Skip to contents

Global-Reporting-Setup

Source: vignettes/Global-Reporting-Setup.Rmd
Global-Reporting-Setup.Rmd

Vignette Build Datetime 

message(paste0('Datetime: ',Sys.Date(),':',Sys.time()))
#> Datetime: 2026-01-21:2026-01-21 14:55:42.074004

Load Libraries

Set Up the Global Environment 

tmpdr <- tempdir()
datdir <- file.path(gsub("\\","/",tmpdr,fixed=TRUE),"datdir")
dir.create(datdir,showWarnings=FALSE)
repfun::copydata(datdir)
outdir <- file.path(gsub("\\","/",tmpdr,fixed=TRUE),"outdir")
dir.create(outdir,showWarnings=FALSE)
suppressMessages(
  repfun::rs_setup(
    D_CENTID="SITEID",
    D_DATADATE=Sys.Date(),
    D_DSPLYNUM=1,
    D_DSPLYTYP=T,
    D_FONTSIZE=10,
    D_FOOT1='1.) Only treatment emergent events related to lipids are displayed.',
    D_FOOT2='2.) Subjects are only counted once within each body system and preferred term.',
    D_KEEPPOPVARS=c('STUDYID','USUBJID','SAFFL'),
    D_OUTFILE=paste0(outdir,"/t_ru_list_1.rtf"),
    D_PGMPTH="./Global-Reporting-Setup.Rmd",
    D_STUDYID='ABCXYZPDQ',
    D_POP="SAFFL",
    D_POPDATA= repfun::adsl %>% dplyr::filter(SAFFL=='Y'),
    D_POPLBL="Safety",
    D_SUBJID=c("STUDYID","USUBJID"),
    D_TITLE1=paste0('Table 1: Summary of Treatment Emergent Adverse Events'),
    D_USERID=Sys.getenv("DOMINO_USER_NAME"),
    R_DICTION="../inst/formats",
    R_MACDIRS=c("."),
    R_DDDATA=paste0(tmpdr,'/t_ru_list_1.rds'),
    R_OTHERDATA=datdir,
    R_INPUTDATA=datdir,
    R_RAWDATA=datdir,
    R_SDTMDATA=datdir,
    R_ADAMDATA=datdir,
    D_RTFYN="Y",
    D_DEBUG=0)
    )

Use Libname to Access and Subset Data 

adae <- repfun:::rfenv$adamdata$adae.rda() %>% dplyr::filter(TRTEMFL=='Y') -> adsl1

Display the Result, add Study ID to Title 

knitr::kable(head(adae[,c(1:10)],10), caption = paste0("TEAEs for Study: ", repfun:::rfenv$G_STUDYID))
TEAEs for Study: ABCXYZPDQ
STUDYID DOMAIN USUBJID AESEQ AESPID AETERM AELLT AELLTCD AEDECOD AEPTCD
CDISCPILOT01 AE 01-701-1015 1 E07 APPLICATION SITE ERYTHEMA APPLICATION SITE REDNESS NA APPLICATION SITE ERYTHEMA NA
CDISCPILOT01 AE 01-701-1015 2 E08 APPLICATION SITE PRURITUS APPLICATION SITE ITCHING NA APPLICATION SITE PRURITUS NA
CDISCPILOT01 AE 01-701-1015 3 E06 DIARRHOEA DIARRHEA NA DIARRHOEA NA
CDISCPILOT01 AE 01-701-1023 2 E09 ERYTHEMA LOCALIZED ERYTHEMA NA ERYTHEMA NA
CDISCPILOT01 AE 01-701-1023 1 E08 ERYTHEMA ERYTHEMA NA ERYTHEMA NA
CDISCPILOT01 AE 01-701-1023 4 E08 ERYTHEMA ERYTHEMA NA ERYTHEMA NA
CDISCPILOT01 AE 01-701-1023 3 E10 ATRIOVENTRICULAR BLOCK SECOND DEGREE AV BLOCK SECOND DEGREE NA ATRIOVENTRICULAR BLOCK SECOND DEGREE NA
CDISCPILOT01 AE 01-701-1028 1 E04 APPLICATION SITE ERYTHEMA APPLICATION SITE ERYTHEMA NA APPLICATION SITE ERYTHEMA NA
CDISCPILOT01 AE 01-701-1028 2 E05 APPLICATION SITE PRURITUS APPLICATION SITE ITCHING NA APPLICATION SITE PRURITUS NA
CDISCPILOT01 AE 01-701-1034 1 E08 APPLICATION SITE PRURITUS APPLICATION SITE ITCHING NA APPLICATION SITE PRURITUS NA