generated from pharmaverse/admiraltemplate
-
Notifications
You must be signed in to change notification settings - Fork 3
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
93 changed files
with
316,450 additions
and
21 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,15 +1,48 @@ | ||
| # Set renv profile base on R version. | ||
| if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) { | ||
| renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") | ||
| if (file.exists("./renv/profile")) { | ||
| message("Using renv profile from `renv/profile` file.") | ||
| } else if (renv_profile %in% c("4.1", "4.2", "4.3")) { | ||
| message("Set renv profile to `", renv_profile, "`") | ||
| Sys.setenv("RENV_PROFILE" = renv_profile) | ||
| .get_dependencies <- function(project_dir) { | ||
|
|
||
| admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE) | ||
| adm_dev_suggests <- if(length(admdev_loc) != 0) { | ||
| renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests")) | ||
| } else { | ||
| data.frame(Packages = character(0)) | ||
| } | ||
| suggests_packages <- renv:::renv_dependencies_discover_description(project_dir, fields = "Suggests") | ||
|
|
||
| packages <- names( | ||
| renv:::renv_package_dependencies( | ||
| unique(c( | ||
| project_dir, | ||
| adm_dev_suggests[["Package"]], | ||
| suggests_packages[["Package"]], | ||
| c("staged.dependencies", "renv", "styler") | ||
| )) | ||
| ) | ||
| ) | ||
| packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "pharmaversesdtm", getwd()))] | ||
| } | ||
|
|
||
| options(renv.snapshot.filter = .get_dependencies) | ||
|
|
||
| .renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") | ||
| if (!file.exists("./renv/profile")) { | ||
| if (.renv_profile %in% c("4.1", "4.2", "4.3")) { | ||
| message("Set renv profile to `", .renv_profile, "`") | ||
| Sys.setenv("RENV_PROFILE" = .renv_profile) | ||
| } else { | ||
| message("This repository do not contains the renv profile for your R version.") | ||
| } | ||
| source("renv/activate.R") | ||
| } else { | ||
| options(repos = c(CRAN = "https://cran.rstudio.com")) | ||
| message( | ||
| "Using renv profile from `renv/profile` file.\n", | ||
| "The `", readLines("./renv/profile"), "` profile will be used." | ||
| ) | ||
| } | ||
|
|
||
| if (Sys.getenv("GITHUB_ACTIONS") != "") { | ||
| options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest")) | ||
| Sys.setenv("RENV_AUTOLOADER_ENABLED" = FALSE) | ||
| } | ||
| Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE) | ||
| Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE) | ||
| source("renv/activate.R") |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| #' Dataset adae | ||
| #' | ||
| #' adae dataset | ||
