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Get-Data-for-Population

Source: vignettes/Get-Data-for-Population.Rmd
Get-Data-for-Population.Rmd

Vignette Build Datetime 

message(paste0('Datetime: ',Sys.Date(),':',Sys.time()))
#> Datetime: 2026-01-21:2026-01-21 14:55:38.494723

Load Libraries

Set Up the Reporting Environment 

tmpdr <- tempdir()
datdir <- file.path(gsub("\\","/",tmpdr,fixed=TRUE),"datdir")
dir.create(datdir,showWarnings=FALSE)
repfun::copydata(datdir)
repfun::rs_setup(D_POP="SAFFL",D_POPLBL="Safety",D_POPDATA=repfun::adsl, 
         D_SUBJID=c("STUDYID","USUBJID"), R_ADAMDATA=datdir)
repfun:::rfenv$G_POPDATA %>% dplyr::mutate(TRT01AN=ifelse(TRT01A=='Placebo',1,ifelse(TRT01A=='Xanomeline Low Dose',2,3)),
                     SAFFL=ifelse((row_number() %% 10) == 0,'N',SAFFL)) %>% 
              repfun::ru_labels(varlabels=list('TRT01AN'='Actual Treatment for Period 01 (n)',
                                       'SAFFL'='Safety Population Flag')) -> G_POPDATA

Read in ADAE, Restrict to Population and Add Population Variables 

adae <- repfun:::rfenv$adamdata$adae.rda() %>% dplyr::select(-c('SAFFL','TRT01A')) %>% 
  repfun::ru_getdata(G_POPDATA, c("STUDYID", "USUBJID"), 
             keeppopvars=c("TRT01AN", "TRT01A", "SAFFL")) %>%
 dplyr::select(STUDYID,USUBJID,AEBODSYS,AEDECOD,SAFFL,TRT01AN,TRT01A) %>% 
  dplyr::arrange(STUDYID,USUBJID,AEBODSYS,AEDECOD,SAFFL,TRT01AN,TRT01A)

Display the Results for AE Body System and Preferred Term 

lbls <- sapply(adae,function(x){attr(x,"label")})
knitr::kable(head(adae,10), col.names=paste(names(lbls),lbls,sep=": "), 
             caption = "Results of Restricting to Population and Adding Population Variables")
Results of Restricting to Population and Adding Population Variables
STUDYID: Study Identifier USUBJID: Unique Subject Identifier AEBODSYS: Body System or Organ Class AEDECOD: Dictionary-Derived Term SAFFL: Safety Population Flag TRT01AN: Actual Treatment for Period 01 (n) TRT01A: Actual Treatment for Period 01
CDISCPILOT01 01-701-1015 GASTROINTESTINAL DISORDERS DIARRHOEA Y 1 Placebo
CDISCPILOT01 01-701-1015 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS APPLICATION SITE ERYTHEMA Y 1 Placebo
CDISCPILOT01 01-701-1015 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS APPLICATION SITE PRURITUS Y 1 Placebo
CDISCPILOT01 01-701-1023 CARDIAC DISORDERS ATRIOVENTRICULAR BLOCK SECOND DEGREE Y 1 Placebo
CDISCPILOT01 01-701-1023 SKIN AND SUBCUTANEOUS TISSUE DISORDERS ERYTHEMA Y 1 Placebo
CDISCPILOT01 01-701-1023 SKIN AND SUBCUTANEOUS TISSUE DISORDERS ERYTHEMA Y 1 Placebo
CDISCPILOT01 01-701-1023 SKIN AND SUBCUTANEOUS TISSUE DISORDERS ERYTHEMA Y 1 Placebo
CDISCPILOT01 01-701-1028 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS APPLICATION SITE ERYTHEMA Y 3 Xanomeline High Dose
CDISCPILOT01 01-701-1028 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS APPLICATION SITE PRURITUS Y 3 Xanomeline High Dose
CDISCPILOT01 01-701-1034 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS APPLICATION SITE PRURITUS Y 3 Xanomeline High Dose