R/UTILS.setParam.R

In leca-dev/RFate: FATE with R

### HEADER #####################################################################
##' @title Replace parameter value(s) from a parameter file
##' 
##' @name .setParam
##'
##' @author Damien Georges, Maya Guéguen
##' 
##' @description This function finds in a text file the value(s) of a given 
##' parameter, and replace it with new value(s).
##' 
##' @param params.lines a \code{string} corresponding to the name of the file 
##' from which to replace the parameter value
##' @param flag a \code{string} corresponding to the parameter name to be 
##' extracted and that must be present into the \code{param.lines} file
##' @param flag.split a \code{string} to choose the concerned type of parameter 
##' (either "\code{ }" or "\code{^--.*--$}"), depending on the type of parameter 
##' file (containing values or filenames)
##' @param value a \code{string} or a \code{numeric} value (it can also be a 
##' \code{vector}) containing the new value of the parameter to be changed
##' 
##' @examples
##' 
##' ## Create a skeleton folder with the default name ('FATE_simulation')
##' if (dir.exists("FATE_simulation")) unlink("FATE_simulation", recursive = TRUE)
##' PRE_FATE.skeletonDirectory()
##' 
##' ## Create a Global_parameters file
##' PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
##'                                  , required.no_PFG = 6
##'                                  , required.no_strata = 5
##'                                  , required.simul_duration = 100
##'                                  , required.seeding_duration = c(10,50)
##'                                  , required.seeding_timestep = 1
##'                                  , required.seeding_input = 100
##'                                  , required.max_abund_low = 30000
##'                                  , required.max_abund_medium = 50000
##'                                  , required.max_abund_high = 90000)
##'                                  
##' readLines("FATE_simulation/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt")
##'                                  
##' ## Change number of PFG
##' .setParam(params.lines = "FATE_simulation/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt"
##'           , flag = "NO_PFG"
##'           , flag.split = " "
##'           , value = 14)
##'           
##' readLines("FATE_simulation/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt")
##' 
##' 
##' ## ----------------------------------------------------------------------------------------- ##
##'                                 
##' ## Load example data
##' 
##' 
##' @export
##'
## END OF HEADER ###############################################################


.setParam = function(params.lines
                     , flag
                     , flag.split
                     , value
){
  
  #############################################################################
  
  .testParam_notChar.m("params.lines", params.lines)
  .testParam_existFile(params.lines)
  .testParam_notChar.m("flag", flag)
  .testParam_notInValues.m("flag.split", flag.split, c(" ", "^--.*--$"))
  if (.testParam_notDef(value) || sum(nchar(value) == 0) > 0)
  {
    stop("No data given!\n (missing `value` information)")
  }
  
  #############################################################################
  
  param.name = params.lines
  params.lines = readLines(params.lines)
  if (flag.split == "^--.*--$")
  {
    if (length(grep("--END_OF_FILE--", params.lines)) == 0)
    {
      stop(paste0("Wrong type of data!\n `flag` (--END_OF_FILE--) "
                  , "is not found within `params.lines` (", param.name, ")"))
    }
  }
  if (length(grep(flag.split, params.lines)) <= ifelse(flag.split == "^--.*--$", 1, 0)){
    stop(paste0("Wrong type of data!\n `flag.split` (", flag.split
                , ") is not found within `params.lines` (", param.name, ")"))
  }
  if (length(grep(flag, params.lines)) == 0){
    stop(paste0("Wrong type of data!\n `flag` (", flag
                , ") is not found within `params.lines` (", param.name, ")"))
  }
  
  #############################################################################
  
  if(flag.split == " "){
    value.line = grep(flag, params.lines, value = TRUE)
    params.lines = sub(value.line
                       , paste(flag
                               , paste0(value, collapse = flag.split)
                               , sep = flag.split)
                       , params.lines)
  } else {
    ind.flag.split = grep(flag.split, params.lines)
    ind.flag = grep(paste0("--", flag, "--"), params.lines)
    if (length(ind.flag) == 0)
    {
      stop(paste0("Wrong type of data!\n `flag` (", flag
                  , ") is not found within `params.lines` (", param.name, ")"))
    }
    ind.start = which(ind.flag.split == ind.flag)
    if (ind.flag.split[ind.start + 1] == ind.start + 1)
    {
      stop(paste0("Wrong type of data!\n `flag` (", flag
                  , ") does not contain any value"))
    }
    
    ind1 = (ind.flag.split[ind.start] + 1)
    ind2 = ifelse(length(ind.flag.split) == 1
                  , max(length(params.lines), ind1)
                  , ind.flag.split[ind.start + 1] - 1)
    if (length(ind1:ind2) == length(value)){
      params.lines[ind1:ind2] = value
    } else {
      stop(paste0("Wrong dimension(s) of data!\n `value` does not "
                  , "have the same number of elements ("
                  , length(value), ") than `flag` (", flag
                  , ", ", length(ind1:ind2), ")"))
    }
  }
  cat(params.lines, sep = "\n", file = param.name, append = FALSE)
  message(paste0("The parameter file ", param.name
                 , " has been successfully corrected !\n"))
}