| #' | ||
| #' @name adae | ||
| #' @docType data | ||
| #' @format A data frame with 101 columns: | ||
| #' \describe{ | ||
| #' \item{ STUDYID }{STUDYID} | ||
| #' \item{ DOMAIN }{DOMAIN} | ||
| #' \item{ USUBJID }{USUBJID} | ||
| #' \item{ AESEQ }{AESEQ} | ||
| #' \item{ AESPID }{AESPID} | ||
| #' \item{ AETERM }{AETERM} | ||
| #' \item{ AELLT }{AELLT} | ||
| #' \item{ AELLTCD }{AELLTCD} | ||
| #' \item{ AEDECOD }{AEDECOD} | ||
| #' \item{ AEPTCD }{AEPTCD} | ||
| #' \item{ AEHLT }{AEHLT} | ||
| #' \item{ AEHLTCD }{AEHLTCD} | ||
| #' \item{ AEHLGT }{AEHLGT} | ||
| #' \item{ AEHLGTCD }{AEHLGTCD} | ||
| #' \item{ AEBODSYS }{AEBODSYS} | ||
| #' \item{ AEBDSYCD }{AEBDSYCD} | ||
| #' \item{ AESOC }{AESOC} | ||
| #' \item{ AESOCCD }{AESOCCD} | ||
| #' \item{ AESEV }{AESEV} | ||
| #' \item{ AESER }{AESER} | ||
| #' \item{ AEACN }{AEACN} | ||
| #' \item{ AEREL }{AEREL} | ||
| #' \item{ AEOUT }{AEOUT} | ||
| #' \item{ AESCAN }{AESCAN} | ||
| #' \item{ AESCONG }{AESCONG} | ||
| #' \item{ AESDISAB }{AESDISAB} | ||
| #' \item{ AESDTH }{AESDTH} | ||
| #' \item{ AESHOSP }{AESHOSP} | ||
| #' \item{ AESLIFE }{AESLIFE} | ||
| #' \item{ AESOD }{AESOD} | ||
| #' \item{ AEDTC }{AEDTC} | ||
| #' \item{ AESTDTC }{AESTDTC} | ||
| #' \item{ AEENDTC }{AEENDTC} | ||
| #' \item{ AESTDY }{AESTDY} | ||
| #' \item{ AEENDY }{AEENDY} | ||
| #' \item{ TRTSDT }{TRTSDT} | ||
| #' \item{ TRTEDT }{TRTEDT} | ||
| #' \item{ DTHDT }{DTHDT} | ||
| #' \item{ EOSDT }{EOSDT} | ||
| #' \item{ ASTDTM }{ASTDTM} | ||
| #' \item{ ASTDTF }{ASTDTF} | ||
| #' \item{ ASTTMF }{ASTTMF} | ||
| #' \item{ AENDTM }{AENDTM} | ||
| #' \item{ AENDTF }{AENDTF} | ||
| #' \item{ AENTMF }{AENTMF} | ||
| #' \item{ ASTDT }{ASTDT} | ||
| #' \item{ AENDT }{AENDT} | ||
| #' \item{ ASTDY }{ASTDY} | ||
| #' \item{ AENDY }{AENDY} | ||
| #' \item{ ADURN }{ADURN} | ||
| #' \item{ ADURU }{ADURU} | ||
| #' \item{ LDOSEDTM }{LDOSEDTM} | ||
| #' \item{ ASEV }{ASEV} | ||
| #' \item{ AREL }{AREL} | ||
| #' \item{ TRTEMFL }{TRTEMFL} | ||
| #' \item{ ASEVN }{ASEVN} | ||
| #' \item{ AOCCIFL }{AOCCIFL} | ||
| #' \item{ SUBJID }{SUBJID} | ||
| #' \item{ RFSTDTC }{RFSTDTC} | ||
| #' \item{ RFENDTC }{RFENDTC} | ||
| #' \item{ RFXSTDTC }{RFXSTDTC} | ||
| #' \item{ RFXENDTC }{RFXENDTC} | ||
| #' \item{ RFICDTC }{RFICDTC} | ||
| #' \item{ RFPENDTC }{RFPENDTC} | ||
| #' \item{ DTHDTC }{DTHDTC} | ||
| #' \item{ DTHFL }{DTHFL} | ||
| #' \item{ SITEID }{SITEID} | ||
| #' \item{ AGE }{AGE} | ||
| #' \item{ AGEU }{AGEU} | ||
| #' \item{ SEX }{SEX} | ||
| #' \item{ RACE }{RACE} | ||
| #' \item{ ETHNIC }{ETHNIC} | ||
| #' \item{ ARMCD }{ARMCD} | ||
| #' \item{ ARM }{ARM} | ||
| #' \item{ ACTARMCD }{ACTARMCD} | ||
| #' \item{ ACTARM }{ACTARM} | ||
| #' \item{ COUNTRY }{COUNTRY} | ||
