | \item{QEVAL}{Evaluator} 20 | } 21 | } 22 | \source{ 23 | Constructed by {admiralpeds} developers 24 | } 25 | \usage{ 26 | suppis_vaccine 27 | } 28 | \description{ 29 | An example SDTM SUPPIS dataset for vaccine studies 30 | } 31 | \details{ 32 | Supplemental Qualifiers for Immunogenicity Specimen Assessments for Vaccine 33 | 34 | An example SDTM SUPPIS dataset for vaccine studies 35 | } 36 | \keyword{dataset} 37 | \keyword{vaccine} 38 | -------------------------------------------------------------------------------- /man/suppds.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppds.R 3 | \docType{data} 4 | \name{suppds} 5 | \alias{suppds} 6 | \title{Supplemental Disposition} 7 | \format{ 8 | A data frame with 9 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{RDOMAIN}{Related Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QLABEL}{Qualifier Variable Label} 17 | \item{QVAL}{Data Value} 18 | \item{QORIG}{Origin} 19 | } 20 | } 21 | \source{ 22 | \href{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppdm.xpt?raw=true}{Access the source of the Supplemental Disposition dataset.} 23 | } 24 | \usage{ 25 | suppds 26 | } 27 | \description{ 28 | A SDTM SUPPDS dataset from the CDISC pilot project 29 | } 30 | \details{ 31 | Supplemental Disposition 32 | 33 | A SDTM SUPPDS dataset from the CDISC pilot project 34 | } 35 | \keyword{dataset} 36 | \keyword{generic} 37 | -------------------------------------------------------------------------------- /.github/CODEOWNERS: -------------------------------------------------------------------------------- 1 | # This a CODEOWNERS file, where you can establish code owners. 2 | # Code owners are automatically requested for review when someone opens a pull request 3 | # that modifies code that they own. 4 | 5 | # admiral.test 6 | data-raw/pc.R @toni-1991 7 | data-raw/pp.R @toni-1991 8 | data-raw/query_databases.R @bundfussr 9 | 10 | # admiralonco 11 | data-raw/rs_onco.R @bundfussr 12 | data-raw/tr_onco.R @bundfussr 13 | data-raw/tu_onco.R @bundfussr 14 | 15 | # admiralophtha 16 | data-raw/ae_ophtha.R @manciniedoardo 17 | data-raw/ex_ophtha.R @manciniedoardo 18 | data-raw/oe_ophtha.R @manciniedoardo 19 | data-raw/qs_ophtha.R @manciniedoardo 20 | data-raw/sc_ophtha.R @manciniedoardo 21 | 22 | # admiralpeds 23 | data-raw/dm_peds.R @fanny-gautier 24 | data-raw/vs_peds.R @fanny-gautier 25 | 26 | # admiralmetabolic 27 | data-raw/dm_metabolic.R @andersaskeland 28 | data-raw/lb_metabolic.R @andersaskeland 29 | data-raw/qs_metabolic.R @andersaskeland 30 | data-raw/vs_metabolic.R @andersaskeland 31 | 32 | # admiralneuro 33 | data-raw/dm_neuro.R @jwang-lilly 34 | data-raw/nv_neuro.R @jwang-lilly 35 | data-raw/suppnv_neuro.R @jwang-lilly 36 | data-raw/ag_neuro.R @jwang-lilly 37 | -------------------------------------------------------------------------------- /R/suppce_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Qualifiers for Clinical Events for Vaccine 5 | #' 6 | #' An example SDTM SUPPCE for vaccine studies 7 | #' 8 | #' @name suppce_vaccine 9 | #' @title Supplemental Qualifiers for Clinical Events for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM SUPPCE for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 9 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{USUBJID}{Unique Subject Identifier} 17 | #' \item{RDOMAIN}{Related Domain Abbreviation} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QVAL}{Data Value} 22 | #' \item{QLABEL}{Qualifier Variable Label} 23 | #' \item{QORIG}{Origin} 24 | #' } 25 | #' 26 | #' @source Constructed by {admiralvaccine} developers 27 | "suppce_vaccine" 28 | -------------------------------------------------------------------------------- /R/suppex_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Qualifiers for Exposures for Vaccine 5 | #' 6 | #' An example SDTM SUPPEX dataset for vaccine studies 7 | #' 8 | #' @name suppex_vaccine 9 | #' @title Supplemental Qualifiers for Exposures for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM SUPPEX dataset for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 9 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{USUBJID}{Unique Subject Identifier} 17 | #' \item{RDOMAIN}{Related Domain Abbreviation} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QVAL}{Data Value} 22 | #' \item{QLABEL}{Qualifier Variable Label} 23 | #' \item{QORIG}{Origin} 24 | #' } 25 | #' 26 | #' @source Constructed by {admiralvaccine} developers 27 | "suppex_vaccine" 28 | -------------------------------------------------------------------------------- /data-raw/batch_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # direct copy from CDISC pilot 3 | Rscript data-raw/ex.R 4 | Rscript data-raw/cm.R 5 | Rscript data-raw/sv.R 6 | Rscript data-raw/ts.R 7 | Rscript data-raw/vs.R 8 | Rscript data-raw/dm.R 9 | 10 | # Update from CDISC pilot 11 | Rscript data-raw/ae.R 12 | Rscript data-raw/ds.R 13 | Rscript data-raw/lb.R 14 | Rscript data-raw/mh.R 15 | Rscript data-raw/qs.R 16 | 17 | # build from program 18 | Rscript data-raw/pc.R 19 | Rscript data-raw/pp.R 20 | Rscript data-raw/query_databases.R # sdg_db, smq_db 21 | 22 | 23 | # admiralophtha 24 | Rscript data-raw/ex_ophtha.R 25 | Rscript data-raw/qs_ophtha.R 26 | # admiralophtha build from program 27 | Rscript data-raw/oe_ophtha.R 28 | Rscript data-raw/sc_ophtha.R 29 | 30 | 31 | # admiralonco build from program 32 | Rscript data-raw/tr_onco.R 33 | Rscript data-raw/tu_onco.R 34 | Rscript data-raw/rs_onco.R 35 | 36 | # admiralpeds build from program 37 | Rscript data-raw/dm_peds.R 38 | Rscript data-raw/vs_peds.R 39 | 40 | # admiralmetabolic build from program 41 | Rscript data-raw/dm_metabolic.R 42 | Rscript data-raw/vs_metabolic.R 43 | Rscript data-raw/qs_metabolic.R 44 | Rscript data-raw/lb_metabolic.R 45 | 46 | -------------------------------------------------------------------------------- /man/suppnv_neuro.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppnv_neuro.R 3 | \docType{data} 4 | \name{suppnv_neuro} 5 | \alias{suppnv_neuro} 6 | \title{Supplemental for Neurological Assessment Dataset-neuro} 7 | \format{ 8 | A data frame with 10 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{RDOMAIN}{Related Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QLABEL}{Qualifier Variable Label} 17 | \item{QVAL}{Data Value} 18 | \item{QORIG}{Origin} 19 | \item{QEVAL}{Evaluator} 20 | } 21 | } 22 | \source{ 23 | Constructed by {admiralneuro} developers 24 | } 25 | \usage{ 26 | suppnv_neuro 27 | } 28 | \description{ 29 | A SDTM SUPPNV dataset containing additional information about neurological assessments or test results 30 | } 31 | \details{ 32 | Supplemental for Neurological Assessment Dataset-neuro 33 | 34 | A SDTM SUPPNV dataset containing additional information about neurological assessments or test results 35 | } 36 | \keyword{dataset} 37 | \keyword{neurology} 38 | -------------------------------------------------------------------------------- /R/suppdm_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Qualifiers for Demographics for Vaccine 5 | #' 6 | #' An example SDTM SUPPDM dataset for vaccine studies 7 | #' 8 | #' @name suppdm_vaccine 9 | #' @title Supplemental Qualifiers for Demographics for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM SUPPDM dataset for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 9 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{USUBJID}{Unique Subject Identifier} 17 | #' \item{RDOMAIN}{Related Domain Abbreviation} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QVAL}{Data Value} 22 | #' \item{QLABEL}{Qualifier Variable Label} 23 | #' \item{QORIG}{Origin} 24 | #' } 25 | #' 26 | #' @source Constructed by {admiralvaccine} developers 27 | "suppdm_vaccine" 28 | -------------------------------------------------------------------------------- /man/ag_neuro.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ag_neuro.R 3 | \docType{data} 4 | \name{ag_neuro} 5 | \alias{ag_neuro} 6 | \title{Procedure Agents Dataset-neuro} 7 | \format{ 8 | A data frame with 13 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{AGSEQ}{Sequence Number} 14 | \item{AGTRT}{Reported Agent Name} 15 | \item{AGCAT}{Category for Agent} 16 | \item{AGDOSE}{Dose per Administration} 17 | \item{AGDOSEU}{Dose Units} 18 | \item{AGROUTE}{Route of Administration} 19 | \item{AGLNKID}{Link ID} 20 | \item{VISITNUM}{Visit Number} 21 | \item{VISIT}{Visit Name} 22 | \item{AGSTDTC}{Start Date/Time of Agent} 23 | } 24 | } 25 | \source{ 26 | Constructed by {admiralneuro} developers 27 | } 28 | \usage{ 29 | ag_neuro 30 | } 31 | \description{ 32 | A SDTM AG dataset recording details of agents such as a PET tracer used in procedures 33 | } 34 | \details{ 35 | Procedure Agents Dataset-neuro 36 | 37 | A SDTM AG dataset recording details of agents such as a PET tracer used in procedures 38 | } 39 | \keyword{dataset} 40 | \keyword{neurology} 41 | -------------------------------------------------------------------------------- /man/suppae.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/suppae.R 3 | \docType{data} 4 | \name{suppae} 5 | \alias{suppae} 6 | \title{Supplemental Adverse Events} 7 | \format{ 8 | A data frame with 10 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{RDOMAIN}{Related Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QLABEL}{Qualifier Variable Label} 17 | \item{QVAL}{Data Value} 18 | \item{QORIG}{Origin} 19 | \item{QEVAL}{Evaluator} 20 | } 21 | } 22 | \source{ 23 | \href{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true}{Access the source of the Supplemental Adverse Events dataset.} 24 | } 25 | \usage{ 26 | suppae 27 | } 28 | \description{ 29 | A SDTM SUPPAE dataset from the CDISC pilot project 30 | } 31 | \details{ 32 | Supplemental Adverse Events 33 | 34 | A SDTM SUPPAE dataset from the CDISC pilot project 35 | } 36 | \keyword{dataset} 37 | \keyword{generic} 38 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/03_docs_update.yml: -------------------------------------------------------------------------------- 1 | name: Updates or Enhancements for Documentation 2 | description: Documents out of date? Examples need reworking? Got an idea for a new article? 3 | title: "Documentation: " 4 | labels: ["vignettes", "website", "documentation"] 5 | assignees: 6 | - octocat 7 | body: 8 | - type: markdown 9 | attributes: 10 | value: | 11 | The admiral team loves documentation! Help us keep it up to date and fresh! 12 | - type: dropdown 13 | id: browsers 14 | attributes: 15 | label: Please select a category the issue is focused on? 16 | multiple: true 17 | options: 18 | - Function Documentation 19 | - User Guides 20 | - Developer Guides 21 | - Other 22 | - I have a new documentation idea! Yay! 23 | - type: textarea 24 | id: docs-out-if-sync 25 | attributes: 26 | label: Let us know where something needs a refresh or put your idea here! 27 | description: Screen shots are super helpful here! You can do a screenshot and cut and paste it here right in here. 28 | placeholder: "Something is out of sync or needs a refresh" 29 | validations: 30 | required: true 31 | -------------------------------------------------------------------------------- /R/suppface_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Qualifiers for Findings About for Clinical Events for Vaccine 5 | #' 6 | #' An example SDTM SUPPFACE dataset for vaccine studies 7 | #' 8 | #' @name suppface_vaccine 9 | #' @title Supplemental Qualifiers for Findings About for Clinical Events for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM SUPPFACE dataset for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 9 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{USUBJID}{Unique Subject Identifier} 17 | #' \item{RDOMAIN}{Related Domain Abbreviation} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QVAL}{Data Value} 22 | #' \item{QLABEL}{Qualifier Variable Label} 23 | #' \item{QORIG}{Origin} 24 | #' } 25 | #' 26 | #' @source Constructed by {admiralvaccine} developers 27 | "suppface_vaccine" 28 | -------------------------------------------------------------------------------- /man/supptr_onco.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/supptr_onco.R 3 | \docType{data} 4 | \name{supptr_onco} 5 | \alias{supptr_onco} 6 | \title{Supplemental Tumor Results for Oncology} 7 | \format{ 8 | A data frame with 9 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{RDOMAIN}{Related Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QLABEL}{Qualifier Variable Label} 17 | \item{QVAL}{Data Value} 18 | \item{QORIG}{Origin} 19 | } 20 | } 21 | \source{ 22 | \href{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ts.xpt?raw=true}{Access the source of the Supplemental Tumor Results for Oncology dataset.} 23 | } 24 | \usage{ 25 | supptr_onco 26 | } 27 | \description{ 28 | A SDTM SUPPTR dataset simulated by Gopi Vegesna 29 | } 30 | \details{ 31 | Supplemental Tumor Results for Oncology 32 | 33 | A SDTM SUPPTR dataset simulated by Gopi Vegesna 34 | } 35 | \author{ 36 | Gopi Vegesna 37 | } 38 | \keyword{dataset} 39 | \keyword{oncology} 40 | -------------------------------------------------------------------------------- /R/suppis_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Qualifiers for Immunogenicity Specimen Assessments for Vaccine 5 | #' 6 | #' An example SDTM SUPPIS dataset for vaccine studies 7 | #' 8 | #' @name suppis_vaccine 9 | #' @title Supplemental Qualifiers for Immunogenicity Specimen Assessments for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM SUPPIS dataset for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 10 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{RDOMAIN}{Related Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QLABEL}{Qualifier Variable Label} 22 | #' \item{QVAL}{Data Value} 23 | #' \item{QORIG}{Origin} 24 | #' \item{QEVAL}{Evaluator} 25 | #' } 26 | #' 27 | #' @source Constructed by {admiralpeds} developers 28 | "suppis_vaccine" 29 | -------------------------------------------------------------------------------- /data-raw/dm_metabolic.R: -------------------------------------------------------------------------------- 1 | # Dataset: dm_metabolic 2 | # Description: Crate DM test SDTM dataset for metabolic studies 3 | 4 | # Load libraries ---- 5 | library(dplyr) 6 | library(admiral) 7 | library(purrr) 8 | 9 | # Import DM data from `pharmaversesdtm` ---- 10 | dm <- pharmaversesdtm::dm 11 | 12 | # Subset to first 5 subjects ---- 13 | dm_subset <- dm %>% 14 | filter(USUBJID %in% c( 15 | "01-701-1015", "01-701-1023", "01-701-1028", 16 | "01-701-1033", "01-701-1034" 17 | )) 18 | 19 | # Change treatment arms ---- 20 | dm_metabolic <- dm_subset %>% 21 | mutate( 22 | ARMCD = case_when( 23 | ARMCD == "Pbo" ~ "Pbo", 24 | ARMCD %in% c("Xan_Hi", "Xan_Lo") ~ "Ins" 25 | ), 26 | ARM = case_when( 27 | ARM == "Placebo" ~ "Placebo", 28 | ARM %in% c( 29 | "Xanomeline High Dose", 30 | "Xanomeline Low Dose" 31 | ) ~ "Insulin" 32 | ), 33 | ACTARMCD = ARMCD, 34 | ACTARM = ARM 35 | ) 36 | 37 | # Restore attributes ---- 38 | common_cols <- intersect(names(dm_metabolic), names(dm)) 39 | walk( 40 | .x = common_cols, 41 | .f = \(x) attr(dm_metabolic[[x]], "label") <<- attr(dm[[x]], "label") 42 | ) 43 | 44 | # Save data inside data folder---- 45 | usethis::use_data(dm_metabolic, overwrite = TRUE) 46 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/06_general_issue.yml: -------------------------------------------------------------------------------- 1 | name: General Issue 2 | description: Issue that is difficult to fit into bug, feature or documentation issue. 3 | title: "General Issue: " 4 | labels: ["general issue"] 5 | assignees: 6 | - octocat 7 | body: 8 | - type: markdown 9 | attributes: 10 | value: | 11 | **Example:** General Issue: Linked In Blog Post for updates on the latest admiral release? 12 | - type: textarea 13 | id: background 14 | attributes: 15 | label: Background Information 16 | description: Please provide the context and purpose of this piece of work. Links and screenshots are encouraged. 17 | placeholder: "Example: Use changelog/news.md file to gather relevant changes and create into a nice post for Linked In. The more information the better and the faster we can get this issue completed." 18 | validations: 19 | required: true 20 | - type: textarea 21 | id: done 22 | attributes: 23 | label: Definition of Done 24 | description: Please define the deliverable or the desired outcome. 25 | placeholder: "Example: All changes since last release are highlighted in Blog Post and posted to Linked In" 26 | validations: 27 | required: false 28 | -------------------------------------------------------------------------------- /data-raw/ae_ophtha.R: -------------------------------------------------------------------------------- 1 | # Dataset: ae_ophtha 2 | # Description: Add ophtha-specific AELAT variable to existing AE dataset 3 | 4 | # Load libraries ----- 5 | library(dplyr) 6 | library(admiral) 7 | library(metatools) 8 | library(haven) 9 | 10 | # Create ae_ophtha ---- 11 | # Start from standard AE dataset from this package - this should be 12 | # in the environment already if devtools::load_all() has been run 13 | ae_ophtha <- ae 14 | 15 | ## Create possible AELAT values - as collected on CRF ---- 16 | lat <- c("LEFT", "RIGHT", "BOTH") 17 | 18 | ## Create AELAT, AELOC variable ---- 19 | # Use random assignment of lat values where AESOC is "EYE DISORDERS" 20 | # Set seed so that result stays the same for each run 21 | set.seed(1) 22 | 23 | ae_ophtha$AELAT <- if_else(ae_ophtha$AESOC == "EYE DISORDERS", 24 | apply(ae_ophtha, 1, function(x) sample(lat, 1)), 25 | NA_character_ 26 | ) 27 | 28 | ae_ophtha <- ae_ophtha %>% 29 | mutate(AELOC = if_else(AESOC == "EYE DISORDERS", "EYE", NA_character_)) 30 | 31 | ae_ophtha <- ae_ophtha %>% 32 | add_labels(AELAT = "Laterality") %>% 33 | add_labels(AELOC = "Location") 34 | 35 | # Label dataset ---- 36 | attr(ae_ophtha, "label") <- "Adverse Events" 37 | 38 | # Save dataset ---- 39 | usethis::use_data(ae_ophtha, overwrite = TRUE) 40 | -------------------------------------------------------------------------------- /man/ds.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ds.R 3 | \docType{data} 4 | \name{ds} 5 | \alias{ds} 6 | \title{Disposition} 7 | \format{ 8 | A data frame with 13 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{DSSEQ}{Sequence Number} 14 | \item{DSSPID}{Sponsor-Defined Identifier} 15 | \item{DSTERM}{Reported Term for the Disposition Event} 16 | \item{DSDECOD}{Standardized Disposition Term} 17 | \item{DSCAT}{Category for Disposition Event} 18 | \item{VISITNUM}{Visit Number} 19 | \item{VISIT}{Visit Name} 20 | \item{DSDTC}{Date/Time of Collection} 21 | \item{DSSTDTC}{Start Date/Time of Disposition Event} 22 | \item{DSSTDY}{Study Day of Start of Disposition Event} 23 | } 24 | } 25 | \source{ 26 | \href{https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/ds.rda}{Access the source of the Disposition dataset.} 27 | } 28 | \usage{ 29 | ds 30 | } 31 | \description{ 32 | An updated SDTM DS dataset that uses the CDISC pilot project 33 | } 34 | \details{ 35 | Disposition 36 | 37 | An updated SDTM DS dataset that uses the CDISC pilot project 38 | } 39 | \author{ 40 | Gopi Vegesna 41 | } 42 | \keyword{dataset} 43 | \keyword{generic} 44 | -------------------------------------------------------------------------------- /R/suppds.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Disposition 5 | #' 6 | #' A SDTM SUPPDS dataset from the CDISC pilot project 7 | #' 8 | #' @name suppds 9 | #' @title Supplemental Disposition 10 | #' @keywords dataset generic 11 | #' @description A SDTM SUPPDS dataset from the CDISC pilot project 12 | #' @docType data 13 | #' @format A data frame with 9 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{RDOMAIN}{Related Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QLABEL}{Qualifier Variable Label} 22 | #' \item{QVAL}{Data Value} 23 | #' \item{QORIG}{Origin} 24 | #' } 25 | #' 26 | #' @source [Access the source of the Supplemental Disposition dataset.](https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppdm.xpt?raw=true) 27 | "suppds" 28 | -------------------------------------------------------------------------------- /man/supprs_onco_ca125.