inst/program/t_ae.R

In kismet303/lopo3000: LoPo 3000 Experimental package using RShiny for interactive LoPo

ADSL1 <- read_sas(paste0(main_path,"Studies/",study,"/data/ADAM/adsl.sas7bdat"))
ADAE1 <- read_sas(paste0(main_path,"Studies/",study,"/data/ADAM/adae.sas7bdat"))

fff <- filters(ADSL1,ADAE1,FilterL)
ADSL <- fff[[1]]
ADAE <- fff[[2]]

 
ADSLa<-ADSL[,c("USUBJID","ARMCD")]

ADAE <- ADAE %>% 
  left_join(ADSLa, by = "USUBJID")  
 
 


##Prepare data ADAE  
if (any(ADAE$AEBODSYS=="")) {
  ADAE[ADAE$AEBODSYS=="",]$AEBODSYS<-"NOT CODED YET" 
}
if (any(ADAE$AEDECOD=="")) {
  ADAE[ADAE$AEDECOD=="",]$AEDECOD<-"NOT CODED YET" 
} 
 

if (dim(ADAE)[1] > 0 ) {


## @knitr answer
cat(fff[[3]])   ##subtitle related to filter
cat("      ")

options(warn=-1)

a<-t_events_per_term_id(
  terms = ADAE[, c("AEBODSYS", "AEDECOD")],
  id = ADAE$USUBJID,
  col_by = factor(ADAE$ARMCD),
  col_N = table(ADSL$ARMCD),
  total = "All Patients"
)

options(warn=0) 
print(a) 
date() 
    
} else { 


## @knitr answer
cat(fff[[3]])   ##subtitle related to filter
cat("      ")
options(warn=-1)

 print("No observation")

options(warn=0) 

date()  
 
  }