| #' \item{ DMDTC }{DMDTC} | ||
| #' \item{ DMDY }{DMDY} | ||
| #' \item{ TRT01P }{TRT01P} | ||
| #' \item{ TRT01A }{TRT01A} | ||
| #' \item{ TRTSDTM }{TRTSDTM} | ||
| #' \item{ TRTSTMF }{TRTSTMF} | ||
| #' \item{ TRTEDTM }{TRTEDTM} | ||
| #' \item{ TRTETMF }{TRTETMF} | ||
| #' \item{ TRTDURD }{TRTDURD} | ||
| #' \item{ SCRFDT }{SCRFDT} | ||
| #' \item{ EOSSTT }{EOSSTT} | ||
| #' \item{ FRVDT }{FRVDT} | ||
| #' \item{ RANDDT }{RANDDT} | ||
| #' \item{ DTHADY }{DTHADY} | ||
| #' \item{ LDDTHELD }{LDDTHELD} | ||
| #' \item{ LSTALVDT }{LSTALVDT} | ||
| #' \item{ AGEGR1 }{AGEGR1} | ||
| #' \item{ SAFFL }{SAFFL} | ||
| #' \item{ RACEGR1 }{RACEGR1} | ||
| #' \item{ REGION1 }{REGION1} | ||
| #' \item{ LDDTHGR1 }{LDDTHGR1} | ||
| #' \item{ DTH30FL }{DTH30FL} | ||
| #' \item{ DTHA30FL }{DTHA30FL} | ||
| #' \item{ DTHB30FL }{DTHB30FL} | ||
| #' } | ||
| #' | ||
| #' @source Generated from pharmaverse/admiral. | ||
| #' @references None | ||
| #' | ||
| #' @examples | ||
| #' data("adae") | ||
| "adae" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,132 @@ | ||
| #' Dataset adbcva_ophtha | ||
| #' | ||
| #' adbcva_ophtha dataset | ||
| #' | ||
| #' @name adbcva_ophtha | ||
| #' @docType data | ||
| #' @format A data frame with 116 columns: | ||
| #' \describe{ | ||
| #' \item{ STUDYID }{STUDYID} | ||
| #' \item{ DOMAIN }{DOMAIN} | ||
| #' \item{ USUBJID }{USUBJID} | ||
| #' \item{ OESEQ }{OESEQ} | ||
| #' \item{ OECAT }{OECAT} | ||
| #' \item{ OESCAT }{OESCAT} | ||
| #' \item{ OEDTC }{OEDTC} | ||
| #' \item{ VISIT }{VISIT} | ||
| #' \item{ VISITNUM }{VISITNUM} | ||
| #' \item{ VISITDY }{VISITDY} | ||
| #' \item{ OESTRESN }{OESTRESN} | ||
| #' \item{ OESTRESC }{OESTRESC} | ||
| #' \item{ OEORRES }{OEORRES} | ||
| #' \item{ OETEST }{OETEST} | ||
| #' \item{ OETESTCD }{OETESTCD} | ||
| #' \item{ OETSTDTL }{OETSTDTL} | ||
| #' \item{ OELAT }{OELAT} | ||
| #' \item{ OELOC }{OELOC} | ||
| #' \item{ OEDY }{OEDY} | ||
| #' \item{ OEMETHOD }{OEMETHOD} | ||
| #' \item{ OEORRESU }{OEORRESU} | ||
| #' \item{ OESTRESU }{OESTRESU} | ||
| #' \item{ OESTAT }{OESTAT} | ||
| #' \item{ OETPT }{OETPT} | ||
| #' \item{ OETPTNUM }{OETPTNUM} | ||
| #' \item{ TRTSDT }{TRTSDT} | ||
| #' \item{ TRTEDT }{TRTEDT} | ||
| #' \item{ TRT01A }{TRT01A} | ||
| #' \item{ TRT01P }{TRT01P} | ||
| #' \item{ STUDYEYE }{STUDYEYE} | ||
| #' \item{ AVAL }{AVAL} | ||
| #' \item{ AVALU }{AVALU} | ||
| #' \item{ DTYPE }{DTYPE} | ||
| #' \item{ AFEYE }{AFEYE} | ||
| #' \item{ PARAM }{PARAM} | ||
| #' \item{ PARAMCD }{PARAMCD} | ||
| #' \item{ AVALC }{AVALC} | ||
| #' \item{ ADT }{ADT} | ||
| #' \item{ ADY }{ADY} | ||
| #' \item{ ATPTN }{ATPTN} | ||
| #' \item{ ATPT }{ATPT} | ||
| #' \item{ AVISIT }{AVISIT} | ||
| #' \item{ AVISITN }{AVISITN} | ||
