R/calculate_all_light_response_parameters.R

In SamLoontjens/HandlingLicorFiles: Handling LI-6400 and LI-6800 output files

#' A function that calculates all light response curve parameters
#' for multiple files.
#'
#' @description
#'   A function that calculates all light response curve parameters
#'   for all files.
#'   The directory it reads is
#'   "input_directory_licorfiles/light_response_data/".
#'   For all the files it calculates all the parameters.
#'   It returns a dataframe with all the parameters.
#'
#'   This makes it easy to drop files in the light response data directory
#'   and run just one line to fit all the data.
#' @author Sam Loontjens
#' @param manual_check A boolean that regulates if the fits are checked.
#' @param write_excel A boolean that regulates if the dataframe
#'                    is written to an excel file.
#' @param write_folder a string of the foldername for writing excel files.
#' @param save_plots A boolean that regulates is the plots are saved.
#' @param save_path A pathname where to save the plots if save_plots is TRUE.
#' @param name_parameters
#' A character vector of the parameters in the filename.
#' Default is a list of date description, light,
#' relative humidity, CO2, species, measurement and plant.
#' @export
#' @return
#' Returns a dataframe with all the parameters.
#' @examples
#' mydata <- calculate_all_light_response_parameters()
#'
calculate_all_light_response_parameters <- function(manual_check = TRUE,
                                                    write_excel = FALSE,
                                                    write_folder = "output_directory_licorfiles/excel_files/",
                                                    save_plots = FALSE,
                                                    save_path = "output_directory_licorfiles/light_response_plots/",
                                                    name_parameters = c("date",
                                                                        "description",
                                                                        "light",
                                                                        "relative humidity",
                                                                        "CO2",
                                                                        "species",
                                                                        "measurement",
                                                                        "plant")) {

  #list the files that will be used
  light_response_file_list <- list_licorfiles("input_directory_licorfiles/light_response_data")

  #make an empty data frame
  light_response_dataframe <- data.frame()

  #calculate the photosynthetic induction parameters for all files
  for (filename in light_response_file_list) {

    #create the pathname
    input_pathname <- paste0("input_directory_licorfiles/",
                             "light_response_data/",
                             filename)

    #call the function to calculate the parameters from the filepath
    parameterlist <- calculate_light_response_parameters(pathname = input_pathname,
                                                         manual_check = manual_check,
                                                         save_plot = save_plots,
                                                         save_path = save_path,
                                                         name_parameters = name_parameters)

    #change the list to a dataframe row
    datarow <- data.frame(parameterlist)

    #add them to the dataframe
    light_response_dataframe <- rbind(light_response_dataframe, datarow)
  }

  #write the dataframe to excel for further analysis
  if (write_excel) {

    #create the pathname
    output_pathname <- paste(write_folder, Sys.time(), " LRC fitting.xlsx", sep = "")

    #change the colons of the time
    output_pathname <- sub(":", "h", output_pathname)
    output_pathname <- sub(":", "m", output_pathname)

    #writing the xlsx
    writexl::write_xlsx(x = light_response_dataframe,
                        path = output_pathname,
                        col_names = TRUE,
                        format_headers = FALSE)

    #confirmation
    print(paste("Writing", output_pathname))
  }


  #return a dataframe with all the parameters
  return(light_response_dataframe)
}