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/supprs_onco_ca125.R 3 | \docType{data} 4 | \name{supprs_onco_ca125} 5 | \alias{supprs_onco_ca125} 6 | \title{Supplemental Qualifiers for RS_ONCO_CA125} 7 | \format{ 8 | A data frame with 9 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{RDOMAIN}{Related Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QLABEL}{Qualifier Variable Label} 17 | \item{QVAL}{Data Value} 18 | \item{QORIG}{Origin} 19 | } 20 | } 21 | \source{ 22 | Generated dataset (\href{https://github.com/pharmaverse/pharmaversesdtm/blob/main/data-raw/rs_supprs_onco_ca125.R}{rs_supprs_onco_ca125.R}) 23 | } 24 | \usage{ 25 | supprs_onco_ca125 26 | } 27 | \description{ 28 | A SDTM supplemental RS dataset using GCIG criteria. It is intended to be used together with \code{rs_onco_ca125}. 29 | } 30 | \details{ 31 | Supplemental Qualifiers for RS_ONCO_CA125 32 | 33 | A SDTM supplemental RS dataset using GCIG criteria. It is intended to be used together with \code{rs_onco_ca125}. 34 | } 35 | \author{ 36 | Vinh Nguyen 37 | } 38 | \keyword{dataset} 39 | \keyword{oncology} 40 | -------------------------------------------------------------------------------- /R/suppnv_neuro.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental for Neurological Assessment Dataset-neuro 5 | #' 6 | #' A SDTM SUPPNV dataset containing additional information about neurological assessments or test results 7 | #' 8 | #' @name suppnv_neuro 9 | #' @title Supplemental for Neurological Assessment Dataset-neuro 10 | #' @keywords dataset neurology 11 | #' @description A SDTM SUPPNV dataset containing additional information about neurological assessments or test results 12 | #' @docType data 13 | #' @format A data frame with 10 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{RDOMAIN}{Related Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QLABEL}{Qualifier Variable Label} 22 | #' \item{QVAL}{Data Value} 23 | #' \item{QORIG}{Origin} 24 | #' \item{QEVAL}{Evaluator} 25 | #' } 26 | #' 27 | #' @source Constructed by {admiralneuro} developers 28 | "suppnv_neuro" 29 | -------------------------------------------------------------------------------- /man/ex_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ex_vaccine.R 3 | \docType{data} 4 | \name{ex_vaccine} 5 | \alias{ex_vaccine} 6 | \title{Exposures for Vaccine} 7 | \format{ 8 | A data frame with 19 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{EXSEQ}{Sequence Number} 14 | \item{EXLNKGRP}{Link Group ID} 15 | \item{EXLNKID}{Link ID} 16 | \item{EXTRT}{Name of Actual Treatment} 17 | \item{EXCAT}{Category of Treatment} 18 | \item{EXDOSE}{Dose per Administration} 19 | \item{EXDOSU}{Dose Units} 20 | \item{EXDOSFRM}{Dose Form} 21 | \item{EXROUTE}{Route of Administration} 22 | \item{EXLOC}{Location of Dose Administration} 23 | \item{EXLAT}{Laterality} 24 | \item{VISITNUM}{Visit Number} 25 | \item{VISIT}{Visit Name} 26 | \item{EPOCH}{Epoch} 27 | \item{EXSTDTC}{Start Date/Time of Treatment} 28 | \item{EXENDTC}{End Date/Time of Treatment} 29 | } 30 | } 31 | \source{ 32 | Constructed by {admiralvaccine} developers 33 | } 34 | \usage{ 35 | ex_vaccine 36 | } 37 | \description{ 38 | An example SDTM EX dataset for vaccine studies 39 | } 40 | \details{ 41 | Exposures for Vaccine 42 | 43 | An example SDTM EX dataset for vaccine studies 44 | } 45 | \keyword{dataset} 46 | \keyword{vaccine} 47 | -------------------------------------------------------------------------------- /R/suppae.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Adverse Events 5 | #' 6 | #' A SDTM SUPPAE dataset from the CDISC pilot project 7 | #' 8 | #' @name suppae 9 | #' @title Supplemental Adverse Events 10 | #' @keywords dataset generic 11 | #' @description A SDTM SUPPAE dataset from the CDISC pilot project 12 | #' @docType data 13 | #' @format A data frame with 10 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{RDOMAIN}{Related Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QLABEL}{Qualifier Variable Label} 22 | #' \item{QVAL}{Data Value} 23 | #' \item{QORIG}{Origin} 24 | #' \item{QEVAL}{Evaluator} 25 | #' } 26 | #' 27 | #' @source [Access the source of the Supplemental Adverse Events dataset.](https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true) 28 | "suppae" 29 | -------------------------------------------------------------------------------- /R/ag_neuro.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Procedure Agents Dataset-neuro 5 | #' 6 | #' A SDTM AG dataset recording details of agents such as a PET tracer used in procedures 7 | #' 8 | #' @name ag_neuro 9 | #' @title Procedure Agents Dataset-neuro 10 | #' @keywords dataset neurology 11 | #' @description A SDTM AG dataset recording details of agents such as a PET tracer used in procedures 12 | #' @docType data 13 | #' @format A data frame with 13 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{AGSEQ}{Sequence Number} 19 | #' \item{AGTRT}{Reported Agent Name} 20 | #' \item{AGCAT}{Category for Agent} 21 | #' \item{AGDOSE}{Dose per Administration} 22 | #' \item{AGDOSEU}{Dose Units} 23 | #' \item{AGROUTE}{Route of Administration} 24 | #' \item{AGLNKID}{Link ID} 25 | #' \item{VISITNUM}{Visit Number} 26 | #' \item{VISIT}{Visit Name} 27 | #' \item{AGSTDTC}{Start Date/Time of Agent} 28 | #' } 29 | #' 30 | #' @source Constructed by {admiralneuro} developers 31 | "ag_neuro" 32 | -------------------------------------------------------------------------------- /R/supptr_onco.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Tumor Results for Oncology 5 | #' 6 | #' A SDTM SUPPTR dataset simulated by Gopi Vegesna 7 | #' 8 | #' @name supptr_onco 9 | #' @title Supplemental Tumor Results for Oncology 10 | #' @keywords dataset oncology 11 | #' @description A SDTM SUPPTR dataset simulated by Gopi Vegesna 12 | #' @docType data 13 | #' @format A data frame with 9 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{RDOMAIN}{Related Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QLABEL}{Qualifier Variable Label} 22 | #' \item{QVAL}{Data Value} 23 | #' \item{QORIG}{Origin} 24 | #' } 25 | #' 26 | #' @source [Access the source of the Supplemental Tumor Results for Oncology dataset.](https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ts.xpt?raw=true) 27 | #' @author Gopi Vegesna 28 | "supptr_onco" 29 | -------------------------------------------------------------------------------- /man/supprs_onco_imwg.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/supprs_onco_imwg.R 3 | \docType{data} 4 | \name{supprs_onco_imwg} 5 | \alias{supprs_onco_imwg} 6 | \title{Supplemental Qualifiers for RS_ONCO_IMWG} 7 | \format{ 8 | A data frame with 9 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{RDOMAIN}{Related Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{IDVAR}{Identifying Variable} 14 | \item{IDVARVAL}{Identifying Variable Value} 15 | \item{QNAM}{Qualifier Variable Name} 16 | \item{QLABEL}{Qualifier Variable Label} 17 | \item{QVAL}{Data Value} 18 | \item{QORIG}{Origin} 19 | } 20 | } 21 | \source{ 22 | \href{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true}{Access the source of the Supplemental Qualifiers for RS_ONCO_IMWG dataset.} 23 | } 24 | \usage{ 25 | supprs_onco_imwg 26 | } 27 | \description{ 28 | A SDTM supplemental RS dataset using IMWG criteria intended to be used with \code{rs_onco_imwg} 29 | } 30 | \details{ 31 | Supplemental Qualifiers for RS_ONCO_IMWG 32 | 33 | A SDTM supplemental RS dataset using IMWG criteria intended to be used with \code{rs_onco_imwg} 34 | } 35 | \author{ 36 | Vinh Nguyen 37 | } 38 | \keyword{dataset} 39 | \keyword{oncology} 40 | -------------------------------------------------------------------------------- /man/sc_ophtha.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/sc_ophtha.R 3 | \docType{data} 4 | \name{sc_ophtha} 5 | \alias{sc_ophtha} 6 | \title{Subject Characteristic for Ophthalmology} 7 | \format{ 8 | A data frame with 12 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{SCSEQ}{Sequence Number} 14 | \item{SCTESTCD}{Subject Characteristic Short Name} 15 | \item{SCTEST}{Subject Characteristic} 16 | \item{SCCAT}{Category for Subject Characteristic} 17 | \item{SCORRES}{Result or Finding in Original Units} 18 | \item{SCSTRESC}{Character Result/Finding in Std Format} 19 | \item{EPOCH}{Epoch} 20 | \item{SCDTC}{Date/Time of Collection} 21 | \item{SCDY}{Study Day of Examination} 22 | } 23 | } 24 | \source{ 25 | Generated dataset. 26 | } 27 | \usage{ 28 | sc_ophtha 29 | } 30 | \description{ 31 | A SDTM SC dataset simulated by Ophthalmology team 32 | } 33 | \details{ 34 | Subject Characteristic for Ophthalmology 35 | 36 | A SDTM SC dataset simulated by Ophthalmology team 37 | 38 | Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 39 | \strong{SCTESTCD} \tab \strong{SCTEST} \cr 40 | FOCID \tab Focus of Study-Specific Interest 41 | } 42 | } 43 | \author{ 44 | Gordon Miller 45 | } 46 | \keyword{dataset} 47 | \keyword{ophthalmology} 48 | -------------------------------------------------------------------------------- /R/supprs_onco_ca125.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Qualifiers for RS_ONCO_CA125 5 | #' 6 | #' A SDTM supplemental RS dataset using GCIG criteria. It is intended to be used together with `rs_onco_ca125`. 7 | #' 8 | #' @name supprs_onco_ca125 9 | #' @title Supplemental Qualifiers for RS_ONCO_CA125 10 | #' @keywords dataset oncology 11 | #' @description A SDTM supplemental RS dataset using GCIG criteria. It is intended to be used together with `rs_onco_ca125`. 12 | #' @docType data 13 | #' @format A data frame with 9 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{RDOMAIN}{Related Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QLABEL}{Qualifier Variable Label} 22 | #' \item{QVAL}{Data Value} 23 | #' \item{QORIG}{Origin} 24 | #' } 25 | #' 26 | #' @source Generated dataset ([rs_supprs_onco_ca125.R](https://github.com/pharmaverse/pharmaversesdtm/blob/main/data-raw/rs_supprs_onco_ca125.R)) 27 | #' @author Vinh Nguyen 28 | "supprs_onco_ca125" 29 | -------------------------------------------------------------------------------- /man/ex.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ex.R 3 | \docType{data} 4 | \name{ex} 5 | \alias{ex} 6 | \title{Exposure} 7 | \format{ 8 | A data frame with 17 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{EXSEQ}{Sequence Number} 14 | \item{EXTRT}{Name of Actual Treatment} 15 | \item{EXDOSE}{Dose per Administration} 16 | \item{EXDOSU}{Dose Units} 17 | \item{EXDOSFRM}{Dose Form} 18 | \item{EXDOSFRQ}{Dosing Frequency per Interval} 19 | \item{EXROUTE}{Route of Administration} 20 | \item{VISITNUM}{Visit Number} 21 | \item{VISIT}{Visit Name} 22 | \item{VISITDY}{Planned Study Day of Visit} 23 | \item{EXSTDTC}{Start Date/Time of Treatment} 24 | \item{EXENDTC}{End Date/Time of Treatment} 25 | \item{EXSTDY}{Study Day of Start of Treatment} 26 | \item{EXENDY}{Study Day of End of Treatment} 27 | } 28 | } 29 | \source{ 30 | \href{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}{Access the source of the Exposure dataset.} 31 | } 32 | \usage{ 33 | ex 34 | } 35 | \description{ 36 | A SDTM EX dataset from the CDISC pilot project 37 | } 38 | \details{ 39 | Exposure 40 | 41 | A SDTM EX dataset from the CDISC pilot project 42 | } 43 | \keyword{dataset} 44 | \keyword{generic} 45 | -------------------------------------------------------------------------------- /R/ds.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Disposition 5 | #' 6 | #' An updated SDTM DS dataset that uses the CDISC pilot project 7 | #' 8 | #' @name ds 9 | #' @title Disposition 10 | #' @keywords dataset generic 11 | #' @description An updated SDTM DS dataset that uses the CDISC pilot project 12 | #' @docType data 13 | #' @format A data frame with 13 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{DSSEQ}{Sequence Number} 19 | #' \item{DSSPID}{Sponsor-Defined Identifier} 20 | #' \item{DSTERM}{Reported Term for the Disposition Event} 21 | #' \item{DSDECOD}{Standardized Disposition Term} 22 | #' \item{DSCAT}{Category for Disposition Event} 23 | #' \item{VISITNUM}{Visit Number} 24 | #' \item{VISIT}{Visit Name} 25 | #' \item{DSDTC}{Date/Time of Collection} 26 | #' \item{DSSTDTC}{Start Date/Time of Disposition Event} 27 | #' \item{DSSTDY}{Study Day of Start of Disposition Event} 28 | #' } 29 | #' 30 | #' @source [Access the source of the Disposition dataset.](https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/ds.rda) 31 | #' @author Gopi Vegesna 32 | "ds" 33 | -------------------------------------------------------------------------------- /R/supprs_onco_imwg.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Supplemental Qualifiers for RS_ONCO_IMWG 5 | #' 6 | #' A SDTM supplemental RS dataset using IMWG criteria intended to be used with `rs_onco_imwg` 7 | #' 8 | #' @name supprs_onco_imwg 9 | #' @title Supplemental Qualifiers for RS_ONCO_IMWG 10 | #' @keywords dataset oncology 11 | #' @description A SDTM supplemental RS dataset using IMWG criteria intended to be used with `rs_onco_imwg` 12 | #' @docType data 13 | #' @format A data frame with 9 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{RDOMAIN}{Related Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{IDVAR}{Identifying Variable} 19 | #' \item{IDVARVAL}{Identifying Variable Value} 20 | #' \item{QNAM}{Qualifier Variable Name} 21 | #' \item{QLABEL}{Qualifier Variable Label} 22 | #' \item{QVAL}{Data Value} 23 | #' \item{QORIG}{Origin} 24 | #' } 25 | #' 26 | #' @source [Access the source of the Supplemental Qualifiers for RS_ONCO_IMWG dataset.](https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true) 27 | #' @author Vinh Nguyen 28 | "supprs_onco_imwg" 29 | -------------------------------------------------------------------------------- /man/rs_onco_recist.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rs_onco_recist.R 3 | \docType{data} 4 | \name{rs_onco_recist} 5 | \alias{rs_onco_recist} 6 | \title{Disease Response (RECIST 1.1) for Oncology} 7 | \format{ 8 | A data frame with 14 columns: 9 | \describe{ 10 | \item{DOMAIN}{Domain Abbreviation} 11 | \item{STUDYID}{Study Identifier} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{VISITNUM}{Visit Number} 14 | \item{VISIT}{Visit Name} 15 | \item{RSTESTCD}{Assessment Short Name} 16 | \item{RSTEST}{Assessment Name} 17 | \item{RSORRES}{Result or Finding in Original Units} 18 | \item{RSSTRESC}{Character Result/Finding in Std Format} 19 | \item{RSEVAL}{Evaluator} 20 | \item{RSEVALID}{Evaluator Identifier} 21 | \item{RSACPTFL}{Accepted Record Flag} 22 | \item{RSDTC}{Date/Time of Assessment} 23 | \item{RSSEQ}{Sequence Number} 24 | } 25 | } 26 | \source{ 27 | Generated dataset. 28 | } 29 | \usage{ 30 | rs_onco_recist 31 | } 32 | \description{ 33 | A SDTM RS dataset using RECIST 1.1 intended for examples of ADaM dataset creation 34 | } 35 | \details{ 36 | Disease Response (RECIST 1.1) for Oncology 37 | 38 | A SDTM RS dataset using RECIST 1.1 intended for examples of ADaM dataset creation 39 | 40 | Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 41 | \strong{RSTESTCD} \tab \strong{RSTEST} \cr 42 | OVRLRESP \tab Overall Response 43 | } 44 | } 45 | \author{ 46 | Stefan Bundfuss 47 | } 48 | \keyword{dataset} 49 | \keyword{oncology} 50 | -------------------------------------------------------------------------------- /data-raw/dm_peds.R: -------------------------------------------------------------------------------- 1 | # Dataset: dm_peds 2 | # Description: Create DM test SDTM dataset for pediatric studies 3 | 4 | # Load libraries ----- 5 | library(dplyr) 6 | library(admiral) 7 | 8 | # Read input test data from pharmaversesdtm ---- 9 | dm <- pharmaversesdtm::dm 10 | 11 | # Convert blank to NA ---- 12 | dm <- convert_blanks_to_na(dm) 13 | 14 | # Subset to first 5 patients only (which is enough for our examples) ---- 15 | dm_subset <- dm %>% 16 | filter(USUBJID %in% c( 17 | "01-701-1015", "01-701-1023", "01-701-1028", 18 | "01-701-1033", "01-701-1034" 19 | )) 20 | 21 | # Add birth dates/age realistic for pediatrics in line with treatment dates ---- 22 | dm_peds <- dm_subset %>% 23 | mutate(BRTHDTC = case_when( 24 | USUBJID == "01-701-1015" ~ "2013-01-02", 25 | USUBJID == "01-701-1023" ~ "2010-08-05", 26 | USUBJID == "01-701-1028" ~ "2010-07-19", 27 | USUBJID == "01-701-1033" ~ "2014-01-01", 28 | USUBJID == "01-701-1034" ~ "2014-06-01" 29 | )) %>% 30 | mutate(AGE = case_when( 31 | USUBJID == "01-701-1015" ~ 1, 32 | USUBJID == "01-701-1023" ~ 2, 33 | USUBJID == "01-701-1028" ~ 3, 34 | USUBJID == "01-701-1033" ~ 0, 35 | USUBJID == "01-701-1034" ~ 0 36 | )) 37 | 38 | # Variable labels ---- 39 | attr(dm_peds$BRTHDTC, "label") <- "Date/Time of Birth" 40 | attr(dm_peds$AGE, "label") <- "Age" 41 | 42 | # Label dataset ---- 43 | attr(dm_peds, "label") <- "Demographics" 44 | 45 | # Save dataset ---- 46 | usethis::use_data(dm_peds, overwrite = TRUE) 47 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/01_bug_report.yml: -------------------------------------------------------------------------------- 1 | name: Bug Report 2 | description: Something is not working correctly or is not working at all! 3 | title: "Bug: " 4 | labels: ["bug", "programming"] 5 | assignees: 6 | - octocat 7 | body: 8 | - type: markdown 9 | attributes: 10 | value: | 11 | **Example:** Bug: derive_vars_dtm() is returning NA values when using preserve argument 12 | - type: textarea 13 | id: what-happened 14 | attributes: 15 | label: What happened? 16 | description: Also tell us what were you expecting to happen before the bug? 17 | placeholder: "A bug happened!" 18 | validations: 19 | required: true 20 | - type: textarea 21 | id: session-info 22 | attributes: 23 | label: Session Information 24 | description: Use `sessionInfo()` in the R console to gather all the details of your environment when the bug happened. 25 | placeholder: "Place the console output here" 26 | validations: 27 | required: false 28 | - type: textarea 29 | id: logs 30 | attributes: 31 | label: Reproducible Example 32 | description: We love code that can reproduce the example. Check out [reprex](https://reprex.tidyverse.org/articles/reprex-dos-and-donts.html) 33 | placeholder: "Please give us as many details as you can! The faster we can recreate the bug, the faster we can get a fix in the works. Warning, Error Messages and Screenshots are also great." 34 | validations: 35 | required: false 36 | -------------------------------------------------------------------------------- /R/ex_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Exposures for Vaccine 5 | #' 6 | #' An example SDTM EX dataset for vaccine studies 7 | #' 8 | #' @name ex_vaccine 9 | #' @title Exposures for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM EX dataset for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 19 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{EXSEQ}{Sequence Number} 19 | #' \item{EXLNKGRP}{Link Group ID} 20 | #' \item{EXLNKID}{Link ID} 21 | #' \item{EXTRT}{Name of Actual Treatment} 22 | #' \item{EXCAT}{Category of Treatment} 23 | #' \item{EXDOSE}{Dose per Administration} 24 | #' \item{EXDOSU}{Dose Units} 25 | #' \item{EXDOSFRM}{Dose Form} 26 | #' \item{EXROUTE}{Route of Administration} 27 | #' \item{EXLOC}{Location of Dose Administration} 28 | #' \item{EXLAT}{Laterality} 29 | #' \item{VISITNUM}{Visit Number} 30 | #' \item{VISIT}{Visit Name} 31 | #' \item{EPOCH}{Epoch} 32 | #' \item{EXSTDTC}{Start Date/Time of Treatment} 33 | #' \item{EXENDTC}{End Date/Time of Treatment} 34 | #' } 35 | #' 36 | #' @source Constructed by {admiralvaccine} developers 37 | "ex_vaccine" 38 | -------------------------------------------------------------------------------- /man/ex_ophtha.