| #' \item{ BASETYPE }{BASETYPE} | ||
| #' \item{ ONTRTFL }{ONTRTFL} | ||
| #' \item{ ABLFL }{ABLFL} | ||
| #' \item{ ANL01FL }{ANL01FL} | ||
| #' \item{ ANL02FL }{ANL02FL} | ||
| #' \item{ WORS01FL }{WORS01FL} | ||
| #' \item{ BASE }{BASE} | ||
| #' \item{ BASEC }{BASEC} | ||
| #' \item{ CHG }{CHG} | ||
| #' \item{ PCHG }{PCHG} | ||
| #' \item{ ASEQ }{ASEQ} | ||
| #' \item{ SUBJID }{SUBJID} | ||
| #' \item{ RFSTDTC }{RFSTDTC} | ||
| #' \item{ RFENDTC }{RFENDTC} | ||
| #' \item{ RFXSTDTC }{RFXSTDTC} | ||
| #' \item{ RFXENDTC }{RFXENDTC} | ||
| #' \item{ RFICDTC }{RFICDTC} | ||
| #' \item{ RFPENDTC }{RFPENDTC} | ||
| #' \item{ DTHDTC }{DTHDTC} | ||
| #' \item{ DTHFL }{DTHFL} | ||
| #' \item{ SITEID }{SITEID} | ||
| #' \item{ AGE }{AGE} | ||
| #' \item{ AGEU }{AGEU} | ||
| #' \item{ SEX }{SEX} | ||
| #' \item{ RACE }{RACE} | ||
| #' \item{ ETHNIC }{ETHNIC} | ||
| #' \item{ ARMCD }{ARMCD} | ||
| #' \item{ ARM }{ARM} | ||
| #' \item{ ACTARMCD }{ACTARMCD} | ||
| #' \item{ ACTARM }{ACTARM} | ||
| #' \item{ COUNTRY }{COUNTRY} | ||
| #' \item{ DMDTC }{DMDTC} | ||
| #' \item{ DMDY }{DMDY} | ||
| #' \item{ TRTSDTM }{TRTSDTM} | ||
| #' \item{ TRTSTMF }{TRTSTMF} | ||
| #' \item{ TRTEDTM }{TRTEDTM} | ||
| #' \item{ TRTETMF }{TRTETMF} | ||
| #' \item{ TRTDURD }{TRTDURD} | ||
| #' \item{ SCRFDT }{SCRFDT} | ||
| #' \item{ EOSDT }{EOSDT} | ||
| #' \item{ EOSSTT }{EOSSTT} | ||
| #' \item{ FRVDT }{FRVDT} | ||
| #' \item{ RANDDT }{RANDDT} | ||
| #' \item{ DTHDT }{DTHDT} | ||
| #' \item{ DTHADY }{DTHADY} | ||
| #' \item{ LDDTHELD }{LDDTHELD} | ||
| #' \item{ LSTALVDT }{LSTALVDT} | ||
| #' \item{ AGEGR1 }{AGEGR1} | ||
| #' \item{ SAFFL }{SAFFL} | ||
| #' \item{ RACEGR1 }{RACEGR1} | ||
| #' \item{ REGION1 }{REGION1} | ||
| #' \item{ LDDTHGR1 }{LDDTHGR1} | ||
| #' \item{ DTH30FL }{DTH30FL} | ||
| #' \item{ DTHA30FL }{DTHA30FL} | ||
| #' \item{ DTHB30FL }{DTHB30FL} | ||
| #' \item{ CRIT1 }{CRIT1} | ||
| #' \item{ CRIT1FL }{CRIT1FL} | ||
| #' \item{ CRIT2 }{CRIT2} | ||
| #' \item{ CRIT2FL }{CRIT2FL} | ||
| #' \item{ CRIT3 }{CRIT3} | ||
| #' \item{ CRIT3FL }{CRIT3FL} | ||
| #' \item{ CRIT4 }{CRIT4} | ||
| #' \item{ CRIT4FL }{CRIT4FL} | ||
| #' \item{ CRIT5 }{CRIT5} | ||
| #' \item{ CRIT5FL }{CRIT5FL} | ||
| #' \item{ CRIT6 }{CRIT6} | ||
| #' \item{ CRIT6FL }{CRIT6FL} | ||
| #' \item{ CRIT7 }{CRIT7} | ||
| #' \item{ CRIT7FL }{CRIT7FL} | ||
| #' \item{ CRIT8 }{CRIT8} | ||
| #' \item{ CRIT8FL }{CRIT8FL} | ||
| #' \item{ AVALCA1N }{AVALCA1N} | ||
| #' \item{ AVALCAT1 }{AVALCAT1} | ||
| #' } | ||
| #' | ||
| #' @source Generated from pharmaverse/admiralophtha. | ||
| #' @references None | ||
| #' | ||
| #' @examples | ||
| #' data("adbcva_ophtha") | ||
| "adbcva_ophtha" |
Oops, something went wrong.