R/data_puller_C.R

In catrinanowakowski/ProcessIsodataOuts: What the Package Does (One Line, Title Case)

#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param file_data PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples 
#' \dontrun{
#' if(interactive()){
#'  #EXAMPLE1
#'  }
#' }
#' @rdname data_puller_C
#' @export 
data_puller_C <- function(file_data){
  # file_data = file_data
  ##############################################################################
  ## Pulls names from the folder
  file_names <- list.files(path = file_data)
  file_names <- file_names[!file_names %in% c("cache")]
  
  library(isoreader)
  # Drop the extra columns!
  keeps <- c("Rt.s.", "Rt..s.", "Rt (s)", "Rt", 
             "Ampl..44.mV.", "Ampl..44..mV.", "Ampl  44 (mV)", "Ampl.44",
             "BGD.44.mV.", "BGD.44..mV.", "BGD 44 (mV)","BGD.44", 
             "Area.All.Vs.", "Area.All..Vs.", "Area All (Vs)", "Intensity.All",
             "d 13C/12C (per mil) vs  VPDB", "d.13C.12C.per.mil.vs..VPDB", "d.13C.12C..per.mil..vs..VPDB","d.13C.12C",
             "file_name")
  
  # Read in all files, bind them togehter
  setwd(file_data)
  df_all <- iso_read_continuous_flow(file_names[1])
  df_all <- data.frame(df_all$vendor_data_table)
  df_all$file_name <- file_names[1]
  df_all <- df_all[,names(df_all) %in% keeps]
  
  numerics <- c("Rt", "Ampl.44", "BGD.44", "Intensity.All", "d.13C.12C")
  for(i in 1:length(numerics)){
    df_all[,numerics[i]] <- as.numeric(df_all[,numerics[i]])
  }
  if(length(file_names) > 2){
    for(i in 2:length(file_names)){
      print(i)
      df <- iso_read_continuous_flow(file_names[i])
      df <- data.frame(df$vendor_data_table)
      df$file_name <- file_names[i]
      df <- df[,names(df) %in% keeps]
      
      numerics <- c("Rt", "Ampl.44", "BGD.44", "Intensity.All", "d.13C.12C")
      for(i in 1:length(numerics)){
        df[,numerics[i]] <- as.numeric(df[,numerics[i]])
      }#for
      
      df_all <- rbind(df_all, df)
      rm(df)
    } #for
  } #if
  
  
  # names(df_all) <- c("Rt..s.", "Ampl..44..mV.", "BGD.44..mV.", "Area.All..Vs.", "d.13C.12C..per.mil..vs..VPDB", "file_name")
  names(df_all) <- c("Rt.s.", "Ampl..44.mV.", "BGD.44.mV.", "Area.All.Vs.", "d.13C.12C.per.mil.vs..VPDB", "file_name")
  
  # numerics <- c("Rt.s.", "Ampl..44.mV.", "BGD.44.mV.", "Area.All.Vs.", "d.13C.12C.per.mil.vs..VPDB")
  # for(i in 1:length(numerics)){
  #   df_all[,numerics[i]] <- as.numeric(df_all[,numerics[i]])
  # }
  
  # Split the sample name off
  df_all$date <- NA
  df_all$time <- NA
  df_all$garb_1 <- NA
  df_all$smp <- NA
  df_all$CN <- NA
  df_all$run <- NA
  df_all$last_name <- NA
  df_all$notes <- NA
  
  
  for(i in 1:nrow(df_all)){
    df_all[i,(ncol(df_all)-7):ncol(df_all)] <- unlist(strsplit(df_all$file_name,'_',fixed=TRUE)[i])
  }
  
  # # Clean the run number and the CN id 
  # for(i in 1:nrow(df_all)){
  #   df_all$CN[i] <- unlist(strsplit(df_all$CN[i],'.',fixed=TRUE))[1]
  # }
  
  for(i in 1:nrow(df_all)){
    df_all$run[i] <- unlist(strsplit(df_all$run[i],'R',fixed=TRUE))[2]
  }
  df_all$run <- as.numeric(df_all$run)
  
  CN_id <- df_all$CN[1]
  df_all <- df_all[,!names(df_all) %in% c("CN")]

  
  
  
  
  return(list(df_all = df_all, 
              CN_id = CN_id))
}