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ex_ophtha.R 3 | \docType{data} 4 | \name{ex_ophtha} 5 | \alias{ex_ophtha} 6 | \title{Exposure for Ophthalmology} 7 | \format{ 8 | A data frame with 19 columns: 9 | \describe{ 10 | \item{USUBJID}{Unique Subject Identifier} 11 | \item{STUDYID}{Study Identifier} 12 | \item{DOMAIN}{Domain Abbreviation} 13 | \item{EXSEQ}{Sequence Number} 14 | \item{EXTRT}{Name of Actual Treatment} 15 | \item{EXDOSE}{Dose per Administration} 16 | \item{EXDOSU}{Dose Units} 17 | \item{EXDOSFRM}{Dose Form} 18 | \item{EXDOSFRQ}{Dose Frequency per Interval} 19 | \item{EXROUTE}{Route of Administration} 20 | \item{EXLOC}{Location of Dose Administration} 21 | \item{EXLAT}{Laterality} 22 | \item{VISITNUM}{Visit Number} 23 | \item{VISIT}{Visit Name} 24 | \item{VISITDY}{Planned Study Day of Visit} 25 | \item{EXSTDTC}{Start Date/Time of Treatment} 26 | \item{EXENDTC}{End Date/Time of Treatment} 27 | \item{EXSTDY}{Study Day of Start of Treatment} 28 | \item{EXENDY}{Study Day of End of Treatment} 29 | } 30 | } 31 | \source{ 32 | Constructed using ex from the {pharmaversesdtm} package 33 | } 34 | \usage{ 35 | ex_ophtha 36 | } 37 | \description{ 38 | An example Exposure SDTM dataset with ophthalmology-specific variables such as \code{EXLOC} and \code{EXLAT} 39 | } 40 | \details{ 41 | Exposure for Ophthalmology 42 | 43 | An example Exposure SDTM dataset with ophthalmology-specific variables such as \code{EXLOC} and \code{EXLAT} 44 | } 45 | \keyword{dataset} 46 | \keyword{ophthalmology} 47 | -------------------------------------------------------------------------------- /R/sc_ophtha.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Subject Characteristic for Ophthalmology 5 | #' 6 | #' A SDTM SC dataset simulated by Ophthalmology team 7 | #' 8 | #' @name sc_ophtha 9 | #' @title Subject Characteristic for Ophthalmology 10 | #' @keywords dataset ophthalmology 11 | #' @description A SDTM SC dataset simulated by Ophthalmology team 12 | #' @docType data 13 | #' @format A data frame with 12 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{SCSEQ}{Sequence Number} 19 | #' \item{SCTESTCD}{Subject Characteristic Short Name} 20 | #' \item{SCTEST}{Subject Characteristic} 21 | #' \item{SCCAT}{Category for Subject Characteristic} 22 | #' \item{SCORRES}{Result or Finding in Original Units} 23 | #' \item{SCSTRESC}{Character Result/Finding in Std Format} 24 | #' \item{EPOCH}{Epoch} 25 | #' \item{SCDTC}{Date/Time of Collection} 26 | #' \item{SCDY}{Study Day of Examination} 27 | #' } 28 | #' 29 | #' @source Generated dataset. 30 | #' @author Gordon Miller 31 | #' @details Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 32 | #' \strong{SCTESTCD} \tab \strong{SCTEST} \cr 33 | #' FOCID \tab Focus of Study-Specific Interest 34 | #' } 35 | 36 | "sc_ophtha" 37 | -------------------------------------------------------------------------------- /man/tu_onco.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/tu_onco.R 3 | \docType{data} 4 | \name{tu_onco} 5 | \alias{tu_onco} 6 | \title{Tumor Identification for Oncology} 7 | \format{ 8 | A data frame with 18 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{TUSEQ}{Sequence Number} 14 | \item{TULNKID}{Link ID} 15 | \item{TUTESTCD}{Tumor Identification Short Name} 16 | \item{TUTEST}{Tumor Identification Test Name} 17 | \item{TUORRES}{Tumor Identification Result} 18 | \item{TUSTRESC}{Tumor Identification Result Std. Format} 19 | \item{TULOC}{Location of the Tumor} 20 | \item{TUMETHOD}{Method of Identification} 21 | \item{TUEVAL}{Evaluator} 22 | \item{TUEVALID}{Evaluator Identifier} 23 | \item{TUACPTFL}{Accepted Record Flag} 24 | \item{VISITNUM}{Visit Number} 25 | \item{VISIT}{Visit Name} 26 | \item{TUDTC}{Date/Time of Tumor Identification} 27 | \item{TUDY}{Study Day of Tumor Identification} 28 | } 29 | } 30 | \source{ 31 | Generated dataset. 32 | } 33 | \usage{ 34 | tu_onco 35 | } 36 | \description{ 37 | A SDTM TU dataset simulated by Gopi Vegesna 38 | } 39 | \details{ 40 | Tumor Identification for Oncology 41 | 42 | A SDTM TU dataset simulated by Gopi Vegesna 43 | 44 | Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 45 | \strong{TUTESTCD} \tab \strong{TUTEST} \cr 46 | TUMIDENT \tab Tumor Identification 47 | } 48 | } 49 | \author{ 50 | Gopi Vegesna 51 | } 52 | \keyword{dataset} 53 | \keyword{oncology} 54 | -------------------------------------------------------------------------------- /man/rs_onco_imwg.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rs_onco_imwg.R 3 | \docType{data} 4 | \name{rs_onco_imwg} 5 | \alias{rs_onco_imwg} 6 | \title{Disease Response (IMWG)} 7 | \format{ 8 | A data frame with 17 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{RSSEQ}{Sequence Number} 14 | \item{RSLNKGRP}{Link Group ID} 15 | \item{RSTESTCD}{Assessment Short Name} 16 | \item{RSTEST}{Assessment Name} 17 | \item{RSCAT}{Category for Assessment} 18 | \item{RSORRES}{Result or Finding in Original Units} 19 | \item{RSSTRESC}{Character Result/Finding in Std Format} 20 | \item{RSSTAT}{Completion Status} 21 | \item{RSREASND}{Reason Not Done} 22 | \item{RSEVAL}{Evaluator} 23 | \item{VISITNUM}{Visit Number} 24 | \item{VISIT}{Visit Name} 25 | \item{RSDTC}{Date/Time of Assessment} 26 | \item{RSDY}{Study Day of Assessment} 27 | } 28 | } 29 | \source{ 30 | Derived from tr_onco_recist 31 | } 32 | \usage{ 33 | rs_onco_imwg 34 | } 35 | \description{ 36 | A SDTM RS dataset using IMWG criteria intended for examples of ADaM dataset creation 37 | } 38 | \details{ 39 | Disease Response (IMWG) 40 | 41 | A SDTM RS dataset using IMWG criteria intended for examples of ADaM dataset creation 42 | 43 | Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 44 | \strong{RSTESTCD} \tab \strong{RSTEST} \cr 45 | OVRLRESP \tab Overall Response 46 | } 47 | } 48 | \author{ 49 | Vinh Nguyen 50 | } 51 | \keyword{dataset} 52 | \keyword{oncology} 53 | -------------------------------------------------------------------------------- /man/tu_onco_recist.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/tu_onco_recist.R 3 | \docType{data} 4 | \name{tu_onco_recist} 5 | \alias{tu_onco_recist} 6 | \title{Tumor Identification (RECIST 1.1) for Oncology} 7 | \format{ 8 | A data frame with 16 columns: 9 | \describe{ 10 | \item{DOMAIN}{Domain Abbreviation} 11 | \item{STUDYID}{Study Identifier} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{VISIT}{Visit Name} 14 | \item{VISITNUM}{Visit Number} 15 | \item{TULOC}{Location of the Tumor/Lesion} 16 | \item{TUTESTCD}{Tumor/Lesion ID Short Name} 17 | \item{TUTEST}{Tumor/Lesion ID Test Name} 18 | \item{TUORRES}{Tumor/Lesion ID Result} 19 | \item{TUSTRESC}{Tumor/Lesion ID Result Std. Format} 20 | \item{TUMETHOD}{Method of Identification} 21 | \item{TULNKID}{Link ID} 22 | \item{TUEVAL}{Evaluator} 23 | \item{TUEVALID}{Evaluator Identifier} 24 | \item{TUACPTFL}{Accepted Record Flag} 25 | \item{TUSEQ}{Sequence Number} 26 | } 27 | } 28 | \source{ 29 | Generated dataset. 30 | } 31 | \usage{ 32 | tu_onco_recist 33 | } 34 | \description{ 35 | A SDTM TU dataset using RECIST 1.1 intended for examples of ADaM dataset creation 36 | } 37 | \details{ 38 | Tumor Identification (RECIST 1.1) for Oncology 39 | 40 | A SDTM TU dataset using RECIST 1.1 intended for examples of ADaM dataset creation 41 | 42 | Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 43 | \strong{TUTESTCD} \tab \strong{TUTEST} \cr 44 | TUMIDENT \tab Tumor Identification 45 | } 46 | } 47 | \author{ 48 | Stefan Bundfuss 49 | } 50 | \keyword{dataset} 51 | \keyword{oncology} 52 | -------------------------------------------------------------------------------- /R/ex.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Exposure 5 | #' 6 | #' A SDTM EX dataset from the CDISC pilot project 7 | #' 8 | #' @name ex 9 | #' @title Exposure 10 | #' @keywords dataset generic 11 | #' @description A SDTM EX dataset from the CDISC pilot project 12 | #' @docType data 13 | #' @format A data frame with 17 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{EXSEQ}{Sequence Number} 19 | #' \item{EXTRT}{Name of Actual Treatment} 20 | #' \item{EXDOSE}{Dose per Administration} 21 | #' \item{EXDOSU}{Dose Units} 22 | #' \item{EXDOSFRM}{Dose Form} 23 | #' \item{EXDOSFRQ}{Dosing Frequency per Interval} 24 | #' \item{EXROUTE}{Route of Administration} 25 | #' \item{VISITNUM}{Visit Number} 26 | #' \item{VISIT}{Visit Name} 27 | #' \item{VISITDY}{Planned Study Day of Visit} 28 | #' \item{EXSTDTC}{Start Date/Time of Treatment} 29 | #' \item{EXENDTC}{End Date/Time of Treatment} 30 | #' \item{EXSTDY}{Study Day of Start of Treatment} 31 | #' \item{EXENDY}{Study Day of End of Treatment} 32 | #' } 33 | #' 34 | #' @source [Access the source of the Exposure dataset.](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) 35 | "ex" 36 | -------------------------------------------------------------------------------- /data-raw/ex_ophtha.R: -------------------------------------------------------------------------------- 1 | # Dataset: ex_ophtha 2 | # Description: Add ophtha-specific EXLOC, EXLAT variables to existing EX dataset 3 | # and modify EXROUTE, EXDOSFRM, EXDOSFRQ to something eye-related 4 | 5 | # Load libraries ----- 6 | library(dplyr) 7 | library(tidyselect) 8 | 9 | # Make ex_ophtha dataset 10 | dm <- pharmaversesdtm::dm 11 | ex <- pharmaversesdtm::ex 12 | 13 | ex_ophtha <- dm %>% 14 | ## Merge on ophtha_dm to use the SUBJID variable ---- 15 | select(USUBJID, SUBJID) %>% 16 | right_join(ex, by = c("USUBJID"), multiple = "all") %>% 17 | ## Create EXLOC & EXLAT, change EXROUTE & EXDOSFRM ---- 18 | mutate( 19 | EXLOC = "EYE", 20 | EXDOSFRM = "INJECTION", 21 | EXDOSFRQ = "ONCE", 22 | EXLAT = ifelse(as.integer(SUBJID) %% 2 == 0, "LEFT", "RIGHT"), 23 | EXROUTE = "INTRAVITREAL" 24 | ) %>% 25 | # Drop SUBJID and reorder variables 26 | select( 27 | "USUBJID", "STUDYID", "DOMAIN", "EXSEQ", "EXTRT", "EXDOSE", 28 | "EXDOSU", "EXDOSFRM", "EXDOSFRQ", "EXROUTE", "EXLOC", 29 | "EXLAT", "VISITNUM", "VISIT", "VISITDY", "EXSTDTC", 30 | "EXENDTC", "EXSTDY", "EXENDY" 31 | ) 32 | 33 | ## Label new variables ---- 34 | attr(ex_ophtha$EXLOC, "label") <- "Location of Dose Administration" 35 | attr(ex_ophtha$EXLAT, "label") <- "Laterality" 36 | attr(ex_ophtha$EXROUTE, "label") <- "Route of Administration" 37 | attr(ex_ophtha$EXDOSFRM, "label") <- "Dose Form" 38 | attr(ex_ophtha$EXDOSFRQ, "label") <- "Dose Frequency per Interval" 39 | 40 | # Label dataset ---- 41 | attr(ex_ophtha, "label") <- "Exposure" 42 | 43 | # Save dataset ---- 44 | usethis::use_data(ex_ophtha, overwrite = TRUE) 45 | -------------------------------------------------------------------------------- /man/rs_onco_ca125.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rs_onco_ca125.R 3 | \docType{data} 4 | \name{rs_onco_ca125} 5 | \alias{rs_onco_ca125} 6 | \title{Disease Response (GCIG)} 7 | \format{ 8 | A data frame with 13 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{RSSEQ}{Sequence Number} 14 | \item{RSTESTCD}{Assessment Short Name} 15 | \item{RSTEST}{Assessment Name} 16 | \item{RSCAT}{Category for Assessment} 17 | \item{RSORRES}{Result or Finding in Original Units} 18 | \item{RSSTRESC}{Character Result/Finding in Std Format} 19 | \item{RSEVAL}{Evaluator} 20 | \item{VISITNUM}{Visit Number} 21 | \item{VISIT}{Visit Name} 22 | \item{RSDTC}{Date/Time of Assessment} 23 | } 24 | } 25 | \source{ 26 | Generated dataset (\href{https://github.com/pharmaverse/pharmaversesdtm/blob/main/data-raw/rs_supprs_onco_ca125.R}{rs_supprs_onco_ca125.R}) 27 | } 28 | \usage{ 29 | rs_onco_ca125 30 | } 31 | \description{ 32 | A SDTM RS dataset using GCIG criteria. The dataset contains just a few patients. It is intended for vignettes and examples of ADaM dataset creation. 33 | } 34 | \details{ 35 | Disease Response (GCIG) 36 | 37 | A SDTM RS dataset using GCIG criteria. The dataset contains just a few patients. It is intended for vignettes and examples of ADaM dataset creation. 38 | 39 | Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 40 | \strong{RSTESTCD} \tab \strong{RSTEST} \cr 41 | OVRLRESP \tab Overall Response 42 | } 43 | } 44 | \author{ 45 | Vinh Nguyen 46 | } 47 | \keyword{dataset} 48 | \keyword{oncology} 49 | -------------------------------------------------------------------------------- /man/dm_peds.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/dm_peds.R 3 | \docType{data} 4 | \name{dm_peds} 5 | \alias{dm_peds} 6 | \title{Demographic Dataset-pediatrics} 7 | \format{ 8 | A data frame with 26 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{SUBJID}{Subject Identifier for the Study} 14 | \item{RFSTDTC}{Subject Reference Start Date/Time} 15 | \item{RFENDTC}{Subject Reference End Date/Time} 16 | \item{RFXSTDTC}{Date/Time of First Study Treatment} 17 | \item{RFXENDTC}{Date/Time of Last Study Treatment} 18 | \item{RFICDTC}{Date/Time of Informed Consent} 19 | \item{RFPENDTC}{Date/Time of End of Participation} 20 | \item{DTHDTC}{Date/Time of Death} 21 | \item{DTHFL}{Subject Death Flag} 22 | \item{SITEID}{Study Site Identifier} 23 | \item{AGE}{Age} 24 | \item{AGEU}{Age Units} 25 | \item{SEX}{Sex} 26 | \item{RACE}{Race} 27 | \item{ETHNIC}{Ethnicity} 28 | \item{ARMCD}{Planned Arm Code} 29 | \item{ARM}{Description of Planned Arm} 30 | \item{ACTARMCD}{Actual Arm Code} 31 | \item{ACTARM}{Description of Actual Arm} 32 | \item{COUNTRY}{Country} 33 | \item{DMDTC}{Date/Time of Collection} 34 | \item{DMDY}{Study Day of Collection} 35 | \item{BRTHDTC}{Date/Time of Birth} 36 | } 37 | } 38 | \source{ 39 | Constructed by {admiralpeds} developers 40 | } 41 | \usage{ 42 | dm_peds 43 | } 44 | \description{ 45 | An updated SDTM DM dataset with pediatric patients 46 | } 47 | \details{ 48 | Demographic Dataset-pediatrics 49 | 50 | An updated SDTM DM dataset with pediatric patients 51 | } 52 | \keyword{dataset} 53 | \keyword{pediatrics} 54 | -------------------------------------------------------------------------------- /man/dm_metabolic.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/dm_metabolic.R 3 | \docType{data} 4 | \name{dm_metabolic} 5 | \alias{dm_metabolic} 6 | \title{Demographic Dataset-metabolic} 7 | \format{ 8 | A data frame with 26 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{SUBJID}{Subject Identifier for the Study} 14 | \item{RFSTDTC}{Subject Reference Start Date/Time} 15 | \item{RFENDTC}{Subject Reference End Date/Time} 16 | \item{RFXSTDTC}{Date/Time of First Study Treatment} 17 | \item{RFXENDTC}{Date/Time of Last Study Treatment} 18 | \item{RFICDTC}{Date/Time of Informed Consent} 19 | \item{RFPENDTC}{Date/Time of End of Participation} 20 | \item{DTHDTC}{Date/Time of Death} 21 | \item{DTHFL}{Subject Death Flag} 22 | \item{SITEID}{Study Site Identifier} 23 | \item{BRTHDTC}{Date/Time of Birth} 24 | \item{AGE}{Age} 25 | \item{AGEU}{Age Units} 26 | \item{SEX}{Sex} 27 | \item{RACE}{Race} 28 | \item{ETHNIC}{Ethnicity} 29 | \item{ARMCD}{Planned Arm Code} 30 | \item{ARM}{Description of Planned Arm} 31 | \item{ACTARMCD}{Actual Arm Code} 32 | \item{ACTARM}{Description of Actual Arm} 33 | \item{COUNTRY}{Country} 34 | \item{DMDTC}{Date/Time of Collection} 35 | \item{DMDY}{Study Day of Collection} 36 | } 37 | } 38 | \source{ 39 | Constructed by {admiralmetabolic} developers 40 | } 41 | \usage{ 42 | dm_metabolic 43 | } 44 | \description{ 45 | A SDTM DM dataset for metabolic studies 46 | } 47 | \details{ 48 | Demographic Dataset-metabolic 49 | 50 | A SDTM DM dataset for metabolic studies 51 | } 52 | \keyword{dataset} 53 | \keyword{metabolic} 54 | -------------------------------------------------------------------------------- /R/rs_onco_recist.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Disease Response (RECIST 1.1) for Oncology 5 | #' 6 | #' A SDTM RS dataset using RECIST 1.1 intended for examples of ADaM dataset creation 7 | #' 8 | #' @name rs_onco_recist 9 | #' @title Disease Response (RECIST 1.1) for Oncology 10 | #' @keywords dataset oncology 11 | #' @description A SDTM RS dataset using RECIST 1.1 intended for examples of ADaM dataset creation 12 | #' @docType data 13 | #' @format A data frame with 14 columns: 14 | #' \describe{ 15 | #' \item{DOMAIN}{Domain Abbreviation} 16 | #' \item{STUDYID}{Study Identifier} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{VISITNUM}{Visit Number} 19 | #' \item{VISIT}{Visit Name} 20 | #' \item{RSTESTCD}{Assessment Short Name} 21 | #' \item{RSTEST}{Assessment Name} 22 | #' \item{RSORRES}{Result or Finding in Original Units} 23 | #' \item{RSSTRESC}{Character Result/Finding in Std Format} 24 | #' \item{RSEVAL}{Evaluator} 25 | #' \item{RSEVALID}{Evaluator Identifier} 26 | #' \item{RSACPTFL}{Accepted Record Flag} 27 | #' \item{RSDTC}{Date/Time of Assessment} 28 | #' \item{RSSEQ}{Sequence Number} 29 | #' } 30 | #' 31 | #' @source Generated dataset. 32 | #' @author Stefan Bundfuss 33 | #' @details Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 34 | #' \strong{RSTESTCD} \tab \strong{RSTEST} \cr 35 | #' OVRLRESP \tab Overall Response 36 | #' } 37 | 38 | "rs_onco_recist" 39 | -------------------------------------------------------------------------------- /data-raw/suppnv_neuro.R: -------------------------------------------------------------------------------- 1 | # Dataset: suppnv_neuro 2 | # Description: Create SUPPNV test SDTM dataset for Alzheimer's Disease (neuro studies) 3 | 4 | # Load libraries ---- 5 | library(admiral) 6 | library(dplyr) 7 | 8 | # Read input data ---- 9 | nv_neuro <- pharmaversesdtm::nv_neuro 10 | 11 | # Convert blank to NA ---- 12 | nv_neuro <- convert_blanks_to_na(nv_neuro) 13 | 14 | suppnv_neuro <- nv_neuro %>% 15 | filter(!is.na(NVLOC)) %>% 16 | mutate( 17 | RDOMAIN = "NV", IDVAR = "NVSEQ", IDVARVAL = NVSEQ, QNAM = "REFREG", 18 | QLABEL = "Reference Region" 19 | ) %>% 20 | mutate(QVAL = case_when( 21 | NVCAT %in% c("FBP", "FBB") ~ "Whole Cerebellum", 22 | NVCAT == "FTP" ~ "Inferior Cerebellar Gray Matter", 23 | TRUE ~ NA_character_ 24 | )) %>% 25 | mutate(QORIG = "Assigned", QEVAL = "STATISTICIAN") %>% 26 | select(STUDYID, RDOMAIN, USUBJID, IDVAR, IDVARVAL, QNAM, QLABEL, QVAL, QORIG, QEVAL) 27 | 28 | # Add labels to variables ---- 29 | labels <- list( 30 | STUDYID = "Study Identifier", 31 | RDOMAIN = "Related Domain Abbreviation", 32 | USUBJID = "Unique Subject Identifier", 33 | IDVAR = "Identifying Variable", 34 | IDVARVAL = "Identifying Variable Value", 35 | QNAM = "Qualifier Variable Name", 36 | QLABEL = "Qualifier Variable Label", 37 | QVAL = "Data Value", 38 | QORIG = "Origin", 39 | QEVAL = "Evaluator" 40 | ) 41 | 42 | for (var in names(labels)) { 43 | attr(suppnv_neuro[[var]], "label") <- labels[[var]] 44 | } 45 | 46 | # Label SUPPNV dataset ---- 47 | attr(suppnv_neuro, "label") <- "Supplemental Qualifiers for Nervous System Findings" 48 | 49 | # Save dataset ---- 50 | usethis::use_data(suppnv_neuro, overwrite = TRUE) 51 | -------------------------------------------------------------------------------- /man/cm.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/cm.R 3 | \docType{data} 4 | \name{cm} 5 | \alias{cm} 6 | \title{Concomitant Medication} 7 | \format{ 8 | A data frame with 22 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{CMSEQ}{Sequence Number} 14 | \item{CMSPID}{Sponsor-Defined Identifier} 15 | \item{CMTRT}{Reported Name of Drug, Med, or Therapy} 16 | \item{CMDECOD}{Standardized Medication Name} 17 | \item{CMINDC}{Indication} 18 | \item{CMCLAS}{Medication Class} 19 | \item{CMDOSE}{Dose per Administration} 20 | \item{CMDOSU}{Dose Units} 21 | \item{CMDOSFRQ}{Dosing Frequency per Interval} 22 | \item{CMROUTE}{Route of Administration} 23 | \item{VISITNUM}{Visit Number} 24 | \item{VISIT}{Visit Name} 25 | \item{VISITDY}{Planned Study Day of Visit} 26 | \item{CMDTC}{Date/Time of Collection} 27 | \item{CMSTDTC}{Start Date/Time of Medication} 28 | \item{CMENDTC}{End Date/Time of Medication} 29 | \item{CMSTDY}{Study Day of Start of Medication} 30 | \item{CMENDY}{Study Day of End of Medication} 31 | \item{CMENRTPT}{End Relative to Reference Time Point} 32 | } 33 | } 34 | \source{ 35 | \href{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}{Access the source of the Concomitant Medication dataset.