R/timeseries.peaks.R

In andersonjake1988/peak.gas: timeseries peak data processing package

#' A function to combine and name timeseries text files
#'
#' This function will loop through a folder containing text file outputs to combine and assign sample names, outputing a single timeseries
#'
#' @keywords LiCor, Peak, CO2, Li-Cor, gas, plot
#' @param directory Path to directory containing the files to be processed. Defaults to user selection window.
#' @param verbose A logical argument stating whether or not to display all function processing information. Defaults to TRUE
#' @import dplyr
#' @import lubridate
#' @import tidyr
#' @examples
#' ts.output <- timeseries.peaks(directory = path.package("peak.gas"))
#' @export timeseries.peaks

timeseries.peaks <- function(directory = choose.dir(), verbose = TRUE){
  setwd(directory)
  if(verbose == TRUE){
    message("Working directory set to:")
    message(getwd())
  }
  filelist <- list.files(pattern = c(".txt", ".TXT"))
  output.raw <- data.frame()
  if(verbose == TRUE){
    print("Looping through Folder:")
    progress_bar <- txtProgressBar(min = 0, max = length(filelist), style = 3)
  }
  for(i in 1:length(filelist)){
    if(verbose == TRUE){
      setTxtProgressBar(progress_bar, i)
    }
    b <- read.table(filelist[i], header = TRUE, sep = "\t", fill = TRUE, strip.white = TRUE, check.names = FALSE)
    data.1 <- mutate(b, Sample = NA, .before = 1)
    names(data.1) <- c("Sample", "Test", "Time", "CO2")
    data.1 <- cbind(data.1, File = filelist[i])
    data.2 <- filter(data.1, Test != "--------------------------------------------------------------")
    data.3 <- data.2
    for(i in 1:nrow(data.2)){
      if(is.na(data.2[i,4])==TRUE){
        data.3[i,1] <- as.character(data.2[i,2])
      } else {
        next
      }
    }
    data.4 <- na.omit(fill(data.3, Sample, .direction = "down"))
    output.raw <- rbind(output.raw, data.4)
  }
  output.raw$Time <- as_datetime(output.raw$Time)
  output_final <- output.raw[, c(5,1,3,4)]
  class(output_final) <- c("timeseries", class(output_final))
  return(output_final)
}