Script to remove dates from files and convert them to days since initial visit

Date_to_Day_TEV.R

date_to_day <- function(file_name, first_date){
  data <- read.table(file_name, header=TRUE, sep='\t', quote = NULL, row.names = NULL, check.names = FALSE)
  data$Date <- as.character(data$Date)
  data <- data[order(as.Date(data$Date, "%m/%d/%y")), ]
  data$Date <- as.Date(data$Date, "%m/%d/%y")
  if(is.null(first_date) == TRUE){
    first_date <- data[1, ]$Date
  }
  else{
    first_date <- as.Date(first_date, "%m/%d/%y")
  }
  Day <- rep(NA, times=nrow(data))
  data$Day <- Day
  for(i in seq(nrow(data))){
    data[i, ]$Day <- data[i, ]$Date - first_date
  }
  
  #Uncomment the lines below to delete the dates from the file
  
  #col_to_remove <- which(names(data) == "Date")
  #data <- data[-c(col_to_remove)]
  write.table(data, file=file_name, quote=FALSE, sep='\t', row.names = FALSE)
  
  #Return data so user can preview in R
  return(data)
}

file <- 'RCL-IDH-029.txt'

#Make sure you are in the directory where your files are stored
#The first parameter is the name of the file
#The second paramter is the first date the patient was tested
#If the patient hasn't been used in TEV yet, leave as NULL and the earliest date in the file
#Will be used as timepoint 0
#Otherwise supply earliest date used in TEV in the format 'm/d/yy', i.e '5/14/16'
data <- date_to_day(file, NULL)