} 36 | } 37 | \usage{ 38 | cm 39 | } 40 | \description{ 41 | A SDTM CM dataset from the CDISC pilot project 42 | } 43 | \details{ 44 | Concomitant Medication 45 | 46 | A SDTM CM dataset from the CDISC pilot project 47 | } 48 | \keyword{dataset} 49 | \keyword{generic} 50 | -------------------------------------------------------------------------------- /man/dm_neuro.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/dm_neuro.R 3 | \docType{data} 4 | \name{dm_neuro} 5 | \alias{dm_neuro} 6 | \title{Demographic Dataset-neuro} 7 | \format{ 8 | A data frame with 26 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{SUBJID}{Subject Identifier for the Study} 14 | \item{RFSTDTC}{Subject Reference Start Date/Time} 15 | \item{RFENDTC}{Subject Reference End Date/Time} 16 | \item{RFXSTDTC}{Date/Time of First Study Treatment} 17 | \item{RFXENDTC}{Date/Time of Last Study Treatment} 18 | \item{RFICDTC}{Date/Time of Informed Consent} 19 | \item{RFPENDTC}{Date/Time of End of Participation} 20 | \item{DTHDTC}{Date/Time of Death} 21 | \item{DTHFL}{Subject Death Flag} 22 | \item{SITEID}{Study Site Identifier} 23 | \item{AGE}{Age} 24 | \item{BRTHDTC}{Date/Time of Birth} 25 | \item{AGEU}{Age Units} 26 | \item{SEX}{Sex} 27 | \item{RACE}{Race} 28 | \item{ETHNIC}{Ethnicity} 29 | \item{ARMCD}{Planned Arm Code} 30 | \item{ARM}{Description of Planned Arm} 31 | \item{ACTARMCD}{Actual Arm Code} 32 | \item{ACTARM}{Description of Actual Arm} 33 | \item{COUNTRY}{Country} 34 | \item{DMDTC}{Date/Time of Collection} 35 | \item{DMDY}{Study Day of Collection} 36 | \item{ARMNRS}{Reason Arm and/or Actual Arm is Null} 37 | } 38 | } 39 | \source{ 40 | Constructed by {admiralneuro} developers 41 | } 42 | \usage{ 43 | dm_neuro 44 | } 45 | \description{ 46 | A SDTM DM dataset for Alzheimer's disease studies 47 | } 48 | \details{ 49 | Demographic Dataset-neuro 50 | 51 | A SDTM DM dataset for Alzheimer's disease studies 52 | } 53 | \keyword{dataset} 54 | \keyword{neurology} 55 | -------------------------------------------------------------------------------- /man/rs_onco_pcwg3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rs_onco_pcwg3.R 3 | \docType{data} 4 | \name{rs_onco_pcwg3} 5 | \alias{rs_onco_pcwg3} 6 | \title{Disease Response (PCWG3) for Oncology} 7 | \format{ 8 | A data frame with 14 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{RSSEQ}{Sequence Number} 14 | \item{RSTESTCD}{Response Assessment Short Name} 15 | \item{RSTEST}{Response Assessment Name} 16 | \item{RSCAT}{Category for Response Assessment} 17 | \item{RSORRES}{Response Assessment Original Result} 18 | \item{RSSTRESC}{Response Assessment Result in Std Format} 19 | \item{RSEVAL}{Evaluator} 20 | \item{VISITNUM}{Visit Number} 21 | \item{VISIT}{Visit Name} 22 | \item{RSDTC}{Date/Time of Response Assessment} 23 | \item{RSDY}{Study Day of Response Assessment} 24 | } 25 | } 26 | \source{ 27 | Generated dataset 28 | } 29 | \usage{ 30 | rs_onco_pcwg3 31 | } 32 | \description{ 33 | A SDTM RS dataset for oncology studies using PCWG3 criteria intended for examples of ADaM dataset creation 34 | } 35 | \details{ 36 | Disease Response (PCWG3) for Oncology 37 | 38 | A SDTM RS dataset for oncology studies using PCWG3 criteria intended for examples of ADaM dataset creation 39 | 40 | Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 41 | \strong{RSTESTCD} \tab \strong{RSTEST} \cr 42 | BONERESP \tab Bone Response \cr 43 | OVRLRESP \tab Overall Response \cr 44 | SFTSRESP \tab Soft Tissue Response \cr 45 | TMRESP \tab Tumor Marker Response 46 | } 47 | } 48 | \author{ 49 | Tomoyuki Namai 50 | } 51 | \keyword{dataset} 52 | \keyword{oncology} 53 | -------------------------------------------------------------------------------- /R/ex_ophtha.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Exposure for Ophthalmology 5 | #' 6 | #' An example Exposure SDTM dataset with ophthalmology-specific variables such as `EXLOC` and `EXLAT` 7 | #' 8 | #' @name ex_ophtha 9 | #' @title Exposure for Ophthalmology 10 | #' @keywords dataset ophthalmology 11 | #' @description An example Exposure SDTM dataset with ophthalmology-specific variables such as `EXLOC` and `EXLAT` 12 | #' @docType data 13 | #' @format A data frame with 19 columns: 14 | #' \describe{ 15 | #' \item{USUBJID}{Unique Subject Identifier} 16 | #' \item{STUDYID}{Study Identifier} 17 | #' \item{DOMAIN}{Domain Abbreviation} 18 | #' \item{EXSEQ}{Sequence Number} 19 | #' \item{EXTRT}{Name of Actual Treatment} 20 | #' \item{EXDOSE}{Dose per Administration} 21 | #' \item{EXDOSU}{Dose Units} 22 | #' \item{EXDOSFRM}{Dose Form} 23 | #' \item{EXDOSFRQ}{Dose Frequency per Interval} 24 | #' \item{EXROUTE}{Route of Administration} 25 | #' \item{EXLOC}{Location of Dose Administration} 26 | #' \item{EXLAT}{Laterality} 27 | #' \item{VISITNUM}{Visit Number} 28 | #' \item{VISIT}{Visit Name} 29 | #' \item{VISITDY}{Planned Study Day of Visit} 30 | #' \item{EXSTDTC}{Start Date/Time of Treatment} 31 | #' \item{EXENDTC}{End Date/Time of Treatment} 32 | #' \item{EXSTDY}{Study Day of Start of Treatment} 33 | #' \item{EXENDY}{Study Day of End of Treatment} 34 | #' } 35 | #' 36 | #' @source Constructed using ex from the {pharmaversesdtm} package 37 | "ex_ophtha" 38 | -------------------------------------------------------------------------------- /data-raw/suppdm_vaccine.R: -------------------------------------------------------------------------------- 1 | # Dataset: suppdm_vaccine 2 | # Description: SUPPDM SDTM dataset for Vaccine studies 3 | 4 | 5 | # Load libraries ---- 6 | library(tibble) 7 | library(dplyr) 8 | library(purrr) 9 | library(metatools) 10 | 11 | # create suppdm 12 | ## Read input data ---- 13 | dm_vaccine <- pharmaversesdtm::dm_vaccine 14 | 15 | suppdm <- tribble( 16 | ~STUDYID, 17 | "ABC" 18 | ) 19 | 20 | vx_suppdm <- suppdm %>% 21 | mutate( 22 | STUDYID = "ABC", 23 | USUBJID = "ABC-1001", 24 | RDOMAIN = "DM", 25 | IDVAR = "", 26 | IDVARVAL = "", 27 | QNAM = "RACIALD", 28 | QVAL = "OTHER", 29 | QLABEL = "Racial Designation", 30 | QORIG = "CRF" 31 | ) %>% 32 | add_row( 33 | STUDYID = "ABC", 34 | USUBJID = "ABC-1002", 35 | RDOMAIN = "DM", 36 | IDVAR = "", 37 | IDVARVAL = "", 38 | QNAM = "RACIALD", 39 | QVAL = "OTHER", 40 | QLABEL = "Racial Designation", 41 | QORIG = "CRF" 42 | ) 43 | 44 | # get common column names 45 | common_cols <- intersect(names(vx_suppdm), names(dm_vaccine)) 46 | 47 | # assign labels to vx_suppdm 48 | walk(common_cols, \(x) attr(vx_suppdm[[x]], "label") <<- 49 | attr(dm_vaccine[[x]], "label")) 50 | 51 | suppdm_vaccine <- vx_suppdm %>% 52 | add_labels( 53 | RDOMAIN = "Related Domain Abbreviation", 54 | IDVAR = "Identifying Variable", 55 | IDVARVAL = "Identifying Variable Value", 56 | QNAM = "Qualifier Variable Name", 57 | QLABEL = "Qualifier Variable Label", 58 | QVAL = "Data Value", 59 | QORIG = "Origin" 60 | ) 61 | 62 | # Label SUPPDM dataset ---- 63 | attr(suppdm_vaccine, "label") <- "Supplemental Qualifiers for Demographics" 64 | 65 | # Save dataset ---- 66 | usethis::use_data(suppdm_vaccine, overwrite = TRUE) 67 | -------------------------------------------------------------------------------- /man/dm_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/dm_vaccine.R 3 | \docType{data} 4 | \name{dm_vaccine} 5 | \alias{dm_vaccine} 6 | \title{Demographics for Vaccine} 7 | \format{ 8 | A data frame with 28 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{SUBJID}{Subject Identifier for the Study} 14 | \item{RFSTDTC}{Subject Reference Start Date/Time} 15 | \item{RFENDTC}{Subject Reference End Date/Time} 16 | \item{RFXSTDTC}{Date/Time of First Study Treatment} 17 | \item{RFXENDTC}{Date/Time of Last Study Treatment} 18 | \item{RFICDTC}{Date/Time of Informed Consent} 19 | \item{RFPENDTC}{Date/Time of End of Participation} 20 | \item{DTHDTC}{Date/Time of Death} 21 | \item{DTHFL}{Subject Death Flag} 22 | \item{SITEID}{Study Site Identifier} 23 | \item{INVID}{Investigator Identifier} 24 | \item{INVNAM}{Investigator Name} 25 | \item{BRTHDTC}{Date/Time of Birth} 26 | \item{AGE}{Age} 27 | \item{AGEU}{Age Units} 28 | \item{SEX}{Sex} 29 | \item{RACE}{Race} 30 | \item{ETHNIC}{Ethnicity} 31 | \item{ARMCD}{Planned Arm Code} 32 | \item{ARM}{Description of Planned Arm} 33 | \item{ACTARMCD}{Actual Arm Code} 34 | \item{ACTARM}{Description of Actual Arm} 35 | \item{COUNTRY}{Country} 36 | \item{DMDTC}{Date/Time of Collection} 37 | \item{DMDY}{Study Day of Collection} 38 | } 39 | } 40 | \source{ 41 | Constructed by {admiralvaccine} developers 42 | } 43 | \usage{ 44 | dm_vaccine 45 | } 46 | \description{ 47 | An example SDTM DM dataset for vaccine studies 48 | } 49 | \details{ 50 | Demographics for Vaccine 51 | 52 | An example SDTM DM dataset for vaccine studies 53 | } 54 | \keyword{dataset} 55 | \keyword{vaccine} 56 | -------------------------------------------------------------------------------- /man/vs_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/vs_vaccine.R 3 | \docType{data} 4 | \name{vs_vaccine} 5 | \alias{vs_vaccine} 6 | \title{Vital Signs for Vaccine} 7 | \format{ 8 | A data frame with 23 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{VSSEQ}{Sequence Number} 14 | \item{VSLNKID}{Link ID} 15 | \item{VSLNKGRP}{Link Group ID} 16 | \item{VSTESTCD}{Vital Signs Test Short Name} 17 | \item{VSTEST}{Vital Signs Test Name} 18 | \item{VSCAT}{Category for Vital Signs} 19 | \item{VSSCAT}{Subcategory for Vital Signs} 20 | \item{VSORRES}{Result or Finding in Original Units} 21 | \item{VSORRESU}{Original Units} 22 | \item{VSSTRESC}{Character Result/Finding in Std Format} 23 | \item{VSSTRESN}{Numeric Result/Finding in Standard Units} 24 | \item{VSSTRESU}{Standard Units} 25 | \item{VSEVAL}{Evaluator} 26 | \item{VSLOC}{Location of Vital Signs Measurement} 27 | \item{EPOCH}{Epoch} 28 | \item{VSDTC}{Date/Time of Measurements} 29 | \item{VSDY}{Study Day of Vital Signs} 30 | \item{VSTPT}{Planned Time Point Name} 31 | \item{VSTPTNUM}{Planned Time Point Number} 32 | \item{VSTPTREF}{Time Point Reference} 33 | } 34 | } 35 | \source{ 36 | Constructed by {admiralvaccine} developers 37 | } 38 | \usage{ 39 | vs_vaccine 40 | } 41 | \description{ 42 | An example SDTM VS dataset for vaccine studies 43 | } 44 | \details{ 45 | Vital Signs for Vaccine 46 | 47 | An example SDTM VS dataset for vaccine studies 48 | 49 | Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 50 | \strong{VSTESTCD} \tab \strong{VSTEST} \cr 51 | TEMP \tab Temperature 52 | } 53 | } 54 | \keyword{dataset} 55 | \keyword{vaccine} 56 | -------------------------------------------------------------------------------- /man/dm.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/dm.R 3 | \docType{data} 4 | \name{dm} 5 | \alias{dm} 6 | \title{Demography} 7 | \format{ 8 | A data frame with 26 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{SUBJID}{Subject Identifier for the Study} 14 | \item{RFSTDTC}{Subject Reference Start Date/Time} 15 | \item{RFENDTC}{Subject Reference End Date/Time} 16 | \item{RFXSTDTC}{Date/Time of First Study Treatment} 17 | \item{RFXENDTC}{Date/Time of Last Study Treatment} 18 | \item{RFICDTC}{Date/Time of Informed Consent} 19 | \item{RFPENDTC}{Date/Time of End of Participation} 20 | \item{DTHDTC}{Date/Time of Death} 21 | \item{DTHFL}{Subject Death Flag} 22 | \item{SITEID}{Study Site Identifier} 23 | \item{BRTHDTC}{Date/Time of Birth} 24 | \item{AGE}{Age} 25 | \item{AGEU}{Age Units} 26 | \item{SEX}{Sex} 27 | \item{RACE}{Race} 28 | \item{ETHNIC}{Ethnicity} 29 | \item{ARMCD}{Planned Arm Code} 30 | \item{ARM}{Description of Planned Arm} 31 | \item{ACTARMCD}{Actual Arm Code} 32 | \item{ACTARM}{Description of Actual Arm} 33 | \item{COUNTRY}{Country} 34 | \item{DMDTC}{Date/Time of Collection} 35 | \item{DMDY}{Study Day of Collection} 36 | } 37 | } 38 | \source{ 39 | \href{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}{Access the source of the Demography dataset.} 40 | } 41 | \usage{ 42 | dm 43 | } 44 | \description{ 45 | A SDTM DM dataset from the CDISC pilot project 46 | } 47 | \details{ 48 | Demography 49 | 50 | A SDTM DM dataset from the CDISC pilot project 51 | } 52 | \keyword{dataset} 53 | \keyword{generic} 54 | -------------------------------------------------------------------------------- /R/rs_onco_imwg.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Disease Response (IMWG) 5 | #' 6 | #' A SDTM RS dataset using IMWG criteria intended for examples of ADaM dataset creation 7 | #' 8 | #' @name rs_onco_imwg 9 | #' @title Disease Response (IMWG) 10 | #' @keywords dataset oncology 11 | #' @description A SDTM RS dataset using IMWG criteria intended for examples of ADaM dataset creation 12 | #' @docType data 13 | #' @format A data frame with 17 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{RSSEQ}{Sequence Number} 19 | #' \item{RSLNKGRP}{Link Group ID} 20 | #' \item{RSTESTCD}{Assessment Short Name} 21 | #' \item{RSTEST}{Assessment Name} 22 | #' \item{RSCAT}{Category for Assessment} 23 | #' \item{RSORRES}{Result or Finding in Original Units} 24 | #' \item{RSSTRESC}{Character Result/Finding in Std Format} 25 | #' \item{RSSTAT}{Completion Status} 26 | #' \item{RSREASND}{Reason Not Done} 27 | #' \item{RSEVAL}{Evaluator} 28 | #' \item{VISITNUM}{Visit Number} 29 | #' \item{VISIT}{Visit Name} 30 | #' \item{RSDTC}{Date/Time of Assessment} 31 | #' \item{RSDY}{Study Day of Assessment} 32 | #' } 33 | #' 34 | #' @source Derived from tr_onco_recist 35 | #' @author Vinh Nguyen 36 | #' @details Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 37 | #' \strong{RSTESTCD} \tab \strong{RSTEST} \cr 38 | #' OVRLRESP \tab Overall Response 39 | #' } 40 | 41 | "rs_onco_imwg" 42 | -------------------------------------------------------------------------------- /R/tu_onco_recist.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Tumor Identification (RECIST 1.1) for Oncology 5 | #' 6 | #' A SDTM TU dataset using RECIST 1.1 intended for examples of ADaM dataset creation 7 | #' 8 | #' @name tu_onco_recist 9 | #' @title Tumor Identification (RECIST 1.1) for Oncology 10 | #' @keywords dataset oncology 11 | #' @description A SDTM TU dataset using RECIST 1.1 intended for examples of ADaM dataset creation 12 | #' @docType data 13 | #' @format A data frame with 16 columns: 14 | #' \describe{ 15 | #' \item{DOMAIN}{Domain Abbreviation} 16 | #' \item{STUDYID}{Study Identifier} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{VISIT}{Visit Name} 19 | #' \item{VISITNUM}{Visit Number} 20 | #' \item{TULOC}{Location of the Tumor/Lesion} 21 | #' \item{TUTESTCD}{Tumor/Lesion ID Short Name} 22 | #' \item{TUTEST}{Tumor/Lesion ID Test Name} 23 | #' \item{TUORRES}{Tumor/Lesion ID Result} 24 | #' \item{TUSTRESC}{Tumor/Lesion ID Result Std. Format} 25 | #' \item{TUMETHOD}{Method of Identification} 26 | #' \item{TULNKID}{Link ID} 27 | #' \item{TUEVAL}{Evaluator} 28 | #' \item{TUEVALID}{Evaluator Identifier} 29 | #' \item{TUACPTFL}{Accepted Record Flag} 30 | #' \item{TUSEQ}{Sequence Number} 31 | #' } 32 | #' 33 | #' @source Generated dataset. 34 | #' @author Stefan Bundfuss 35 | #' @details Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 36 | #' \strong{TUTESTCD} \tab \strong{TUTEST} \cr 37 | #' TUMIDENT \tab Tumor Identification 38 | #' } 39 | 40 | "tu_onco_recist" 41 | -------------------------------------------------------------------------------- /R/tu_onco.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Tumor Identification for Oncology 5 | #' 6 | #' A SDTM TU dataset simulated by Gopi Vegesna 7 | #' 8 | #' @name tu_onco 9 | #' @title Tumor Identification for Oncology 10 | #' @keywords dataset oncology 11 | #' @description A SDTM TU dataset simulated by Gopi Vegesna 12 | #' @docType data 13 | #' @format A data frame with 18 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{TUSEQ}{Sequence Number} 19 | #' \item{TULNKID}{Link ID} 20 | #' \item{TUTESTCD}{Tumor Identification Short Name} 21 | #' \item{TUTEST}{Tumor Identification Test Name} 22 | #' \item{TUORRES}{Tumor Identification Result} 23 | #' \item{TUSTRESC}{Tumor Identification Result Std. Format} 24 | #' \item{TULOC}{Location of the Tumor} 25 | #' \item{TUMETHOD}{Method of Identification} 26 | #' \item{TUEVAL}{Evaluator} 27 | #' \item{TUEVALID}{Evaluator Identifier} 28 | #' \item{TUACPTFL}{Accepted Record Flag} 29 | #' \item{VISITNUM}{Visit Number} 30 | #' \item{VISIT}{Visit Name} 31 | #' \item{TUDTC}{Date/Time of Tumor Identification} 32 | #' \item{TUDY}{Study Day of Tumor Identification} 33 | #' } 34 | #' 35 | #' @source Generated dataset. 36 | #' @author Gopi Vegesna 37 | #' @details Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 38 | #' \strong{TUTESTCD} \tab \strong{TUTEST} \cr 39 | #' TUMIDENT \tab Tumor Identification 40 | #' } 41 | 42 | "tu_onco" 43 | -------------------------------------------------------------------------------- /man/pc.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/pc.R 3 | \docType{data} 4 | \name{pc} 5 | \alias{pc} 6 | \title{Pharmacokinetic Concentrations} 7 | \format{ 8 | A data frame with 20 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{PCSEQ}{Sequence Number} 14 | \item{PCTESTCD}{Pharmacokinetic Test Short Name} 15 | \item{PCTEST}{Pharmacokinetic Test Name} 16 | \item{PCORRES}{Result or Finding in Original Units} 17 | \item{PCORRESU}{Original Units} 18 | \item{PCSTRESC}{Character Result/Finding in Std Format} 19 | \item{PCSTRESN}{Numeric Result/Finding in Standard Units} 20 | \item{PCSTRESU}{Standard Units} 21 | \item{PCNAM}{Vendor Name} 22 | \item{PCSPEC}{Specimen Material Type} 23 | \item{PCLLOQ}{Lower Limit of Quantitation} 24 | \item{VISIT}{Visit Name} 25 | \item{VISITNUM}{Visit Number} 26 | \item{PCDTC}{Date/Time of Specimen Collection} 27 | \item{PCDY}{Actual Study Day of Specimen Collection} 28 | \item{PCTPT}{Planned Time Point Name} 29 | \item{PCTPTNUM}{Planned Time Point Number} 30 | } 31 | } 32 | \source{ 33 | \href{https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/pc.rda}{Access the source of the Pharmacokinetic Concentrations dataset.} 34 | } 35 | \usage{ 36 | pc 37 | } 38 | \description{ 39 | A SDTM PC dataset simulated by Antonio Rodriguez Contesti 40 | } 41 | \details{ 42 | Pharmacokinetic Concentrations 43 | 44 | A SDTM PC dataset simulated by Antonio Rodriguez Contesti 45 | 46 | Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 47 | \strong{PCTESTCD} \tab \strong{PCTEST} \cr 48 | XAN \tab XANOMELINE 49 | } 50 | } 51 | \author{ 52 | Antonio Rodriguez Contesti 53 | } 54 | \keyword{dataset} 55 | \keyword{generic} 56 | -------------------------------------------------------------------------------- /man/tr_onco_recist.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/tr_onco_recist.R 3 | \docType{data} 4 | \name{tr_onco_recist} 5 | \alias{tr_onco_recist} 6 | \title{Tumor Results (RECIST 1.1) for Oncology} 7 | \format{ 8 | A data frame with 19 columns: 9 | \describe{ 10 | \item{DOMAIN}{Domain Abbreviation} 11 | \item{STUDYID}{Study Identifier} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{TRGRPID}{Group ID} 14 | \item{TRLNKID}{Link ID} 15 | \item{TRTESTCD}{Tumor/Lesion Assessment Short Name} 16 | \item{TRTEST}{Tumor/Lesion Assessment Test Name} 17 | \item{TRORRES}{Result or Finding in Original Units} 18 | \item{TRORRESU}{Original Units} 19 | \item{TRSTRESC}{Character Result/Finding in Std Format} 20 | \item{TRSTRESN}{Numeric Result/Finding in Standard Units} 21 | \item{TRSTRESU}{Standard Units} 22 | \item{VISITNUM}{Visit Number} 23 | \item{VISIT}{Visit Name} 24 | \item{TREVAL}{Evaluator} 25 | \item{TREVALID}{Evaluator Identifier} 26 | \item{TRACPTFL}{Accepted Record Flag} 27 | \item{TRDTC}{Date/Time of Tumor/Lesion Measurement} 28 | \item{TRSEQ}{Sequence Number} 29 | } 30 | } 31 | \source{ 32 | Generated dataset. 