rNIX/R/modifyData.R

#' Sum columns in data frame df where some of the entries might be NA
#'
#' @param df data frame
#' @param var1 first column
#' @param var2 second column
#' @param outVar which variable to store sum into
#' @param valIfNA which value to use for NA
#'
#' @return updated data frame
#' @export 
#'
## examples df<-sumWithNA(df,'lesionmtv41','metastasesmtv41','totalmtv41',0)

sumWithNA<-function(df,var1='lesionmtv41',var2='metastasesmtv41',outVar='totalmtv41',valIfNA=0){
   v1=df[,var1]
   v2=df[,var2]
   v1[is.na(v1)]=valIfNA
   v2[is.na(v2)]=valIfNA
   df[,outVar]=v1+v2
   df
      
}

#' Map variable time OS status to status at cutoff
#'
#' @param df data frame
#' @param cutoff time instance where OS is evaluated, same units as timeVar
#' @param timeVar name of column where times of status evaluation are recorded (from treatment start)
#' @param osVar name of column with status at evaluation (1-alive/progress free, 2-censored, 3-dead/w/disease)
#' @param targetVar name of target variable holding status at cutoff (0-dead, 1-alive, 2-censored)
#'
#' @return updated data frame with targetVar

selectValid<-function(df,cutoff=2,timeVar='years_to_event',osVar='st_osMAP',targetVar='osAtCutoff'){
   #if alive and ytoevent>c -> alive
   #if censored and ytoe>c -> alive
   #if dod and ytovent>c -> alive
   df[,targetVar]=1



   #if alive and ytoe<c -> censored
   df[(df[,timeVar]<cutoff) & df[,osVar] == 1,targetVar]=2

   #if censored and ytoe<c -> censored
   df[df[,timeVar]<cutoff & df[,osVar] == 2,targetVar]=2

   #if dod and ytovent<c -> dead
   df[df[,timeVar]<cutoff & df[,osVar] == 3,targetVar]=0
   df

}