R/filters.R

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

library(dplyr)

filters <- function(anl,slref,filter_code){ 
  
  vect_filter <- strsplit(filter_code, "_")[[1]]
   title<-c()
  
  for (filts in vect_filter) {
 
    if (filts == "IT")  {
      anl <- anl %>%  filter( ITTFL == "Y")
      title <- c(title,"Intent-to-Treat Population")
    }
    if (filts == "SE")  {
      anl <- anl %>%  filter(SAFFL == "Y")
      title <- c(title,"Safety-Evaluable Population")
    }
    if (filts == "SER")  {
      slref <- slref %>%  filter(AESER == "Y")
      title <- c(title,"Serious Adverse Events")
    }  
    if (filts == "INJ")  {
      slref <- slref %>%  filter(AESCAT  =='LOCAL INJECTION SITE REACTION' | AESCAT  == 'SYSTEMIC INJECTION REACTION') 
      title <- c(title,"Injection Site Reactions")
    } 
    if (filts == "INF")  { 
      slref <- slref %>%  filter(AESCAT  == 'LOCAL INFUSION SITE REACTION' | AESCAT  == 'SYSTEMIC INFUSION REACTION'  )
      title <- c(title,"Infusion Site Reactions")
    }  
    if (filts == "REL")  {
      slref <- slref %>%  filter(AEREL == "Y")
      title <- c(title,"Related to Any Study Treatment")
    }  
    if (filts == "DSCALL")  {
      slref <- slref %>%  filter(AEACN1 == 'DRUG WITHDRAWN' | AEACN2 == 'DRUG WITHDRAWN' | AEACN3 == 'DRUG WITHDRAWN')
      title <- c(title,"Leading to Study Treatment Discontinuation")
    }   
    if (filts  ==  "ATEZOSC")  {
      slref <- slref %>%  filter(toupper(PARCAT2) == "ATEZOLIZUMAB SC"  & toupper(PARCAT1) == "OVERALL")
      title <- c(title,"Atezolizumab SC treatment")
    }    
    if (filts == "RHUPH20")  {
      slref <- slref %>%  filter(toupper(PARCAT2) == "RHUPH20"  & toupper(PARCAT1) == "OVERALL")
      title <- c(title,"RHUPH20 treatment")
    } 
    if (filts == "ATEZOIV")  {
      slref <- slref %>%  filter(toupper(PARCAT2) == "ATEZOLIZUMAB IV" & toupper(PARCAT1) == "OVERALL")
      title <- c(title,"Atezolizumab IV treatment")
    }  
 
  } 
   
   
   
  return(list(anl,slref,title ))
}

 
 


####Lopo as a SQL database  ####
#con <- dbConnect(RSQLite::SQLite(), paste0("Studies/",study,"/meta/FILTERS"))
#dbCreateTable(con, "FILTERS", df_filter)
#dbAppendTable(con, "FILTERS", df_filter)
#dbReadTable(con, "FILTERS")
#dbDisconnect(con)
################################