33 | } 34 | \usage{ 35 | tr_onco_recist 36 | } 37 | \description{ 38 | A SDTM TR dataset using RECIST 1.1 intended for examples of ADaM dataset creation 39 | } 40 | \details{ 41 | Tumor Results (RECIST 1.1) for Oncology 42 | 43 | A SDTM TR dataset using RECIST 1.1 intended for examples of ADaM dataset creation 44 | 45 | Contains a set of 3 unique Test Short Names and Test Names: \tabular{ll}{ 46 | \strong{TRTESTCD} \tab \strong{TRTEST} \cr 47 | LDIAM \tab Longest Diameter \cr 48 | LPERP \tab Longest Perpendicular\cr 49 | TUMSTATE \tab Tumor State 50 | } 51 | } 52 | \author{ 53 | Stefan Bundfuss 54 | } 55 | \keyword{dataset} 56 | \keyword{oncology} 57 | -------------------------------------------------------------------------------- /R/rs_onco_ca125.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Disease Response (GCIG) 5 | #' 6 | #' A SDTM RS dataset using GCIG criteria. The dataset contains just a few patients. It is intended for vignettes and examples of ADaM dataset creation. 7 | #' 8 | #' @name rs_onco_ca125 9 | #' @title Disease Response (GCIG) 10 | #' @keywords dataset oncology 11 | #' @description A SDTM RS dataset using GCIG criteria. The dataset contains just a few patients. It is intended for vignettes and examples of ADaM dataset creation. 12 | #' @docType data 13 | #' @format A data frame with 13 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{RSSEQ}{Sequence Number} 19 | #' \item{RSTESTCD}{Assessment Short Name} 20 | #' \item{RSTEST}{Assessment Name} 21 | #' \item{RSCAT}{Category for Assessment} 22 | #' \item{RSORRES}{Result or Finding in Original Units} 23 | #' \item{RSSTRESC}{Character Result/Finding in Std Format} 24 | #' \item{RSEVAL}{Evaluator} 25 | #' \item{VISITNUM}{Visit Number} 26 | #' \item{VISIT}{Visit Name} 27 | #' \item{RSDTC}{Date/Time of Assessment} 28 | #' } 29 | #' 30 | #' @source Generated dataset ([rs_supprs_onco_ca125.R](https://github.com/pharmaverse/pharmaversesdtm/blob/main/data-raw/rs_supprs_onco_ca125.R)) 31 | #' @author Vinh Nguyen 32 | #' @details Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 33 | #' \strong{RSTESTCD} \tab \strong{RSTEST} \cr 34 | #' OVRLRESP \tab Overall Response 35 | #' } 36 | 37 | "rs_onco_ca125" 38 | -------------------------------------------------------------------------------- /man/nv_neuro.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/nv_neuro.R 3 | \docType{data} 4 | \name{nv_neuro} 5 | \alias{nv_neuro} 6 | \title{Neurological Assessment Dataset-neuro} 7 | \format{ 8 | A data frame with 21 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{NVSEQ}{Sequence Number} 14 | \item{NVLNKID}{Link ID} 15 | \item{NVTESTCD}{Short Name of Nervous System Test} 16 | \item{NVTEST}{Name of Nervous System Test} 17 | \item{NVCAT}{Category for Nervous System Test} 18 | \item{NVLOC}{Location Used for the Measurement} 19 | \item{NVMETHOD}{Method of Test or Examination} 20 | \item{NVNAM}{Vendor Name} 21 | \item{NVORRES}{Result or Finding in Original Units} 22 | \item{NVORRESU}{Original Units} 23 | \item{NVSTRESC}{Character Result/Finding in Std Format} 24 | \item{NVSTRESN}{Numeric Result/Finding in Standard Units} 25 | \item{NVSTRESU}{Standard Units} 26 | \item{VISITNUM}{Visit Number} 27 | \item{VISIT}{Visit Name} 28 | \item{NVDTC}{Date/Time of Collection} 29 | \item{NVDY}{Study Day of Collection} 30 | \item{NVLOBXFL}{Last Observation Before Exposure Flag} 31 | } 32 | } 33 | \source{ 34 | Constructed by {admiralneuro} developers 35 | } 36 | \usage{ 37 | nv_neuro 38 | } 39 | \description{ 40 | A SDTM NV dataset containing neurological assessments or test results 41 | } 42 | \details{ 43 | Neurological Assessment Dataset-neuro 44 | 45 | A SDTM NV dataset containing neurological assessments or test results 46 | 47 | Contains a set of 2 unique Test Short Names and Test Names: \tabular{ll}{ 48 | \strong{NVTESTCD} \tab \strong{NVTEST} \cr 49 | SUVR \tab Standardized Uptake Value Ratio \cr 50 | VR \tab Qualitative Visual Classification 51 | } 52 | } 53 | \keyword{dataset} 54 | \keyword{neurology} 55 | -------------------------------------------------------------------------------- /man/eg.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/eg.R 3 | \docType{data} 4 | \name{eg} 5 | \alias{eg} 6 | \title{Electrocardiogram} 7 | \format{ 8 | A data frame with 23 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{EGSEQ}{Sequence Number} 14 | \item{EGTESTCD}{ECG Test Short Name} 15 | \item{EGTEST}{ECG Test Name} 16 | \item{EGORRES}{Result or Finding in Original Units} 17 | \item{EGORRESU}{Original Units} 18 | \item{EGSTRESC}{Character Result/Finding in Std Format} 19 | \item{EGSTRESN}{Numeric Result/Finding in Standard Units} 20 | \item{EGSTRESU}{Standard Units} 21 | \item{EGSTAT}{Completion Status} 22 | \item{EGLOC}{Location of Vital Signs Measurement} 23 | \item{EGBLFL}{Baseline Flag} 24 | \item{VISITNUM}{Visit Number} 25 | \item{VISIT}{Visit Name} 26 | \item{VISITDY}{Planned Study Day of Visit} 27 | \item{EGDTC}{Date/Time of Measurements} 28 | \item{EGDY}{Study Day of Vital Signs} 29 | \item{EGTPT}{Planned Time Point Number} 30 | \item{EGTPTNUM}{Time Point Number} 31 | \item{EGELTM}{Planned Elapsed Time from Time Point Ref} 32 | \item{EGTPTREF}{Time Point Reference} 33 | } 34 | } 35 | \source{ 36 | Generated dataset. 37 | } 38 | \usage{ 39 | eg 40 | } 41 | \description{ 42 | An example of standard SDTM EG dataset to be used in deriving ADEG dataset 43 | } 44 | \details{ 45 | Electrocardiogram 46 | 47 | An example of standard SDTM EG dataset to be used in deriving ADEG dataset 48 | 49 | Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 50 | \strong{EGTESTCD} \tab \strong{EGTEST} \cr 51 | ECGINT \tab ECG Interpretation\cr 52 | HR \tab Heart Rate \cr 53 | QT \tab QT Duration \cr 54 | RR \tab RR Duration 55 | } 56 | } 57 | \keyword{dataset} 58 | \keyword{generic} 59 | -------------------------------------------------------------------------------- /man/rs_onco.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rs_onco.R 3 | \docType{data} 4 | \name{rs_onco} 5 | \alias{rs_onco} 6 | \title{Disease Response for Oncology} 7 | \format{ 8 | A data frame with 19 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{RSSEQ}{Sequence Number} 14 | \item{RSLNKGRP}{Link Group} 15 | \item{RSTESTCD}{Response Assessment Short Name} 16 | \item{RSTEST}{Response Assessment Name} 17 | \item{RSCAT}{Category for Response Assessment} 18 | \item{RSORRES}{Response Assessment Original Result} 19 | \item{RSSTRESC}{Response Assessment Result in Std Format} 20 | \item{RSSTAT}{Completion Status} 21 | \item{RSREASND}{Reason Response Assessment Not Performed} 22 | \item{RSEVAL}{Evaluator} 23 | \item{RSEVALID}{Evaluator Identifier} 24 | \item{RSACPTFL}{Accepted Record Flag} 25 | \item{VISITNUM}{Visit Number} 26 | \item{VISIT}{Visit Name} 27 | \item{RSDTC}{Date/Time of Response Assessment} 28 | \item{RSDY}{Study Day of Response Assessment} 29 | } 30 | } 31 | \source{ 32 | \href{https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/tr_onco_recist.rda}{Access the source of the Disease Response for Oncology dataset.} 33 | } 34 | \usage{ 35 | rs_onco 36 | } 37 | \description{ 38 | A SDTM RS dataset simulated by Gopi Vegesna 39 | } 40 | \details{ 41 | Disease Response for Oncology 42 | 43 | A SDTM RS dataset simulated by Gopi Vegesna 44 | 45 | Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 46 | \strong{RSTESTCD} \tab \strong{RSTEST} \cr 47 | NEWLPROG \tab New Lesion Progression\cr 48 | NTRGRESP \tab Non-target Response \cr 49 | OVRLRESP \tab Overall Response \cr 50 | TRGRESP \tab Target Response 51 | } 52 | } 53 | \author{ 54 | Gopi Vegesna 55 | } 56 | \keyword{dataset} 57 | \keyword{oncology} 58 | -------------------------------------------------------------------------------- /man/pharmaversesdtm-package.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/pharmaversesdtm-package.R 3 | \docType{package} 4 | \name{pharmaversesdtm-package} 5 | \alias{pharmaversesdtm} 6 | \alias{pharmaversesdtm-package} 7 | \title{pharmaversesdtm: SDTM Test Data for the 'Pharmaverse' Family of Packages} 8 | \description{ 9 | \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} 10 | 11 | A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages. SDTM dataset specifications are described in the CDISC SDTM implementation guide, accessible by creating a free account on \url{https://www.cdisc.org/}. 12 | } 13 | \seealso{ 14 | Useful links: 15 | \itemize{ 16 | \item \url{https://pharmaverse.github.io/pharmaversesdtm/} 17 | \item \url{https://github.com/pharmaverse/pharmaversesdtm/} 18 | } 19 | 20 | } 21 | \author{ 22 | \strong{Maintainer}: Lina Patil \email{lina.patil@cytel.com} 23 | 24 | Authors: 25 | \itemize{ 26 | \item Stefan Bundfuss (\href{https://orcid.org/0009-0005-0027-1198}{ORCID}) 27 | \item Kristin Dahnert 28 | \item Fanny Gautier \email{fanny.gautier@cytel.com} (\href{https://orcid.org/0009-0004-3581-0131}{ORCID}) 29 | \item Edoardo Mancini \email{edoardo.mancini@roche.com} (\href{https://orcid.org/0009-0006-4899-8641}{ORCID}) 30 | \item Tomoyuki Namai 31 | \item Vinh Nguyen 32 | \item Vladyslav Shuliar (\href{https://orcid.org/0009-0008-2354-8999}{ORCID}) 33 | } 34 | 35 | Other contributors: 36 | \itemize{ 37 | \item Cytel Inc. [copyright holder, funder] 38 | \item F. Hoffmann-La Roche AG [copyright holder, funder] 39 | \item GlaxoSmithKline LLC [copyright holder, funder] 40 | } 41 | 42 | } 43 | \keyword{internal} 44 | -------------------------------------------------------------------------------- /man/ce_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ce_vaccine.R 3 | \docType{data} 4 | \name{ce_vaccine} 5 | \alias{ce_vaccine} 6 | \title{Clinical Events for Vaccine} 7 | \format{ 8 | A data frame with 29 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{CESEQ}{Sequence Number} 14 | \item{CELNKID}{Link ID} 15 | \item{CELNKGRP}{Link Group ID} 16 | \item{CETERM}{Reported Term for the Clinical Event} 17 | \item{CEDECOD}{Dictionary-Derived Term} 18 | \item{CELAT}{Laterality of Location of Clinical Event} 19 | \item{CELOC}{Location of Clinical Event} 20 | \item{CECAT}{Category for Clinical Event} 21 | \item{CESCAT}{Subcategory for Clinical Event} 22 | \item{CEPRESP}{Clinical Event Pre-Specified} 23 | \item{CEOCCUR}{Clinical Event Occurrence} 24 | \item{CESEV}{Severity/Intensity} 25 | \item{CEREL}{Causality} 26 | \item{CEOUT}{Outcome of Clinical Event} 27 | \item{EPOCH}{Epoch} 28 | \item{CEDTC}{Date/Time of Event Collection} 29 | \item{CESTDTC}{Start Date/Time of Clinical Event} 30 | \item{CEENDTC}{End Date/Time of Clinical Event} 31 | \item{CEDUR}{Duration of Clinical Event} 32 | \item{CETPT}{Planned Time Point Name} 33 | \item{CETPTNUM}{Planned Time Point Number} 34 | \item{CETPTREF}{Time Point Reference} 35 | \item{CERFTDTC}{Date/Time of Reference Time Point} 36 | \item{CEEVINTX}{Evaluation Interval Text} 37 | \item{CESTAT}{Completion Status} 38 | \item{CEREASND}{Reason Clinical Event Not Collected} 39 | } 40 | } 41 | \source{ 42 | Constructed by {admiralvaccine} developers 43 | } 44 | \usage{ 45 | ce_vaccine 46 | } 47 | \description{ 48 | An example SDTM CE dataset for vaccine studies 49 | } 50 | \details{ 51 | Clinical Events for Vaccine 52 | 53 | An example SDTM CE dataset for vaccine studies 54 | } 55 | \keyword{dataset} 56 | \keyword{vaccine} 57 | -------------------------------------------------------------------------------- /R/rs_onco_pcwg3.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Disease Response (PCWG3) for Oncology 5 | #' 6 | #' A SDTM RS dataset for oncology studies using PCWG3 criteria intended for examples of ADaM dataset creation 7 | #' 8 | #' @name rs_onco_pcwg3 9 | #' @title Disease Response (PCWG3) for Oncology 10 | #' @keywords dataset oncology 11 | #' @description A SDTM RS dataset for oncology studies using PCWG3 criteria intended for examples of ADaM dataset creation 12 | #' @docType data 13 | #' @format A data frame with 14 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{RSSEQ}{Sequence Number} 19 | #' \item{RSTESTCD}{Response Assessment Short Name} 20 | #' \item{RSTEST}{Response Assessment Name} 21 | #' \item{RSCAT}{Category for Response Assessment} 22 | #' \item{RSORRES}{Response Assessment Original Result} 23 | #' \item{RSSTRESC}{Response Assessment Result in Std Format} 24 | #' \item{RSEVAL}{Evaluator} 25 | #' \item{VISITNUM}{Visit Number} 26 | #' \item{VISIT}{Visit Name} 27 | #' \item{RSDTC}{Date/Time of Response Assessment} 28 | #' \item{RSDY}{Study Day of Response Assessment} 29 | #' } 30 | #' 31 | #' @source Generated dataset 32 | #' @author Tomoyuki Namai 33 | #' @details Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 34 | #' \strong{RSTESTCD} \tab \strong{RSTEST} \cr 35 | #' BONERESP \tab Bone Response \cr 36 | #' OVRLRESP \tab Overall Response \cr 37 | #' SFTSRESP \tab Soft Tissue Response \cr 38 | #' TMRESP \tab Tumor Marker Response 39 | #' } 40 | 41 | "rs_onco_pcwg3" 42 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/02_feature_request.yml: -------------------------------------------------------------------------------- 1 | name: Feature Request 2 | description: Enchancement to admiral functionality 3 | title: "Feature Request: " 4 | labels: ["enhancement", "programming"] 5 | assignees: 6 | - octocat 7 | body: 8 | - type: markdown 9 | attributes: 10 | value: | 11 | Thanks for taking the time to fill out this feature request! We love keeping admiral fresh! 12 | - type: textarea 13 | id: feature 14 | attributes: 15 | label: Feature Idea 16 | description: Tell us your idea in as few words as possible 17 | placeholder: "`derive_var_dtm` should do x, y and z" 18 | validations: 19 | required: true 20 | - type: textarea 21 | id: input 22 | attributes: 23 | label: Relevant Input 24 | description: Can you provide what the inputs should look like? 25 | placeholder: "What should the input look like? REMINDER: no patient level data or company sensitive information should be shared via this open public issue" 26 | validations: 27 | required: false 28 | - type: textarea 29 | id: output 30 | attributes: 31 | label: Relevant Output 32 | description: Can you provide what the final output should look like? 33 | placeholder: "What should the output look like? REMINDER: no patient level data or company sensitive information should be shared via this open public issue" 34 | validations: 35 | required: false 36 | - type: textarea 37 | id: code 38 | attributes: 39 | label: Reproducible Example/Pseudo Code 40 | description: Can you provide a working example or a sketch of how the code should work? 41 | placeholder: "We love example code and it will speed up the process! REMINDER: no patient level data or company sensitive information should be shared via this open public issue" 42 | validations: 43 | required: false 44 | -------------------------------------------------------------------------------- /R/dm_metabolic.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Demographic Dataset-metabolic 5 | #' 6 | #' A SDTM DM dataset for metabolic studies 7 | #' 8 | #' @name dm_metabolic 9 | #' @title Demographic Dataset-metabolic 10 | #' @keywords dataset metabolic 11 | #' @description A SDTM DM dataset for metabolic studies 12 | #' @docType data 13 | #' @format A data frame with 26 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{SUBJID}{Subject Identifier for the Study} 19 | #' \item{RFSTDTC}{Subject Reference Start Date/Time} 20 | #' \item{RFENDTC}{Subject Reference End Date/Time} 21 | #' \item{RFXSTDTC}{Date/Time of First Study Treatment} 22 | #' \item{RFXENDTC}{Date/Time of Last Study Treatment} 23 | #' \item{RFICDTC}{Date/Time of Informed Consent} 24 | #' \item{RFPENDTC}{Date/Time of End of Participation} 25 | #' \item{DTHDTC}{Date/Time of Death} 26 | #' \item{DTHFL}{Subject Death Flag} 27 | #' \item{SITEID}{Study Site Identifier} 28 | #' \item{BRTHDTC}{Date/Time of Birth} 29 | #' \item{AGE}{Age} 30 | #' \item{AGEU}{Age Units} 31 | #' \item{SEX}{Sex} 32 | #' \item{RACE}{Race} 33 | #' \item{ETHNIC}{Ethnicity} 34 | #' \item{ARMCD}{Planned Arm Code} 35 | #' \item{ARM}{Description of Planned Arm} 36 | #' \item{ACTARMCD}{Actual Arm Code} 37 | #' \item{ACTARM}{Description of Actual Arm} 38 | #' \item{COUNTRY}{Country} 39 | #' \item{DMDTC}{Date/Time of Collection} 40 | #' \item{DMDY}{Study Day of Collection} 41 | #' } 42 | #' 43 | #' @source Constructed by {admiralmetabolic} developers 44 | "dm_metabolic" 45 | -------------------------------------------------------------------------------- /R/dm_peds.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Demographic Dataset-pediatrics 5 | #' 6 | #' An updated SDTM DM dataset with pediatric patients 7 | #' 8 | #' @name dm_peds 9 | #' @title Demographic Dataset-pediatrics 10 | #' @keywords dataset pediatrics 11 | #' @description An updated SDTM DM dataset with pediatric patients 12 | #' @docType data 13 | #' @format A data frame with 26 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{SUBJID}{Subject Identifier for the Study} 19 | #' \item{RFSTDTC}{Subject Reference Start Date/Time} 20 | #' \item{RFENDTC}{Subject Reference End Date/Time} 21 | #' \item{RFXSTDTC}{Date/Time of First Study Treatment} 22 | #' \item{RFXENDTC}{Date/Time of Last Study Treatment} 23 | #' \item{RFICDTC}{Date/Time of Informed Consent} 24 | #' \item{RFPENDTC}{Date/Time of End of Participation} 25 | #' \item{DTHDTC}{Date/Time of Death} 26 | #' \item{DTHFL}{Subject Death Flag} 27 | #' \item{SITEID}{Study Site Identifier} 28 | #' \item{AGE}{Age} 29 | #' \item{AGEU}{Age Units} 30 | #' \item{SEX}{Sex} 31 | #' \item{RACE}{Race} 32 | #' \item{ETHNIC}{Ethnicity} 33 | #' \item{ARMCD}{Planned Arm Code} 34 | #' \item{ARM}{Description of Planned Arm} 35 | #' \item{ACTARMCD}{Actual Arm Code} 36 | #' \item{ACTARM}{Description of Actual Arm} 37 | #' \item{COUNTRY}{Country} 38 | #' \item{DMDTC}{Date/Time of Collection} 39 | #' \item{DMDY}{Study Day of Collection} 40 | #' \item{BRTHDTC}{Date/Time of Birth} 41 | #' } 42 | #' 43 | #' @source Constructed by {admiralpeds} developers 44 | "dm_peds" 45 | -------------------------------------------------------------------------------- /R/cm.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Concomitant Medication 5 | #' 6 | #' A SDTM CM dataset from the CDISC pilot project 7 | #' 8 | #' @name cm 9 | #' @title Concomitant Medication 10 | #' @keywords dataset generic 11 | #' @description A SDTM CM dataset from the CDISC pilot project 12 | #' @docType data 13 | #' @format A data frame with 22 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{CMSEQ}{Sequence Number} 19 | #' \item{CMSPID}{Sponsor-Defined Identifier} 20 | #' \item{CMTRT}{Reported Name of Drug, Med, or Therapy} 21 | #' \item{CMDECOD}{Standardized Medication Name} 22 | #' \item{CMINDC}{Indication} 23 | #' \item{CMCLAS}{Medication Class} 24 | #' \item{CMDOSE}{Dose per Administration} 25 | #' \item{CMDOSU}{Dose Units} 26 | #' \item{CMDOSFRQ}{Dosing Frequency per Interval} 27 | #' \item{CMROUTE}{Route of Administration} 28 | #' \item{VISITNUM}{Visit Number} 29 | #' \item{VISIT}{Visit Name} 30 | #' \item{VISITDY}{Planned Study Day of Visit} 31 | #' \item{CMDTC}{Date/Time of Collection} 32 | #' \item{CMSTDTC}{Start Date/Time of Medication} 33 | #' \item{CMENDTC}{End Date/Time of Medication} 34 | #' \item{CMSTDY}{Study Day of Start of Medication} 35 | #' \item{CMENDY}{Study Day of End of Medication} 36 | #' \item{CMENRTPT}{End Relative to Reference Time Point} 37 | #' } 38 | #' 39 | #' @source [Access the source of the Concomitant Medication dataset.](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) 40 | "cm" 41 | -------------------------------------------------------------------------------- /man/is_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/is_vaccine.R 3 | \docType{data} 4 | \name{is_vaccine} 5 | \alias{is_vaccine} 6 | \title{Immunogenicity Specimen Assessments for Vaccine} 7 | \format{ 8 | A data frame with 24 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{ISSEQ}{Sequence Number} 14 | \item{ISTESTCD}{Immunogenicity Test/Exam Short Name} 15 | \item{ISTEST}{Immunogenicity Test or Exam Name} 16 | \item{ISCAT}{Category for Immunogenicity Test} 17 | \item{ISORRES}{Result or Finding in Original Units} 18 | \item{ISORRESU}{Original Units} 19 | \item{ISSTRESC}{Character Result/Finding in Std Format} 20 | \item{ISSTRESN}{Numeric Result/Finding in Standard Units} 21 | \item{ISSTRESU}{Standard Units} 22 | \item{ISSTAT}{Completion Status} 23 | \item{ISREASND}{Reason Not Done} 24 | \item{ISNAM}{Vendor Name} 25 | \item{ISSPEC}{Specimen Type} 26 | \item{ISMETHOD}{Method of Test or Examination} 27 | \item{ISBLFL}{Baseline Flag} 28 | \item{ISLLOQ}{Lower Limit of Quantitation} 29 | \item{VISITNUM}{Visit Number} 30 | \item{EPOCH}{Epoch} 31 | \item{ISDTC}{Date/Time of Collection} 32 | \item{ISDY}{Study Day of Collection} 33 | \item{ISULOQ}{Upper Limit of Quantitation} 34 | } 35 | } 36 | \source{ 37 | Constructed by {admiralvaccine} developers 38 | } 39 | \usage{ 40 | is_vaccine 41 | } 42 | \description{ 43 | An example SDTM IS for vaccine studies 44 | } 45 | \details{ 46 | Immunogenicity Specimen Assessments for Vaccine 47 | 48 | An example SDTM IS for vaccine studies 49 | 50 | Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 51 | \strong{ISTESTCD} \tab \strong{ISTEST} \cr 52 | I0019NT \tab I0019NT Antibody\cr 53 | J0033VN \tab J0033VN Antibody\cr 54 | M0019LN \tab M0019LN Antibody\cr 55 | R0003MA \tab R0003MA Antibody 56 | } 57 | } 58 | \keyword{dataset} 59 | \keyword{vaccine} 60 | -------------------------------------------------------------------------------- /man/rs_onco_irecist.