R/racircalbatch.R

In jstinzi/racir: Rapid A/Ci Response (RACiR) Data Analysis

#' Corrects a batch of rapid A/Ci response (RACiR) data
#'
#' \code{racircalbatch} Corrects your RACiR data files based on a calibration file.
#' Produces diagnostic graphs of A vs. Ci for quality control. Output
#' includes a list of data frames with corrected data.
#'
#' @param data List of data frames with the RACiR response data
#' @param caldata Data frame with the calibration data
#' @param mincut Minimum cutoff value for reference CO2 (CO2_r). Used to cut
#' out the data from the initial chamber mixing. Default value is set to the
#' minimum COR_r value.
#' @param maxcut Maximum cutoff value for reference CO2 (CO2_r). Used to cut
#' out the data from the end of the response. Not needed in all cases. Default
#' value is set to the maximum COR_r value.
#' @param title Vector for titles of output graph - useful for batch RACiR
#' corrections. Length must be equal to data list length
#' @param varnames Variable names - this allows for the use of this code with
#' other machines and setups where variable names may differ.
#'
#' @return racircalbatch calibrates a batch of RACiR data
#' @importFrom stats BIC
#' @importFrom stats lm
#' @importFrom stats predict
#' @importFrom graphics legend
#' @importFrom graphics lines
#' @importFrom graphics plot
#' @export
#'@examples \donttest{
#'#Create a list of files
#'files <- c(system.file("extdata", "poplar_1", package = "racir"),
#'           system.file("extdata", "poplar_2", package = "racir"))
#'data <- vector("list", length(files))
#'for(i in seq_along(files)){
#'  data[[i]] <- read_6800(files[i])
#'  names(data)[i] <- files[i]
#'}
#'
#'caldata <- read_6800(system.file("extdata", "cal", package = "racir"))
#'output <- racircalbatch(caldata = caldata, data = data,
#'                        mincut = 300, maxcut = 780, title = files)
#'}
#'
racircalbatch <- function(caldata, data, mincut, maxcut,
                          title, varnames = list(A = "A",
                                                 Ca = "Ca",
                                                 CO2_r = "CO2_r",
                                                 E = "E",
                                                 gtc = "gtc")){

  # Check for title
  title <- ifelse(missing(title) == TRUE, rep(NA, length(data)), title)
  output <- vector("list", length(data))
  for (i in seq_along(data)){
    output[[i]] <- racircal(caldata = caldata,
                            data = data[[i]],
                            mincut = mincut,
                            maxcut = maxcut,
                            title = title[i],
                            varnames = varnames)
    output[[i]]$ID <- title[i]
  }
  return(output)
  }