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rs_onco_irecist.R 3 | \docType{data} 4 | \name{rs_onco_irecist} 5 | \alias{rs_onco_irecist} 6 | \title{Disease Response (iRECIST) for Oncology} 7 | \format{ 8 | A data frame with 19 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{RSSEQ}{Sequence Number} 14 | \item{RSLNKGRP}{Link Group ID} 15 | \item{RSTESTCD}{Assessment Short Name} 16 | \item{RSTEST}{Assessment Name} 17 | \item{RSCAT}{Category for Assessment} 18 | \item{RSORRES}{Result or Finding in Original Units} 19 | \item{RSSTRESC}{Character Result/Finding in Std Format} 20 | \item{RSSTAT}{Completion Status} 21 | \item{RSREASND}{Reason Not Done} 22 | \item{RSEVAL}{Evaluator} 23 | \item{RSEVALID}{Evaluator Identifier} 24 | \item{RSACPTFL}{Accepted Record Flag} 25 | \item{VISITNUM}{Visit Number} 26 | \item{VISIT}{Visit Name} 27 | \item{RSDTC}{Date/Time of Assessment} 28 | \item{RSDY}{Study Day of Assessment} 29 | } 30 | } 31 | \source{ 32 | Generated dataset. 33 | } 34 | \usage{ 35 | rs_onco_irecist 36 | } 37 | \description{ 38 | A SDTM RS dataset using iRECIST intended for examples of ADaM dataset creation 39 | } 40 | \details{ 41 | Disease Response (iRECIST) for Oncology 42 | 43 | A SDTM RS dataset using iRECIST intended for examples of ADaM dataset creation 44 | 45 | Contains a set of 6 unique Test Short Names and Test Names: \tabular{ll}{ 46 | \strong{RSTESTCD} \tab \strong{RSTEST} \cr 47 | IRECLIND \tab Last iRECIST Assessment Indicator\cr 48 | NEWLIND \tab New Lesion Indicator \cr 49 | NEWLPROG \tab New Lesion Progression \cr 50 | NTRGRESP \tab Non-target Response \cr 51 | OVRLRESP \tab Overall Response \cr 52 | TRGRESP \tab Target Response 53 | } 54 | } 55 | \author{ 56 | Rohan Thampi 57 | } 58 | \keyword{dataset} 59 | \keyword{oncology} 60 | -------------------------------------------------------------------------------- /man/vs.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/vs.R 3 | \docType{data} 4 | \name{vs} 5 | \alias{vs} 6 | \title{Vital Signs} 7 | \format{ 8 | A data frame with 24 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{VSSEQ}{Sequence Number} 14 | \item{VSTESTCD}{Vital Signs Test Short Name} 15 | \item{VSTEST}{Vital Signs Test Name} 16 | \item{VSPOS}{Vital Signs Position of Subject} 17 | \item{VSORRES}{Result or Finding in Original Units} 18 | \item{VSORRESU}{Original Units} 19 | \item{VSSTRESC}{Character Result/Finding in Std Format} 20 | \item{VSSTRESN}{Numeric Result/Finding in Standard Units} 21 | \item{VSSTRESU}{Standard Units} 22 | \item{VSSTAT}{Completion Status} 23 | \item{VSLOC}{Location of Vital Signs Measurement} 24 | \item{VSBLFL}{Baseline Flag} 25 | \item{VISITNUM}{Visit Number} 26 | \item{VISIT}{Visit Name} 27 | \item{VISITDY}{Planned Study Day of Visit} 28 | \item{VSDTC}{Date/Time of Measurements} 29 | \item{VSDY}{Study Day of Vital Signs} 30 | \item{VSTPT}{Planned Time Point Name} 31 | \item{VSTPTNUM}{Planned Time Point Number} 32 | \item{VSELTM}{Planned Elapsed Time from Time Point Ref} 33 | \item{VSTPTREF}{Time Point Reference} 34 | } 35 | } 36 | \source{ 37 | Generated dataset. 38 | } 39 | \usage{ 40 | vs 41 | } 42 | \description{ 43 | A SDTM VS dataset from the CDISC pilot project 44 | } 45 | \details{ 46 | Vital Signs 47 | 48 | A SDTM VS dataset from the CDISC pilot project 49 | 50 | Contains a set of 6 unique Test Short Names and Test Names: \tabular{ll}{ 51 | \strong{VSTESTCD} \tab \strong{VSTEST} \cr 52 | DIABP \tab Diastolic Blood Pressure\cr 53 | HEIGHT \tab Height \cr 54 | PULSE \tab Pulse Rate \cr 55 | SYSBP \tab Systolic Blood Pressure \cr 56 | TEMP \tab Temperature \cr 57 | WEIGHT \tab Weight 58 | } 59 | } 60 | \keyword{dataset} 61 | \keyword{generic} 62 | -------------------------------------------------------------------------------- /man/tr_onco.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/tr_onco.R 3 | \docType{data} 4 | \name{tr_onco} 5 | \alias{tr_onco} 6 | \title{Tumor Results for Oncology} 7 | \format{ 8 | A data frame with 24 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{TRSEQ}{Sequence Number} 14 | \item{TRGRPID}{Group ID} 15 | \item{TRLNKGRP}{Link Group} 16 | \item{TRLNKID}{Link ID} 17 | \item{TRTESTCD}{Tumor Assessment Short Name} 18 | \item{TRTEST}{Tumor Assessment Test Name} 19 | \item{TRORRES}{Result or Finding in Original Units} 20 | \item{TRORRESU}{Original Units} 21 | \item{TRSTRESC}{Character Result/Finding in Std Format} 22 | \item{TRSTRESN}{Numeric Result/Finding in Standard Units} 23 | \item{TRSTRESU}{Standard Units} 24 | \item{TRSTAT}{Completion Status} 25 | \item{TRREASND}{Reason Tumor Measurement Not Performed} 26 | \item{TRMETHOD}{Method used to Identify the Tumor} 27 | \item{TREVAL}{Evaluator} 28 | \item{TREVALID}{Evaluator Identifier} 29 | \item{TRACPTFL}{Accepted Record Flag} 30 | \item{VISITNUM}{Visit Number} 31 | \item{VISIT}{Visit Name} 32 | \item{TRDTC}{Date/Time of Tumor Measurement} 33 | \item{TRDY}{Study Day of Tumor Measurement} 34 | } 35 | } 36 | \source{ 37 | Generated dataset. 38 | } 39 | \usage{ 40 | tr_onco 41 | } 42 | \description{ 43 | A SDTM TR dataset simulated by Gopi Vegesna 44 | } 45 | \details{ 46 | Tumor Results for Oncology 47 | 48 | A SDTM TR dataset simulated by Gopi Vegesna 49 | 50 | Contains a set of 5 unique Test Short Names and Test Names: \tabular{ll}{ 51 | \strong{TRTESTCD} \tab \strong{TRTEST} \cr 52 | DIAMETER \tab Diameter \cr 53 | LDIAM \tab Longest Diameter \cr 54 | LPERP \tab Longest Perpendicular\cr 55 | SUMDIAM \tab Sum of Diameter \cr 56 | TUMSTATE \tab Tumor State 57 | } 58 | } 59 | \author{ 60 | Gopi Vegesna 61 | } 62 | \keyword{dataset} 63 | \keyword{oncology} 64 | -------------------------------------------------------------------------------- /R/dm_neuro.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Demographic Dataset-neuro 5 | #' 6 | #' A SDTM DM dataset for Alzheimer's disease studies 7 | #' 8 | #' @name dm_neuro 9 | #' @title Demographic Dataset-neuro 10 | #' @keywords dataset neurology 11 | #' @description A SDTM DM dataset for Alzheimer's disease studies 12 | #' @docType data 13 | #' @format A data frame with 26 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{SUBJID}{Subject Identifier for the Study} 19 | #' \item{RFSTDTC}{Subject Reference Start Date/Time} 20 | #' \item{RFENDTC}{Subject Reference End Date/Time} 21 | #' \item{RFXSTDTC}{Date/Time of First Study Treatment} 22 | #' \item{RFXENDTC}{Date/Time of Last Study Treatment} 23 | #' \item{RFICDTC}{Date/Time of Informed Consent} 24 | #' \item{RFPENDTC}{Date/Time of End of Participation} 25 | #' \item{DTHDTC}{Date/Time of Death} 26 | #' \item{DTHFL}{Subject Death Flag} 27 | #' \item{SITEID}{Study Site Identifier} 28 | #' \item{AGE}{Age} 29 | #' \item{BRTHDTC}{Date/Time of Birth} 30 | #' \item{AGEU}{Age Units} 31 | #' \item{SEX}{Sex} 32 | #' \item{RACE}{Race} 33 | #' \item{ETHNIC}{Ethnicity} 34 | #' \item{ARMCD}{Planned Arm Code} 35 | #' \item{ARM}{Description of Planned Arm} 36 | #' \item{ACTARMCD}{Actual Arm Code} 37 | #' \item{ACTARM}{Description of Actual Arm} 38 | #' \item{COUNTRY}{Country} 39 | #' \item{DMDTC}{Date/Time of Collection} 40 | #' \item{DMDY}{Study Day of Collection} 41 | #' \item{ARMNRS}{Reason Arm and/or Actual Arm is Null} 42 | #' } 43 | #' 44 | #' @source Constructed by {admiralneuro} developers 45 | "dm_neuro" 46 | -------------------------------------------------------------------------------- /man/pp.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/pp.R 3 | \docType{data} 4 | \name{pp} 5 | \alias{pp} 6 | \title{Pharmacokinetic Parameters} 7 | \format{ 8 | A data frame with 14 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{PPSEQ}{Sequence Number} 14 | \item{PPTESTCD}{Parameter Short Name} 15 | \item{PPTEST}{Parameter Name} 16 | \item{PPCAT}{Parameter Category} 17 | \item{PPORRES}{Result or Finding in Original Units} 18 | \item{PPORRESU}{Original Units} 19 | \item{PPSTRESC}{Character Result/Finding in Std Format} 20 | \item{PPSTRESN}{Numeric Result/Finding in Standard Units} 21 | \item{PPSTRESU}{Standard Units} 22 | \item{PPSPEC}{Specimen Material Type} 23 | \item{PPRFDTC}{Date/Time of Reference Point} 24 | } 25 | } 26 | \source{ 27 | \href{https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/pp.rda}{Access the source of the Pharmacokinetic Parameters dataset.} 28 | } 29 | \usage{ 30 | pp 31 | } 32 | \description{ 33 | A SDTM PP dataset simulated by Antonio Rodriguez Contesti 34 | } 35 | \details{ 36 | Pharmacokinetic Parameters 37 | 38 | A SDTM PP dataset simulated by Antonio Rodriguez Contesti 39 | 40 | Contains a set of 10 unique Test Short Names and Test Names: \tabular{ll}{ 41 | \strong{PPTESTCD} \tab \strong{PPTEST} \cr 42 | AUCALL \tab AUC All \cr 43 | AUCLST \tab AUC to Last Nonzero Conc \cr 44 | CLST \tab Last Nonzero Conc \cr 45 | CMAX \tab Max Conc \cr 46 | LAMZ \tab Lambda z \cr 47 | LAMZHL \tab Half-Life Lambda z \cr 48 | LAMZNPT \tab Number of Points for Lambda z\cr 49 | RCAMINT \tab Ae \cr 50 | RENALCL \tab CLR \cr 51 | TMAX \tab Time of CMAX 52 | } 53 | } 54 | \author{ 55 | Antonio Rodriguez Contesti 56 | } 57 | \keyword{dataset} 58 | \keyword{generic} 59 | -------------------------------------------------------------------------------- /data-raw/suppce_vaccine.R: -------------------------------------------------------------------------------- 1 | # Dataset: suppce_vaccine 2 | # Description: SUPPCE test SDTM dataset for Vaccine studies 3 | 4 | 5 | # Load libraries ---- 6 | library(tibble) 7 | library(dplyr) 8 | library(purrr) 9 | library(metatools) 10 | 11 | ## Read input data ---- 12 | suppdm_vaccine <- pharmaversesdtm::suppdm_vaccine 13 | 14 | suppce <- tribble( 15 | ~STUDYID, 16 | "ABC" 17 | ) 18 | 19 | vx_suppce <- suppce %>% 20 | mutate( 21 | STUDYID = "ABC", 22 | USUBJID = "ABC-1001", 23 | RDOMAIN = "CE", 24 | IDVAR = "CESEQ", 25 | IDVARVAL = "1", 26 | QNAM = "CEEVAL", 27 | QVAL = "STUDY SUBJECT", 28 | QLABEL = "Evaluator", 29 | QORIG = "ASSIGNED" 30 | ) %>% 31 | add_row( 32 | STUDYID = "ABC", 33 | USUBJID = "ABC-1001", 34 | RDOMAIN = "CE", 35 | IDVAR = "CESEQ", 36 | IDVARVAL = "2", 37 | QNAM = "CEEVAL", 38 | QVAL = "STUDY SUBJECT", 39 | QLABEL = "Evaluator", 40 | QORIG = "ASSIGNED" 41 | ) %>% 42 | add_row( 43 | STUDYID = "ABC", 44 | USUBJID = "ABC-1002", 45 | RDOMAIN = "CE", 46 | IDVAR = "CESEQ", 47 | IDVARVAL = "1", 48 | QNAM = "CEEVAL", 49 | QVAL = "STUDY SUBJECT", 50 | QLABEL = "Evaluator", 51 | QORIG = "ASSIGNED" 52 | ) %>% 53 | add_row( 54 | STUDYID = "ABC", 55 | USUBJID = "ABC-1002", 56 | RDOMAIN = "CE", 57 | IDVAR = "CESEQ", 58 | IDVARVAL = "2", 59 | QNAM = "CEEVAL", 60 | QVAL = "STUDY SUBJECT", 61 | QLABEL = "Evaluator", 62 | QORIG = "ASSIGNED" 63 | ) 64 | 65 | # get common column names 66 | common_cols <- intersect(names(vx_suppce), names(suppdm_vaccine)) 67 | 68 | # assign labels to vx_suppce 69 | walk(common_cols, \(x) attr(vx_suppce[[x]], "label") <<- 70 | attr(suppdm_vaccine[[x]], "label")) 71 | 72 | suppce_vaccine <- vx_suppce 73 | 74 | # Label SUPPCE dataset ---- 75 | attr(suppce_vaccine, "label") <- "Supplemental Qualifiers for Clinical Events" 76 | 77 | # Save dataset ---- 78 | usethis::use_data(suppce_vaccine, overwrite = TRUE) 79 | -------------------------------------------------------------------------------- /R/dm_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Demographics for Vaccine 5 | #' 6 | #' An example SDTM DM dataset for vaccine studies 7 | #' 8 | #' @name dm_vaccine 9 | #' @title Demographics for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM DM dataset for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 28 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{SUBJID}{Subject Identifier for the Study} 19 | #' \item{RFSTDTC}{Subject Reference Start Date/Time} 20 | #' \item{RFENDTC}{Subject Reference End Date/Time} 21 | #' \item{RFXSTDTC}{Date/Time of First Study Treatment} 22 | #' \item{RFXENDTC}{Date/Time of Last Study Treatment} 23 | #' \item{RFICDTC}{Date/Time of Informed Consent} 24 | #' \item{RFPENDTC}{Date/Time of End of Participation} 25 | #' \item{DTHDTC}{Date/Time of Death} 26 | #' \item{DTHFL}{Subject Death Flag} 27 | #' \item{SITEID}{Study Site Identifier} 28 | #' \item{INVID}{Investigator Identifier} 29 | #' \item{INVNAM}{Investigator Name} 30 | #' \item{BRTHDTC}{Date/Time of Birth} 31 | #' \item{AGE}{Age} 32 | #' \item{AGEU}{Age Units} 33 | #' \item{SEX}{Sex} 34 | #' \item{RACE}{Race} 35 | #' \item{ETHNIC}{Ethnicity} 36 | #' \item{ARMCD}{Planned Arm Code} 37 | #' \item{ARM}{Description of Planned Arm} 38 | #' \item{ACTARMCD}{Actual Arm Code} 39 | #' \item{ACTARM}{Description of Actual Arm} 40 | #' \item{COUNTRY}{Country} 41 | #' \item{DMDTC}{Date/Time of Collection} 42 | #' \item{DMDY}{Study Day of Collection} 43 | #' } 44 | #' 45 | #' @source Constructed by {admiralvaccine} developers 46 | "dm_vaccine" 47 | -------------------------------------------------------------------------------- /R/vs_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Vital Signs for Vaccine 5 | #' 6 | #' An example SDTM VS dataset for vaccine studies 7 | #' 8 | #' @name vs_vaccine 9 | #' @title Vital Signs for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM VS dataset for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 23 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{VSSEQ}{Sequence Number} 19 | #' \item{VSLNKID}{Link ID} 20 | #' \item{VSLNKGRP}{Link Group ID} 21 | #' \item{VSTESTCD}{Vital Signs Test Short Name} 22 | #' \item{VSTEST}{Vital Signs Test Name} 23 | #' \item{VSCAT}{Category for Vital Signs} 24 | #' \item{VSSCAT}{Subcategory for Vital Signs} 25 | #' \item{VSORRES}{Result or Finding in Original Units} 26 | #' \item{VSORRESU}{Original Units} 27 | #' \item{VSSTRESC}{Character Result/Finding in Std Format} 28 | #' \item{VSSTRESN}{Numeric Result/Finding in Standard Units} 29 | #' \item{VSSTRESU}{Standard Units} 30 | #' \item{VSEVAL}{Evaluator} 31 | #' \item{VSLOC}{Location of Vital Signs Measurement} 32 | #' \item{EPOCH}{Epoch} 33 | #' \item{VSDTC}{Date/Time of Measurements} 34 | #' \item{VSDY}{Study Day of Vital Signs} 35 | #' \item{VSTPT}{Planned Time Point Name} 36 | #' \item{VSTPTNUM}{Planned Time Point Number} 37 | #' \item{VSTPTREF}{Time Point Reference} 38 | #' } 39 | #' 40 | #' @source Constructed by {admiralvaccine} developers 41 | #' @details Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 42 | #' \strong{VSTESTCD} \tab \strong{VSTEST} \cr 43 | #' TEMP \tab Temperature 44 | #' } 45 | 46 | "vs_vaccine" 47 | -------------------------------------------------------------------------------- /R/dm.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Demography 5 | #' 6 | #' A SDTM DM dataset from the CDISC pilot project 7 | #' 8 | #' @name dm 9 | #' @title Demography 10 | #' @keywords dataset generic 11 | #' @description A SDTM DM dataset from the CDISC pilot project 12 | #' @docType data 13 | #' @format A data frame with 26 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{SUBJID}{Subject Identifier for the Study} 19 | #' \item{RFSTDTC}{Subject Reference Start Date/Time} 20 | #' \item{RFENDTC}{Subject Reference End Date/Time} 21 | #' \item{RFXSTDTC}{Date/Time of First Study Treatment} 22 | #' \item{RFXENDTC}{Date/Time of Last Study Treatment} 23 | #' \item{RFICDTC}{Date/Time of Informed Consent} 24 | #' \item{RFPENDTC}{Date/Time of End of Participation} 25 | #' \item{DTHDTC}{Date/Time of Death} 26 | #' \item{DTHFL}{Subject Death Flag} 27 | #' \item{SITEID}{Study Site Identifier} 28 | #' \item{BRTHDTC}{Date/Time of Birth} 29 | #' \item{AGE}{Age} 30 | #' \item{AGEU}{Age Units} 31 | #' \item{SEX}{Sex} 32 | #' \item{RACE}{Race} 33 | #' \item{ETHNIC}{Ethnicity} 34 | #' \item{ARMCD}{Planned Arm Code} 35 | #' \item{ARM}{Description of Planned Arm} 36 | #' \item{ACTARMCD}{Actual Arm Code} 37 | #' \item{ACTARM}{Description of Actual Arm} 38 | #' \item{COUNTRY}{Country} 39 | #' \item{DMDTC}{Date/Time of Collection} 40 | #' \item{DMDY}{Study Day of Collection} 41 | #' } 42 | #' 43 | #' @source [Access the source of the Demography dataset.](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) 44 | "dm" 45 | -------------------------------------------------------------------------------- /R/tr_onco_recist.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Tumor Results (RECIST 1.1) for Oncology 5 | #' 6 | #' A SDTM TR dataset using RECIST 1.1 intended for examples of ADaM dataset creation 7 | #' 8 | #' @name tr_onco_recist 9 | #' @title Tumor Results (RECIST 1.1) for Oncology 10 | #' @keywords dataset oncology 11 | #' @description A SDTM TR dataset using RECIST 1.1 intended for examples of ADaM dataset creation 12 | #' @docType data 13 | #' @format A data frame with 19 columns: 14 | #' \describe{ 15 | #' \item{DOMAIN}{Domain Abbreviation} 16 | #' \item{STUDYID}{Study Identifier} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{TRGRPID}{Group ID} 19 | #' \item{TRLNKID}{Link ID} 20 | #' \item{TRTESTCD}{Tumor/Lesion Assessment Short Name} 21 | #' \item{TRTEST}{Tumor/Lesion Assessment Test Name} 22 | #' \item{TRORRES}{Result or Finding in Original Units} 23 | #' \item{TRORRESU}{Original Units} 24 | #' \item{TRSTRESC}{Character Result/Finding in Std Format} 25 | #' \item{TRSTRESN}{Numeric Result/Finding in Standard Units} 26 | #' \item{TRSTRESU}{Standard Units} 27 | #' \item{VISITNUM}{Visit Number} 28 | #' \item{VISIT}{Visit Name} 29 | #' \item{TREVAL}{Evaluator} 30 | #' \item{TREVALID}{Evaluator Identifier} 31 | #' \item{TRACPTFL}{Accepted Record Flag} 32 | #' \item{TRDTC}{Date/Time of Tumor/Lesion Measurement} 33 | #' \item{TRSEQ}{Sequence Number} 34 | #' } 35 | #' 36 | #' @source Generated dataset. 37 | #' @author Stefan Bundfuss 38 | #' @details Contains a set of 3 unique Test Short Names and Test Names: \tabular{ll}{ 39 | #' \strong{TRTESTCD} \tab \strong{TRTEST} \cr 40 | #' LDIAM \tab Longest Diameter \cr 41 | #' LPERP \tab Longest Perpendicular\cr 42 | #' TUMSTATE \tab Tumor State 43 | #' } 44 | 45 | "tr_onco_recist" 46 | -------------------------------------------------------------------------------- /data-raw/suppex_vaccine.R: -------------------------------------------------------------------------------- 1 | # Dataset: suppex_vaccine 2 | # Description: SUPPEX SDTM dataset for Vaccine studies 3 | 4 | # Load libraries ---- 5 | library(tibble) 6 | library(dplyr) 7 | library(purrr) 8 | library(metatools) 9 | 10 | # create suppex 11 | ## Read input data ---- 12 | suppdm_vaccine <- pharmaversesdtm::suppdm_vaccine 13 | 14 | suppex <- tribble( 15 | ~STUDYID, 16 | "ABC" 17 | ) 18 | 19 | vx_suppex <- suppex %>% 20 | mutate( 21 | STUDYID = "ABC", 22 | USUBJID = "ABC-1001", 23 | RDOMAIN = "EX", 24 | IDVAR = "EXSEQ", 25 | IDVARVAL = "1", 26 | QNAM = "EXTDV", 27 | QVAL = "N", 28 | QLABEL = "Temporary Delay of Vaccination", 29 | QORIG = "ASSIGNED" 30 | ) %>% 31 | add_row( 32 | STUDYID = "ABC", 33 | USUBJID = "ABC-1001", 34 | RDOMAIN = "EX", 35 | IDVAR = "EXSEQ", 36 | IDVARVAL = "2", 37 | QNAM = "EXTDV", 38 | QVAL = "Y", 39 | QLABEL = "Temporary Delay of Vaccination", 40 | QORIG = "ASSIGNED" 41 | ) %>% 42 | add_row( 43 | STUDYID = "ABC", 44 | USUBJID = "ABC-1002", 45 | RDOMAIN = "EX", 46 | IDVAR = "EXSEQ", 47 | IDVARVAL = "1", 48 | QNAM = "EXTDV", 49 | QVAL = "N", 50 | QLABEL = "Temporary Delay of Vaccination", 51 | QORIG = "ASSIGNED" 52 | ) %>% 53 | add_row( 54 | STUDYID = "ABC", 55 | USUBJID = "ABC-1002", 56 | RDOMAIN = "EX", 57 | IDVAR = "EXSEQ", 58 | IDVARVAL = "2", 59 | QNAM = "EXTDV", 60 | QVAL = "Y", 61 | QLABEL = "Temporary Delay of Vaccination", 62 | QORIG = "ASSIGNED" 63 | ) 64 | 65 | # get common column names 66 | common_cols <- intersect(names(vx_suppex), names(suppdm_vaccine)) 67 | 68 | # assign labels to vx_suppex 69 | walk(common_cols, \(x) attr(vx_suppex[[x]], "label") <<- 70 | attr(suppdm_vaccine[[x]], "label")) 71 | 72 | suppex_vaccine <- vx_suppex 73 | 74 | # Label suppex dataset ---- 75 | attr(suppex_vaccine, "label") <- "Supplemental Qualifiers for Exposure" 76 | 77 | # Save dataset ---- 78 | usethis::use_data(suppex_vaccine, overwrite = TRUE) 79 | -------------------------------------------------------------------------------- /R/pc.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Pharmacokinetic Concentrations 5 | #' 6 | #' A SDTM PC dataset simulated by Antonio Rodriguez Contesti 7 | #' 8 | #' @name pc 9 | #' @title Pharmacokinetic Concentrations 10 | #' @keywords dataset generic 11 | #' @description A SDTM PC dataset simulated by Antonio Rodriguez Contesti 12 | #' @docType data 13 | #' @format A data frame with 20 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{PCSEQ}{Sequence Number} 19 | #' \item{PCTESTCD}{Pharmacokinetic Test Short Name} 20 | #' \item{PCTEST}{Pharmacokinetic Test Name} 21 | #' \item{PCORRES}{Result or Finding in Original Units} 22 | #' \item{PCORRESU}{Original Units} 23 | #' \item{PCSTRESC}{Character Result/Finding in Std Format} 24 | #' \item{PCSTRESN}{Numeric Result/Finding in Standard Units} 25 | #' \item{PCSTRESU}{Standard Units} 26 | #' \item{PCNAM}{Vendor Name} 27 | #' \item{PCSPEC}{Specimen Material Type} 28 | #' \item{PCLLOQ}{Lower Limit of Quantitation} 29 | #' \item{VISIT}{Visit Name} 30 | #' \item{VISITNUM}{Visit Number} 31 | #' \item{PCDTC}{Date/Time of Specimen Collection} 32 | #' \item{PCDY}{Actual Study Day of Specimen Collection} 33 | #' \item{PCTPT}{Planned Time Point Name} 34 | #' \item{PCTPTNUM}{Planned Time Point Number} 35 | #' } 36 | #' 37 | #' @source [Access the source of the Pharmacokinetic Concentrations dataset.](https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/pc.rda) 38 | #' @author Antonio Rodriguez Contesti 39 | #' @details Contains a set of 1 unique Test Short Name and Test Name: \tabular{ll}{ 40 | #' \strong{PCTESTCD} \tab \strong{PCTEST} \cr 41 | #' XAN \tab XANOMELINE 42 | #' } 43 | 44 | "pc" 45 | -------------------------------------------------------------------------------- /data-raw/suppface_vaccine.R: -------------------------------------------------------------------------------- 1 | # Dataset: suppface_vaccine 2 | # Description: SUPPFACE test SDTM dataset for Vaccine studies 3 | 4 | 5 | # Load libraries ---- 6 | library(tibble) 7 | library(dplyr) 8 | library(purrr) 9 | library(metatools) 10 | 11 | ## Read input data ---- 12 | suppdm_vaccine <- pharmaversesdtm::suppdm_vaccine 13 | 14 | suppface <- tribble( 15 | ~STUDYID, 16 | "ABC" 17 | ) 18 | 19 | vx_suppface <- suppface %>% 20 | mutate( 21 | STUDYID = "ABC", 22 | USUBJID = "ABC-1001", 23 | RDOMAIN = "FACE", 24 | IDVAR = "FASEQ", 25 | IDVARVAL = "1", 26 | QNAM = "CLTYP", 27 | QVAL = "DAIRY", 28 | QLABEL = "Collection Type", 29 | QORIG = "Predecessor" 30 | ) %>% 31 | add_row( 32 | STUDYID = "ABC", 33 | USUBJID = "ABC-1001", 34 | RDOMAIN = "FACE", 35 | IDVAR = "FASEQ", 36 | IDVARVAL = "2", 37 | QNAM = "CLTYP", 38 | QVAL = "DAIRY", 39 | QLABEL = "Collection Type", 40 | QORIG = "Predecessor" 41 | ) %>% 42 | add_row( 43 | STUDYID = "ABC", 44 | USUBJID = "ABC-1002", 45 | RDOMAIN = "FACE", 46 | IDVAR = "FASEQ", 47 | IDVARVAL = "1", 48 | QNAM = "CLTYP", 49 | QVAL = "DAIRY", 50 | QLABEL = "Collection Type", 51 | QORIG = "Predecessor" 52 | ) %>% 53 | add_row( 54 | STUDYID = "ABC", 55 | USUBJID = "ABC-1002", 56 | RDOMAIN = "FACE", 57 | IDVAR = "FASEQ", 58 | IDVARVAL = "2", 59 | QNAM = "CLTYP", 60 | QVAL = "DAIRY", 61 | QLABEL = "Collection Type", 62 | QORIG = "Predecessor" 63 | ) 64 | 65 | # get common column names 66 | common_cols <- intersect(names(vx_suppface), names(suppdm_vaccine)) 67 | 68 | # assign labels to vx_suppface 69 | walk(common_cols, \(x) attr(vx_suppface[[x]], "label") <<- 70 | attr(suppdm_vaccine[[x]], "label")) 71 | 72 | suppface_vaccine <- vx_suppface 73 | 74 | # Label SUPPFACE dataset ---- 75 | attr(suppface_vaccine, "label") <- 76 | "Supplemental Qualifiers for Findings About Clinical Events" 77 | 78 | # Save dataset ---- 79 | usethis::use_data(suppface_vaccine, overwrite = TRUE) 80 | -------------------------------------------------------------------------------- /man/vs_peds.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/vs_peds.R 3 | \docType{data} 4 | \name{vs_peds} 5 | \alias{vs_peds} 6 | \title{Vital signs Dataset-pediatrics} 7 | \format{ 8 | A data frame with 26 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{VSSEQ}{Sequence Number} 14 | \item{VSTESTCD}{Vital Signs Test Short Name} 15 | \item{VSTEST}{Vital Signs Test Name} 16 | \item{VSPOS}{Vital Signs Position of Subject} 17 | \item{VSORRES}{Result or Finding in Original Units} 18 | \item{VSORRESU}{Original Units} 19 | \item{VSSTRESC}{Character Result/Finding in Std Format} 20 | \item{VSSTRESN}{Numeric Result/Finding in Standard Units} 21 | \item{VSSTRESU}{Standard Units} 22 | \item{VSSTAT}{Completion Status} 23 | \item{VSLOC}{Location of Vital Signs Measurement} 24 | \item{VSBLFL}{Baseline Flag} 25 | \item{VISITNUM}{Visit Number} 26 | \item{VISIT}{Visit Name} 27 | \item{VISITDY}{Planned Study Day of Visit} 28 | \item{VSDTC}{Date/Time of Measurements} 29 | \item{VSDY}{Study Day of Vital Signs} 30 | \item{VSTPT}{Planned Time Point Name} 31 | \item{VSTPTNUM}{Planned Time Point Number} 32 | \item{VSELTM}{Planned Elapsed Time from Time Point Ref} 33 | \item{VSTPTREF}{Time Point Reference} 34 | \item{VSEVAL}{Evaluator} 35 | \item{EPOCH}{Epoch} 36 | } 37 | } 38 | \source{ 39 | Constructed by {admiralpeds} developers 40 | } 41 | \usage{ 42 | vs_peds 43 | } 44 | \description{ 45 | An updated SDTM VS dataset with anthropometric measurements for pediatric patients 46 | } 47 | \details{ 48 | Vital signs Dataset-pediatrics 49 | 50 | An updated SDTM VS dataset with anthropometric measurements for pediatric patients 51 | 52 | Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 53 | \strong{VSTESTCD} \tab \strong{VSTEST} \cr 54 | BMI \tab BMI \cr 55 | HDCIRC \tab Head Circumference\cr 56 | HEIGHT \tab Height \cr 57 | WEIGHT \tab Weight 58 | } 59 | } 60 | \keyword{dataset} 61 | \keyword{pediatrics} 62 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Type: Package 2 | Package: pharmaversesdtm 3 | Title: SDTM Test Data for the 'Pharmaverse' Family of Packages 4 | Version: 1.3.1.9009 5 | Authors@R: c( 6 | person("Lina", "Patil", , "lina.patil@cytel.com", role = c("aut", "cre")), 7 | person("Stefan", "Bundfuss", role = "aut", 8 | comment = c(ORCID = "0009-0005-0027-1198")), 9 | person("Kristin", "Dahnert", role = "aut"), 10 | person("Fanny", "Gautier", , "fanny.gautier@cytel.com", role = "aut", 11 | comment = c(ORCID = "0009-0004-3581-0131")), 12 | person("Edoardo", "Mancini", , "edoardo.mancini@roche.com", role = "aut", 13 | comment = c(ORCID = "0009-0006-4899-8641")), 14 | person("Tomoyuki", "Namai", role = "aut"), 15 | person("Vinh", "Nguyen", role = "aut"), 16 | person("Vladyslav", "Shuliar", role = "aut", 17 | comment = c(ORCID = "0009-0008-2354-8999")), 18 | person("Cytel Inc.", role = c("cph", "fnd")), 19 | person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")), 20 | person("GlaxoSmithKline LLC", role = c("cph", "fnd")) 21 | ) 22 | Description: A set of Study Data Tabulation Model (SDTM) datasets from the 23 | Clinical Data Interchange Standards Consortium (CDISC) pilot project 24 | used for testing and developing Analysis Data Model (ADaM) datasets 25 | inside the pharmaverse family of packages. SDTM dataset specifications 26 | are described in the CDISC SDTM implementation guide, accessible by 27 | creating a free account on . 28 | License: Apache License (>= 2.0) 29 | URL: https://pharmaverse.github.io/pharmaversesdtm/, 30 | https://github.com/pharmaverse/pharmaversesdtm/ 31 | Depends: 32 | R (>= 3.5.0) 33 | Suggests: 34 | admiraldev (>= 1.2.0), 35 | cli, 36 | covr, 37 | devtools, 38 | knitr, 39 | lintr, 40 | metatools, 41 | pkgdown, 42 | rmarkdown, 43 | roxygen2, 44 | spelling, 45 | testthat, 46 | usethis 47 | Encoding: UTF-8 48 | Language: en-US 49 | LazyData: true 50 | Roxygen: list(markdown = TRUE) 51 | RoxygenNote: 7.3.3 52 | -------------------------------------------------------------------------------- /R/nv_neuro.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Neurological Assessment Dataset-neuro 5 | #' 6 | #' A SDTM NV dataset containing neurological assessments or test results 7 | #' 8 | #' @name nv_neuro 9 | #' @title Neurological Assessment Dataset-neuro 10 | #' @keywords dataset neurology 11 | #' @description A SDTM NV dataset containing neurological assessments or test results 12 | #' @docType data 13 | #' @format A data frame with 21 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{NVSEQ}{Sequence Number} 19 | #' \item{NVLNKID}{Link ID} 20 | #' \item{NVTESTCD}{Short Name of Nervous System Test} 21 | #' \item{NVTEST}{Name of Nervous System Test} 22 | #' \item{NVCAT}{Category for Nervous System Test} 23 | #' \item{NVLOC}{Location Used for the Measurement} 24 | #' \item{NVMETHOD}{Method of Test or Examination} 25 | #' \item{NVNAM}{Vendor Name} 26 | #' \item{NVORRES}{Result or Finding in Original Units} 27 | #' \item{NVORRESU}{Original Units} 28 | #' \item{NVSTRESC}{Character Result/Finding in Std Format} 29 | #' \item{NVSTRESN}{Numeric Result/Finding in Standard Units} 30 | #' \item{NVSTRESU}{Standard Units} 31 | #' \item{VISITNUM}{Visit Number} 32 | #' \item{VISIT}{Visit Name} 33 | #' \item{NVDTC}{Date/Time of Collection} 34 | #' \item{NVDY}{Study Day of Collection} 35 | #' \item{NVLOBXFL}{Last Observation Before Exposure Flag} 36 | #' } 37 | #' 38 | #' @source Constructed by {admiralneuro} developers 39 | #' @details Contains a set of 2 unique Test Short Names and Test Names: \tabular{ll}{ 40 | #' \strong{NVTESTCD} \tab \strong{NVTEST} \cr 41 | #' SUVR \tab Standardized Uptake Value Ratio \cr 42 | #' VR \tab Qualitative Visual Classification 43 | #' } 44 | 45 | "nv_neuro" 46 | -------------------------------------------------------------------------------- /man/mh.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/mh.R 3 | \docType{data} 4 | \name{mh} 5 | \alias{mh} 6 | \title{Medical History} 7 | \format{ 8 | A data frame with 28 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{MHSEQ}{Sequence Number} 14 | \item{MHSPID}{Sponsor-Defined Identifier} 15 | \item{MHTERM}{Reported Term for the Medical History} 16 | \item{MHLLT}{Lowest Level Term} 17 | \item{MHDECOD}{Dictionary-Derived Term} 18 | \item{MHHLT}{High Level Term} 19 | \item{MHHLGT}{High Level Group Term} 20 | \item{MHCAT}{Category for Medical History} 21 | \item{MHBODSYS}{Body System or Organ Class} 22 | \item{MHSEV}{Severity/Intensity} 23 | \item{VISITNUM}{Visit Number} 24 | \item{VISIT}{Visit Name} 25 | \item{VISITDY}{Planned Study Day of Visit} 26 | \item{MHDTC}{Date/Time of History Collection} 27 | \item{MHSTDTC}{Start Date/Time of Medical History Event} 28 | \item{MHDY}{Study Day of History Collection} 29 | \item{MHENDTC}{End Date/Time of Medical History Event} 30 | \item{MHPRESP}{Medical History Event Pre-Specified} 31 | \item{MHOCCUR}{Medical History Occurrence} 32 | \item{MHSTRTPT}{Start Relative to Reference Time Point} 33 | \item{MHENRTPT}{End Relative to Reference Time Point} 34 | \item{MHSTTPT}{Start Reference Time Point} 35 | \item{MHENTPT}{End Reference Time Point} 36 | \item{MHENRF}{End Relative to Reference Period} 37 | \item{MHSTAT}{Completion Status} 38 | } 39 | } 40 | \source{ 41 | \href{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}{Access the source of the Medical History dataset.} 42 | } 43 | \usage{ 44 | mh 45 | } 46 | \description{ 47 | An updated SDTM MH dataset that uses data from the CDISC pilot project 48 | } 49 | \details{ 50 | Medical History 51 | 52 | An updated SDTM MH dataset that uses data from the CDISC pilot project 53 | } 54 | \author{ 55 | Annie Yang 56 | } 57 | \keyword{dataset} 58 | \keyword{generic} 59 | -------------------------------------------------------------------------------- /man/is_ada.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/is_ada.R 3 | \docType{data} 4 | \name{is_ada} 5 | \alias{is_ada} 6 | \title{Immunogenicity Specimen Assessments for ADA} 7 | \format{ 8 | A data frame with 27 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{ISSEQ}{Sequence Number} 14 | \item{ISTESTCD}{Immunogenicity Test/Exam Short Name} 15 | \item{ISTEST}{Immunogenicity Test or Examination Name} 16 | \item{ISBDAGNT}{Binding Agent} 17 | \item{ISCAT}{Category for Immunogenicity Test} 18 | \item{ISORRES}{Results or Findings in Original Units} 19 | \item{ISORRESU}{Original Units} 20 | \item{ISSTRESC}{Character Result/Finding in Std Format} 21 | \item{ISSTRESN}{Numeric Results/Findings in Std. Units} 22 | \item{ISSTRESU}{Standard Units} 23 | \item{ISSTAT}{Completion Status} 24 | \item{ISREASND}{Reason Not Done} 25 | \item{ISNAM}{Vendor Name} 26 | \item{ISSPEC}{Specimen Type} 27 | \item{ISBLFL}{Baseline Flag} 28 | \item{ISLLOQ}{Lower Limit of Quantitation} 29 | \item{VISITNUM}{Visit Number} 30 | \item{VISIT}{Visit Name} 31 | \item{VISITDY}{Planned Study Day of Visit} 32 | \item{EPOCH}{Epoch} 33 | \item{ISDTC}{Date/Time of Collection} 34 | \item{ISDY}{Study Day of Visit/Collection/Exam} 35 | \item{ISTPT}{Planned Time Point Name} 36 | \item{ISTPTNUM}{Planned Time Point Number} 37 | } 38 | } 39 | \source{ 40 | Generated dataset 41 | } 42 | \usage{ 43 | is_ada 44 | } 45 | \description{ 46 | A SDTM IS dataset containing relevant antidrug antibody assessment studies 47 | } 48 | \details{ 49 | Immunogenicity Specimen Assessments for ADA 50 | 51 | A SDTM IS dataset containing relevant antidrug antibody assessment studies 52 | 53 | Contains a set of 2 unique Test Short Names and Test Names: \tabular{ll}{ 54 | \strong{ISTESTCD} \tab \strong{ISTEST} \cr 55 | ADA_BAB \tab Binding Antidrug Antibody \cr 56 | ADA_NAB \tab Neutralizing Binding Antidrug Antibody 57 | } 58 | } 59 | \author{ 60 | Kristin Dahnert 61 | } 62 | \keyword{dataset} 63 | \keyword{generic} 64 | -------------------------------------------------------------------------------- /R/rs_onco.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Disease Response for Oncology 5 | #' 6 | #' A SDTM RS dataset simulated by Gopi Vegesna 7 | #' 8 | #' @name rs_onco 9 | #' @title Disease Response for Oncology 10 | #' @keywords dataset oncology 11 | #' @description A SDTM RS dataset simulated by Gopi Vegesna 12 | #' @docType data 13 | #' @format A data frame with 19 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{RSSEQ}{Sequence Number} 19 | #' \item{RSLNKGRP}{Link Group} 20 | #' \item{RSTESTCD}{Response Assessment Short Name} 21 | #' \item{RSTEST}{Response Assessment Name} 22 | #' \item{RSCAT}{Category for Response Assessment} 23 | #' \item{RSORRES}{Response Assessment Original Result} 24 | #' \item{RSSTRESC}{Response Assessment Result in Std Format} 25 | #' \item{RSSTAT}{Completion Status} 26 | #' \item{RSREASND}{Reason Response Assessment Not Performed} 27 | #' \item{RSEVAL}{Evaluator} 28 | #' \item{RSEVALID}{Evaluator Identifier} 29 | #' \item{RSACPTFL}{Accepted Record Flag} 30 | #' \item{VISITNUM}{Visit Number} 31 | #' \item{VISIT}{Visit Name} 32 | #' \item{RSDTC}{Date/Time of Response Assessment} 33 | #' \item{RSDY}{Study Day of Response Assessment} 34 | #' } 35 | #' 36 | #' @source [Access the source of the Disease Response for Oncology dataset.](https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/tr_onco_recist.rda) 37 | #' @author Gopi Vegesna 38 | #' @details Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 39 | #' \strong{RSTESTCD} \tab \strong{RSTEST} \cr 40 | #' NEWLPROG \tab New Lesion Progression\cr 41 | #' NTRGRESP \tab Non-target Response \cr 42 | #' OVRLRESP \tab Overall Response \cr 43 | #' TRGRESP \tab Target Response 44 | #' } 45 | 46 | "rs_onco" 47 | -------------------------------------------------------------------------------- /R/eg.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Electrocardiogram 5 | #' 6 | #' An example of standard SDTM EG dataset to be used in deriving ADEG dataset 7 | #' 8 | #' @name eg 9 | #' @title Electrocardiogram 10 | #' @keywords dataset generic 11 | #' @description An example of standard SDTM EG dataset to be used in deriving ADEG dataset 12 | #' @docType data 13 | #' @format A data frame with 23 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{EGSEQ}{Sequence Number} 19 | #' \item{EGTESTCD}{ECG Test Short Name} 20 | #' \item{EGTEST}{ECG Test Name} 21 | #' \item{EGORRES}{Result or Finding in Original Units} 22 | #' \item{EGORRESU}{Original Units} 23 | #' \item{EGSTRESC}{Character Result/Finding in Std Format} 24 | #' \item{EGSTRESN}{Numeric Result/Finding in Standard Units} 25 | #' \item{EGSTRESU}{Standard Units} 26 | #' \item{EGSTAT}{Completion Status} 27 | #' \item{EGLOC}{Location of Vital Signs Measurement} 28 | #' \item{EGBLFL}{Baseline Flag} 29 | #' \item{VISITNUM}{Visit Number} 30 | #' \item{VISIT}{Visit Name} 31 | #' \item{VISITDY}{Planned Study Day of Visit} 32 | #' \item{EGDTC}{Date/Time of Measurements} 33 | #' \item{EGDY}{Study Day of Vital Signs} 34 | #' \item{EGTPT}{Planned Time Point Number} 35 | #' \item{EGTPTNUM}{Time Point Number} 36 | #' \item{EGELTM}{Planned Elapsed Time from Time Point Ref} 37 | #' \item{EGTPTREF}{Time Point Reference} 38 | #' } 39 | #' 40 | #' @source Generated dataset. 41 | #' @details Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 42 | #' \strong{EGTESTCD} \tab \strong{EGTEST} \cr 43 | #' ECGINT \tab ECG Interpretation\cr 44 | #' HR \tab Heart Rate \cr 45 | #' QT \tab QT Duration \cr 46 | #' RR \tab RR Duration 47 | #' } 48 | 49 | "eg" 50 | -------------------------------------------------------------------------------- /data-raw/ex_vaccine.R: -------------------------------------------------------------------------------- 1 | # Dataset: ex_vaccine 2 | # Description: EX SDTM dataset for Vaccine studies 3 | 4 | # Load libraries ---- 5 | library(tibble) 6 | library(dplyr) 7 | library(purrr) 8 | library(metatools) 9 | 10 | # create ex 11 | ## Read input data ---- 12 | ex <- pharmaversesdtm::ex 13 | 14 | vx_ex <- tribble( 15 | ~USUBJID, ~EXSEQ, ~EXSTDTC, ~EXENDTC, ~VISITNUM, 16 | "ABC-1001", 1, "2021-11-03T10:50:00", "2021-11-03T10:50:00", 1, 17 | "ABC-1001", 2, "2021-12-30T09:10:00", "2021-12-30T09:10:00", 2, 18 | "ABC-1002", 1, "2021-10-07T12:48:00", "2021-10-07T12:48:00", 1, 19 | "ABC-1002", 2, "2021-12-16T12:41:00", "2021-12-16T12:41:00", 2 20 | ) %>% 21 | mutate( 22 | STUDYID = "ABC", 23 | DOMAIN = "EX", 24 | EXCAT = "INVESTIGATIONAL PRODUCT", 25 | EXDOSU = "SYRINGE", 26 | EXDOSE = 1, 27 | EXDOSFRM = "INJECTION", 28 | EXROUTE = "INTRAMUSCULAR", 29 | VISIT = case_when( 30 | VISITNUM == 1 ~ "VISIT 1", 31 | VISITNUM == 2 ~ "VISIT 2", 32 | TRUE ~ NA_character_ 33 | ), 34 | EPOCH = ifelse(EXSEQ == 1, "VACCINATION 1", "VACCINATION 2"), 35 | EXLNKGRP = EPOCH, 36 | EXTRT = ifelse(EXSEQ == 1, "VACCINE A", "VACCINE B"), 37 | EXLOC = "DELTOID MUSCLE", 38 | EXLAT = "LEFT", 39 | EXLNKID = paste(EXLNKGRP, EXLOC, EXLAT, sep = "-") 40 | ) %>% 41 | select( 42 | STUDYID, DOMAIN, USUBJID, EXSEQ, EXLNKGRP, EXLNKID, EXTRT, EXCAT, 43 | EXDOSE, EXDOSU, EXDOSFRM, EXROUTE, EXLOC, EXLAT, VISITNUM, VISIT, EPOCH, 44 | EXSTDTC, EXENDTC 45 | ) 46 | 47 | # get common column names 48 | common_cols <- intersect(names(vx_ex), names(ex)) 49 | 50 | # assign labels to vx_ex 51 | walk(common_cols, \(x) attr(vx_ex[[x]], "label") <<- attr(ex[[x]], "label")) 52 | 53 | ex_vaccine <- vx_ex %>% 54 | add_labels( 55 | EXLNKID = "Link ID", 56 | EXLNKGRP = "Link Group ID", 57 | EXLOC = "Location of Dose Administration", 58 | EXLAT = "Laterality", 59 | EPOCH = "Epoch", 60 | EXCAT = "Category of Treatment" 61 | ) 62 | 63 | # Label ex dataset ---- 64 | attr(ex_vaccine, "label") <- "Exposure" 65 | 66 | # Save dataset ---- 67 | usethis::use_data(ex_vaccine, overwrite = TRUE) 68 | -------------------------------------------------------------------------------- /R/ce_vaccine.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Clinical Events for Vaccine 5 | #' 6 | #' An example SDTM CE dataset for vaccine studies 7 | #' 8 | #' @name ce_vaccine 9 | #' @title Clinical Events for Vaccine 10 | #' @keywords dataset vaccine 11 | #' @description An example SDTM CE dataset for vaccine studies 12 | #' @docType data 13 | #' @format A data frame with 29 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{CESEQ}{Sequence Number} 19 | #' \item{CELNKID}{Link ID} 20 | #' \item{CELNKGRP}{Link Group ID} 21 | #' \item{CETERM}{Reported Term for the Clinical Event} 22 | #' \item{CEDECOD}{Dictionary-Derived Term} 23 | #' \item{CELAT}{Laterality of Location of Clinical Event} 24 | #' \item{CELOC}{Location of Clinical Event} 25 | #' \item{CECAT}{Category for Clinical Event} 26 | #' \item{CESCAT}{Subcategory for Clinical Event} 27 | #' \item{CEPRESP}{Clinical Event Pre-Specified} 28 | #' \item{CEOCCUR}{Clinical Event Occurrence} 29 | #' \item{CESEV}{Severity/Intensity} 30 | #' \item{CEREL}{Causality} 31 | #' \item{CEOUT}{Outcome of Clinical Event} 32 | #' \item{EPOCH}{Epoch} 33 | #' \item{CEDTC}{Date/Time of Event Collection} 34 | #' \item{CESTDTC}{Start Date/Time of Clinical Event} 35 | #' \item{CEENDTC}{End Date/Time of Clinical Event} 36 | #' \item{CEDUR}{Duration of Clinical Event} 37 | #' \item{CETPT}{Planned Time Point Name} 38 | #' \item{CETPTNUM}{Planned Time Point Number} 39 | #' \item{CETPTREF}{Time Point Reference} 40 | #' \item{CERFTDTC}{Date/Time of Reference Time Point} 41 | #' \item{CEEVINTX}{Evaluation Interval Text} 42 | #' \item{CESTAT}{Completion Status} 43 | #' \item{CEREASND}{Reason Clinical Event Not Collected} 44 | #' } 45 | #' 46 | #' @source Constructed by {admiralvaccine} developers 47 | "ce_vaccine" 48 | -------------------------------------------------------------------------------- /man/oe_ophtha.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/oe_ophtha.R 3 | \docType{data} 4 | \name{oe_ophtha} 5 | \alias{oe_ophtha} 6 | \title{Ophthalmic Examinations for Ophthalmology} 7 | \format{ 8 | A data frame with 25 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{OESEQ}{Sequence Number} 14 | \item{OECAT}{Category for Ophthalmic Test or Exam} 15 | \item{OESCAT}{Subcategory for Ophthalmic Test or Exam} 16 | \item{OEDTC}{Date/Time of Collection} 17 | \item{VISIT}{Visit Name} 18 | \item{VISITNUM}{Visit Number} 19 | \item{VISITDY}{Planned Study Day of Visit} 20 | \item{OESTRESN}{Numeric Result/Finding in Standard Units} 21 | \item{OESTRESC}{Character Result/Finding in Std Format} 22 | \item{OEORRES}{Result or Finding in Original Units} 23 | \item{OETEST}{Name of Ophthalmic Test or Examination} 24 | \item{OETESTCD}{Short Name of Ophthalmic Test or Exam} 25 | \item{OETSTDTL}{Ophthalmic Test or Exam Detail} 26 | \item{OELAT}{Laterality} 27 | \item{OELOC}{Location Used for the Measurement} 28 | \item{OEDY}{Study Day of Visit/Collection/Exam} 29 | \item{OEMETHOD}{Method of Test or Examination} 30 | \item{OEORRESU}{Original Units} 31 | \item{OESTRESU}{Standard Units} 32 | \item{OESTAT}{Completion Status} 33 | \item{OETPT}{Planned Time Point Name} 34 | \item{OETPTNUM}{Planned Time Point Number} 35 | } 36 | } 37 | \source{ 38 | Generated dataset. 39 | } 40 | \usage{ 41 | oe_ophtha 42 | } 43 | \description{ 44 | A SDTM OE dataset simulated by Ophthalmology team 45 | } 46 | \details{ 47 | Ophthalmic Examinations for Ophthalmology 48 | 49 | A SDTM OE dataset simulated by Ophthalmology team 50 | 51 | Contains a set of 4 unique Test Short Names and Test Names: \tabular{ll}{ 52 | \strong{OETESTCD} \tab \strong{OETEST} \cr 53 | CSUBTH \tab Center Subfield Thickness \cr 54 | DRSSR \tab Diabetic Retinopathy Sev Recode Value\cr 55 | IOP \tab Intraocular Pressure \cr 56 | VACSCORE \tab Visual Acuity Score 57 | } 58 | } 59 | \author{ 60 | Gordon Miller 61 | } 62 | \keyword{dataset} 63 | \keyword{ophthalmology} 64 | -------------------------------------------------------------------------------- /man/face_vaccine.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/face_vaccine.R 3 | \docType{data} 4 | \name{face_vaccine} 5 | \alias{face_vaccine} 6 | \title{Findings About Clinical Events for Vaccine} 7 | \format{ 8 | A data frame with 30 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{FASEQ}{Sequence Number} 14 | \item{FALNKGRP}{Link Group ID} 15 | \item{FALAT}{Laterality} 16 | \item{FALNKID}{Link ID} 17 | \item{FALOC}{Location of the Finding About} 18 | \item{FATESTCD}{Findings About Test Short Name} 19 | \item{FATEST}{Findings About Test Name} 20 | \item{FAOBJ}{Object of the Observation} 21 | \item{FACAT}{Category for Findings About} 22 | \item{FASCAT}{Subcategory for Findings About} 23 | \item{FAEVAL}{Evaluator} 24 | \item{FAORRES}{Result or Finding in Original Units} 25 | \item{FAORRESU}{Original Units} 26 | \item{EPOCH}{Epoch} 27 | \item{FADTC}{Date/Time of Collection} 28 | \item{FADY}{Study Day of Collection} 29 | \item{FATPT}{Planned Time Point Name} 30 | \item{FATPTNUM}{Planned Time Point Number} 31 | \item{FATPTREF}{Time Point Reference} 32 | \item{FARFTDTC}{Date/Time of Reference Time Point} 33 | \item{FAEVLINT}{Evaluation Interval} 34 | \item{FAEVINTX}{Evaluation Interval Text} 35 | \item{FASTAT}{Completion Status} 36 | \item{FAREASND}{Reason Not Performed} 37 | \item{FASTRESC}{Character Result/Finding in Std Format} 38 | \item{FASTRESN}{Numeric Result/Finding in Standard Units} 39 | \item{FASTRESU}{Standard Units} 40 | } 41 | } 42 | \source{ 43 | Constructed by {admiralvaccine} developers 44 | } 45 | \usage{ 46 | face_vaccine 47 | } 48 | \description{ 49 | An example SDTM FACE for vaccine studies 50 | } 51 | \details{ 52 | Findings About Clinical Events for Vaccine 53 | 54 | An example SDTM FACE for vaccine studies 55 | 56 | Contains a set of 3 unique Test Short Names and Test Names: \tabular{ll}{ 57 | \strong{FATESTCD} \tab \strong{FATEST} \cr 58 | DIAMETER \tab Diameter \cr 59 | OCCUR \tab Occurrence Indicator\cr 60 | SEV \tab Severity/Intensity 61 | } 62 | } 63 | \keyword{dataset} 64 | \keyword{vaccine} 65 | -------------------------------------------------------------------------------- /data-raw/dm_neuro.R: -------------------------------------------------------------------------------- 1 | # Dataset: dm_neuro 2 | # Description: Create DM test SDTM dataset for Alzheimer's Disease (Neuro) 3 | 4 | # Load libraries ---- 5 | library(admiral) 6 | library(dplyr) 7 | library(lubridate) 8 | 9 | # Read input test data from pharmaversesdtm ---- 10 | dm <- pharmaversesdtm::dm 11 | 12 | # Convert blank to NA ---- 13 | dm <- convert_blanks_to_na(dm) 14 | 15 | # Subset to 15 patients 16 | dm_neuro <- dm %>% 17 | filter(USUBJID %in% c( 18 | "01-701-1015", "01-701-1023", "01-701-1028", "01-701-1034", 19 | "01-701-1146", "01-701-1153", "01-701-1181", "01-701-1234", 20 | "01-701-1275", "01-701-1302", "01-701-1345", "01-701-1360", 21 | "01-701-1383", "01-701-1392", "01-714-1288" 22 | )) 23 | 24 | # Create a vector of USUBJID values to modify 25 | usubjid_to_modify <- c( 26 | "01-701-1345", "01-714-1288", "01-701-1028", 27 | "01-701-1181", "01-701-1360" 28 | ) 29 | 30 | # Store the labels before modifying 31 | var_labels <- lapply(dm_neuro, function(x) attr(x, "label")) 32 | 33 | # Modify the dataset 34 | dm_neuro <- dm_neuro %>% 35 | mutate( 36 | across(c(ARMCD, ARM, ACTARMCD, ACTARM, RFXSTDTC, RFXENDTC), 37 | ~ if_else(USUBJID %in% usubjid_to_modify, NA_character_, .), 38 | .names = "{.col}" 39 | ), 40 | ARMNRS = case_when( 41 | USUBJID %in% usubjid_to_modify ~ "Observational Study", 42 | TRUE ~ NA_character_ 43 | ), 44 | 45 | # Convert RFSDTC from char to date, -2 days, and convert back to char 46 | RFICDTC = if_else( 47 | !is.na(RFSTDTC), # Check if RFSDTC is not NA 48 | as.character(as.Date(RFSTDTC, format = "%Y-%m-%d") - days(2)), 49 | NA_character_ # Return NA if RFSDTC is NA 50 | ) 51 | ) 52 | 53 | # Restore the labels after modification 54 | for (col in names(var_labels)) { 55 | attr(dm_neuro[[col]], "label") <- var_labels[[col]] 56 | } 57 | 58 | # Assign the label for ARMNRS 59 | attr(dm_neuro$ARMNRS, "label") <- "Reason Arm and/or Actual Arm is Null" 60 | 61 | # Label dataset ---- 62 | attr(dm_neuro, "label") <- "Demographics" 63 | attr(dm_neuro, "variable.labels") <- var_labels 64 | 65 | # Save dataset ---- 66 | usethis::use_data(dm_neuro, overwrite = TRUE) 67 | -------------------------------------------------------------------------------- /R/rs_onco_irecist.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Disease Response (iRECIST) for Oncology 5 | #' 6 | #' A SDTM RS dataset using iRECIST intended for examples of ADaM dataset creation 7 | #' 8 | #' @name rs_onco_irecist 9 | #' @title Disease Response (iRECIST) for Oncology 10 | #' @keywords dataset oncology 11 | #' @description A SDTM RS dataset using iRECIST intended for examples of ADaM dataset creation 12 | #' @docType data 13 | #' @format A data frame with 19 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{RSSEQ}{Sequence Number} 19 | #' \item{RSLNKGRP}{Link Group ID} 20 | #' \item{RSTESTCD}{Assessment Short Name} 21 | #' \item{RSTEST}{Assessment Name} 22 | #' \item{RSCAT}{Category for Assessment} 23 | #' \item{RSORRES}{Result or Finding in Original Units} 24 | #' \item{RSSTRESC}{Character Result/Finding in Std Format} 25 | #' \item{RSSTAT}{Completion Status} 26 | #' \item{RSREASND}{Reason Not Done} 27 | #' \item{RSEVAL}{Evaluator} 28 | #' \item{RSEVALID}{Evaluator Identifier} 29 | #' \item{RSACPTFL}{Accepted Record Flag} 30 | #' \item{VISITNUM}{Visit Number} 31 | #' \item{VISIT}{Visit Name} 32 | #' \item{RSDTC}{Date/Time of Assessment} 33 | #' \item{RSDY}{Study Day of Assessment} 34 | #' } 35 | #' 36 | #' @source Generated dataset. 37 | #' @author Rohan Thampi 38 | #' @details Contains a set of 6 unique Test Short Names and Test Names: \tabular{ll}{ 39 | #' \strong{RSTESTCD} \tab \strong{RSTEST} \cr 40 | #' IRECLIND \tab Last iRECIST Assessment Indicator\cr 41 | #' NEWLIND \tab New Lesion Indicator \cr 42 | #' NEWLPROG \tab New Lesion Progression \cr 43 | #' NTRGRESP \tab Non-target Response \cr 44 | #' OVRLRESP \tab Overall Response \cr 45 | #' TRGRESP \tab Target Response 46 | #' } 47 | 48 | "rs_onco_irecist" 49 | -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- 1 | url: https://pharmaverse.github.io/pharmaversesdtm 2 | 3 | template: 4 | bootstrap: 5 5 | params: 6 | bootswatch: flatly 7 | repo: 8 | url: 9 | home: https://github.com/pharmaverse/pharmaversesdtm 10 | source: https://github.com/pharmaverse/pharmaversesdtm/blob/main/ 11 | issue: https://github.com/pharmaverse/pharmaversesdtm/issues/ 12 | user: https://github.com/ 13 | news: 14 | cran_dates: true 15 | 16 | development: 17 | mode: auto 18 | 19 | authors: 20 | footer: 21 | roles: [aut, cre] 22 | text: "Developed by Cytel Inc., F. Hoffmann-La Roche AG, GlaxoSmithKline LLC, " 23 | sidebar: 24 | roles: [aut, fnd] 25 | Cytel Inc.: 26 | html: "Cytel logo" 27 | href: https://www.cytel.com/ 28 | F. Hoffmann-La Roche AG: 29 | html: "Roche logo" 30 | href: https://www.roche.com/ 31 | GlaxoSmithKline LLC: 32 | html: "GSK logo" 33 | href: https://gsk.com/ 34 | 35 | navbar: 36 | structure: 37 | left: [reference, news] 38 | components: 39 | reference: 40 | text: Reference 41 | href: reference/index.html 42 | 43 | reference: 44 | - title: "Generic Datasets" 45 | contents: 46 | - has_keyword("generic") 47 | 48 | - title: "Metabolism Datasets" 49 | contents: 50 | - has_keyword("metabolic") 51 | 52 | - title: "Neurology Datasets" 53 | contents: 54 | - has_keyword("neurology") 55 | 56 | - title: "Oncology Datasets" 57 | contents: 58 | - has_keyword("oncology") 59 | 60 | - title: "Ophthalmology Datasets" 61 | contents: 62 | - has_keyword("ophthalmology") 63 | 64 | - title: "Pediatrics Datasets" 65 | contents: 66 | - has_keyword("pediatrics") 67 | 68 | - title: "Vaccine Datasets" 69 | contents: 70 | - has_keyword("vaccine") 71 | 72 | - title: "Functions" 73 | desc: "List of all available functions." 74 | contents: 75 | - get_terms 76 | -------------------------------------------------------------------------------- /data-raw/dm_vaccine.R: -------------------------------------------------------------------------------- 1 | # Dataset: dm_vaccine 2 | # Description: DM SDTM dataset for Vaccine studies 3 | 4 | 5 | # Load libraries ---- 6 | library(tibble) 7 | library(dplyr) 8 | library(purrr) 9 | library(metatools) 10 | 11 | # create dm ---- 12 | ## Read input data ---- 13 | dm <- pharmaversesdtm::dm 14 | 15 | vx_dm <- tribble( 16 | ~USUBJID, ~SUBJID, ~RFSTDTC, ~RFENDTC, ~RFXSTDTC, ~RFXENDTC, ~RFICDTC, ~RFPENDTC, ~SITEID, ~INVID, 17 | ~INVNAM, ~BRTHDTC, ~AGE, ~AGEU, ~SEX, ~RACE, ~ETHNIC, 18 | "ABC-1001", "1001", "2021-11-03T10:50:00", "2022-04-27", "2021-11-03T10:50:00", 19 | "2021-12-30T09:10:00", "2021-10-28", "2022-04-27", 1001, 1328, "Potter, Harry", "1947-09-21", 74, 20 | "YEARS", "F", "WHITE", "NOT HISPANIC OR LATINO", 21 | "ABC-1002", "1002", "2021-10-07T12:48:00", "2022-06-14", "2021-10-07T12:48:00", 22 | "2021-12-16T12:41:00", "2021-09-22", "2022-06-14", 1002, 1212, "Gomez, Selena", "1951-07-13", 70, 23 | "YEARS", "F", "BLACK OR AFRICAN AMERICAN", "HISPANIC OR LATINO" 24 | ) %>% 25 | mutate( 26 | STUDYID = "ABC", 27 | DOMAIN = "DM", 28 | DTHDTC = NA_character_, 29 | DTHFL = NA_character_, 30 | ARMCD = "VAXAB", 31 | ARM = "VACCINE A VACCINE B", 32 | ACTARMCD = "VAXAB", 33 | ACTARM = "VACCINE A VACCINE B", 34 | COUNTRY = "USA", 35 | DMDTC = NA_character_, 36 | DMDY = NA_integer_ 37 | ) %>% 38 | # ordering the variables 39 | select( 40 | STUDYID, DOMAIN, USUBJID, SUBJID, RFSTDTC, RFENDTC, RFXSTDTC, RFXENDTC, 41 | RFICDTC, RFPENDTC, DTHDTC, DTHFL, SITEID, INVID, INVNAM, BRTHDTC, AGE, AGEU, 42 | SEX, RACE, ETHNIC, ARMCD, ARM, ACTARMCD, ACTARM, COUNTRY, DMDTC, DMDY 43 | ) 44 | 45 | # get common column names 46 | common_cols <- intersect(names(vx_dm), names(dm)) 47 | 48 | # assign labels to vx_dm 49 | walk(common_cols, \(x) attr(vx_dm[[x]], "label") <<- attr(dm[[x]], "label")) 50 | 51 | dm_vaccine <- vx_dm %>% 52 | add_labels( 53 | INVID = "Investigator Identifier", 54 | INVNAM = "Investigator Name", 55 | BRTHDTC = "Date/Time of Birth" 56 | ) 57 | 58 | # Label dm dataset ---- 59 | attr(dm_vaccine, "label") <- "Demographics" 60 | 61 | # Save dataset ---- 62 | usethis::use_data(dm_vaccine, overwrite = TRUE) 63 | -------------------------------------------------------------------------------- /man/vs_metabolic.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/vs_metabolic.R 3 | \docType{data} 4 | \name{vs_metabolic} 5 | \alias{vs_metabolic} 6 | \title{Vital signs Dataset-metabolic} 7 | \format{ 8 | A data frame with 24 columns: 9 | \describe{ 10 | \item{STUDYID}{Study Identifier} 11 | \item{DOMAIN}{Domain Abbreviation} 12 | \item{USUBJID}{Unique Subject Identifier} 13 | \item{VSSEQ}{Sequence Number} 14 | \item{VSTESTCD}{Vital Signs Test Short Name} 15 | \item{VSTEST}{Vital Signs Test Name} 16 | \item{VSPOS}{Vital Signs Position of Subject} 17 | \item{VSORRES}{Result or Finding in Original Units} 18 | \item{VSORRESU}{Original Units} 19 | \item{VSSTRESC}{Character Result/Finding in Std Format} 20 | \item{VSSTRESN}{Numeric Result/Finding in Standard Units} 21 | \item{VSSTRESU}{Standard Units} 22 | \item{VSSTAT}{Completion Status} 23 | \item{VSLOC}{Location of Vital Signs Measurement} 24 | \item{VSBLFL}{Baseline Flag} 25 | \item{VISITNUM}{Visit Number} 26 | \item{VISIT}{Visit Name} 27 | \item{VISITDY}{Planned Study Day of Visit} 28 | \item{VSDTC}{Date/Time of Measurements} 29 | \item{VSDY}{Study Day of Vital Signs} 30 | \item{VSTPT}{Planned Time Point Name} 31 | \item{VSTPTNUM}{Planned Time Point Number} 32 | \item{VSELTM}{Planned Elapsed Time from Time Point Ref} 33 | \item{VSTPTREF}{Time Point Reference} 34 | } 35 | } 36 | \source{ 37 | Constructed by {admiralmetabolic} developers 38 | } 39 | \usage{ 40 | vs_metabolic 41 | } 42 | \description{ 43 | A SDTM VS dataset for metabolic studies 44 | } 45 | \details{ 46 | Vital signs Dataset-metabolic 47 | 48 | A SDTM VS dataset for metabolic studies 49 | 50 | Contains a set of 9 unique Test Short Names and Test Names: \tabular{ll}{ 51 | \strong{VSTESTCD} \tab \strong{VSTEST} \cr 52 | BMI \tab Body Mass Index \cr 53 | DIABP \tab Diastolic Blood Pressure\cr 54 | HEIGHT \tab Height \cr 55 | HIPCIR \tab Hip Circumference \cr 56 | PULSE \tab Pulse Rate \cr 57 | SYSBP \tab Systolic Blood Pressure \cr 58 | TEMP \tab Temperature \cr 59 | WEIGHT \tab Weight \cr 60 | WSTCIR \tab Waist Circumference 61 | } 62 | } 63 | \keyword{dataset} 64 | \keyword{metabolic} 65 | -------------------------------------------------------------------------------- /R/pp.R: -------------------------------------------------------------------------------- 1 | # This file is automatically generated by data-raw/create_sdtms_data.R. 2 | # For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R. 3 | # Manual edits are not recommended, as changes may be overwritten. 4 | #' Pharmacokinetic Parameters 5 | #' 6 | #' A SDTM PP dataset simulated by Antonio Rodriguez Contesti 7 | #' 8 | #' @name pp 9 | #' @title Pharmacokinetic Parameters 10 | #' @keywords dataset generic 11 | #' @description A SDTM PP dataset simulated by Antonio Rodriguez Contesti 12 | #' @docType data 13 | #' @format A data frame with 14 columns: 14 | #' \describe{ 15 | #' \item{STUDYID}{Study Identifier} 16 | #' \item{DOMAIN}{Domain Abbreviation} 17 | #' \item{USUBJID}{Unique Subject Identifier} 18 | #' \item{PPSEQ}{Sequence Number} 19 | #' \item{PPTESTCD}{Parameter Short Name} 20 | #' \item{PPTEST}{Parameter Name} 21 | #' \item{PPCAT}{Parameter Category} 22 | #' \item{PPORRES}{Result or Finding in Original Units} 23 | #' \item{PPORRESU}{Original Units} 24 | #' \item{PPSTRESC}{Character Result/Finding in Std Format} 25 | #' \item{PPSTRESN}{Numeric Result/Finding in Standard Units} 26 | #' \item{PPSTRESU}{Standard Units} 27 | #' \item{PPSPEC}{Specimen Material Type} 28 | #' \item{PPRFDTC}{Date/Time of Reference Point} 29 | #' } 30 | #' 31 | #' @source [Access the source of the Pharmacokinetic Parameters dataset.](https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/pp.rda) 32 | #' @author Antonio Rodriguez Contesti 33 | #' @details Contains a set of 10 unique Test Short Names and Test Names: \tabular{ll}{ 34 | #' \strong{PPTESTCD} \tab \strong{PPTEST} \cr 35 | #' AUCALL \tab AUC All \cr 36 | #' AUCLST \tab AUC to Last Nonzero Conc \cr 37 | #' CLST \tab Last Nonzero Conc \cr 38 | #' CMAX \tab Max Conc \cr 39 | #' LAMZ \tab Lambda z \cr 40 | #' LAMZHL \tab Half-Life Lambda z \cr 41 | #' LAMZNPT \tab Number of Points for Lambda z\cr 42 | #' RCAMINT \tab Ae \cr 43 | #' RENALCL \tab CLR \cr 44 | #' TMAX \tab Time of CMAX 45 | #' } 46 | 47 | "pp" 48 | --------------------------------------------------------------------------------