R/checkargs.R

In SSDM: Stacked Species Distribution Modelling

.checkargs <- function(Xcol = 'Longitude',
                      Ycol = 'Latitude',
                      Pcol = NULL,
                      Spcol = 'SpeciesID',
                      name = NULL,
                      Spname = NULL,
                      save = FALSE,
                      path = getwd(),
                      PA = NULL,
                      rep = 1,
                      cv = 'holdout',
                      cv.param = c(0.7,2),
                      final.fit.data = 'all',
                      bin.thresh = 'SES',
                      metric = NULL,
                      thresh = 1001,
                      axes.metric = 'Pearson',
                      select = FALSE,
                      select.metric = c('AUC'),
                      select.thresh = c(0.75),
                      verbose = TRUE,
                      GUI = FALSE,
                      uncertainty = TRUE,
                      tmp = FALSE,
                      ensemble.metric = c('AUC'),
                      ensemble.thresh = c(0.75),
                      weight = TRUE,
                      method = 'pSSDM',
                      rep.B = 1000,
                      richness = NULL,
                      GeoRes = TRUE,
                      reso = 1,
                      file = NULL,
                      files = NULL,
                      format = c('.grd','.tif','.asc','.sdat','.rst','.nc','.tif','.envi','.bil','.img'),
                      categorical = NULL,
                      Norm = TRUE,
                      esdm = Ensemble.SDM(),
                      stack = Stacked.SDM(),
                      range = NULL,
                      endemism = 'WEI',
                      cores = 1,
                      MEM = FALSE,
                      eval = TRUE){
  ## Argument checking function
  ## Occurrences, Environment, and part of
  ## X, Y, Pcol are directly defined in functions

  # Col
  if (!inherits(Xcol, "character")) {
    stop("Xcol parameter should be a character (column name).")
  }
  if (!inherits(Ycol, "character")) {
    stop("Ycol parameter should be a character (column name).")
  }
  if (!inherits(Pcol, "character") && !is.null(Pcol)) {
    stop("Pcol parameter should be a character (column name), or NULL if no presence column.")
  }
  if (!inherits(Spcol, "character") && !is.null(Spcol)) {
    stop("Spcol parameter should be a character (column name), or NULL if no species column..")
  }

  # Name and Spname
  if (!inherits(name, "character") && !is.null(name)) {
    stop("name parameter should be a character, or NULL to be automatically defined.")
  }
  if (!inherits(Spname, "character") && !is.null(Spname)) {
    stop("Spname parameter should be a character, or NULL to be automatically defined.")
  }

  # PA
  if (!inherits(PA, "list") && !is.null(PA)) {
    stop("PA parameter should be a list, or NULL to be automatically defined.")
  }
  if (!is.null(PA) && (is.null(PA$nb) || is.null(PA$strat))) {
    stop("PA should be a list containing as PA = list('nb'=..., 'strat'=...).")
  }
  if (!is.null(PA) && !is.null(PA$nb) && (abs(PA$nb - round(PA$nb)) != 0 ||
                                          PA$nb < 1)) {
    stop("PA$nb should be an integer > 0.")
  }
  if (!is.null(PA) && !is.null(PA$strat) && !(PA$strat %in% c("random", "disk","geobuffer"))) {
    stop("PA$strat should be random, disk or geobuffer (see help).")
  }

  # rep
  if (!inherits(rep, "numeric") || abs(thresh - round(thresh)) != 0 || thresh <
      1) {
    stop("rep parameter should be an integer > 1.")
  }

  # CV
  if (!inherits(cv, "character")) {
    stop("cv parameter should be a character.")
  }
  if (!(cv %in% c("k-fold", "holdout", "LOO"))) {
    stop("cv parameter should be k-fold, holdout or LOO (see help).")
  }
  if (!inherits(cv.param, "numeric") || is.null(cv.param)) {
    stop("cv.param parameter should be a numeric")
  }
  if (cv != "LOO" && length(cv.param) < 2) {
    stop("cv.param parameter should be of length 2")
  }
  if (cv == "k-fold" && ((abs(cv.param[1] - round(cv.param[1])) != 0 || abs(cv.param[2] -
                                                                            round(cv.param[2])) != 0) || (cv.param[1] == 0 || cv.param[2] == 0))) {
    stop("cv.param parameters (k and repetitions) should be both integers > 0 (see help).")
  }
  if (cv == "holdout" && (abs(cv.param[2] - round(cv.param[2])) != 0 || cv.param[2] ==
                          0)) {
    stop("cv.param[2] (repetitions) parameters should be an integer > 0 (see help).")
  }
  if (cv == "holdout" && (cv.param[1] < 0 || cv.param[1] > 1)) {
    stop("cv.param[1] (train fraction) parameters should be a float between 0 and 1 (see help).")
  }
  
  # final.fit.data
  if (!inherits(final.fit.data,c("character","numeric"))) {
    stop("final.fit.data should be a character string or numeric.")
  }
  
  if (inherits(final.fit.data,"character") && !(final.fit.data %in% c("all", "holdout"))) {
    stop("final.fit.data should be one of 'all', 'holdout' or numeric (between 0-1).")
  }

  # bin.thresh
  if (!inherits(bin.thresh, "character") || !(bin.thresh %in% c("Kappa", "NOM", "TSS","SES", "EP"))) {
    stop("bin.thresh parameter should be Kappa, NOM, TSS, SES, or EP (see help).")
  }
  
  # thresh
  if (!inherits(thresh, "numeric") || abs(thresh - round(thresh)) != 0) {
    stop("thresh parameter should be an integer.")
  }

  # metric
  if (!inherits(metric, c("character","NULL")) || (inherits(metric, "character") && !(metric %in% c("Kappa", "CCR", "TSS","SES", "LW", "ROC")))) {
    stop("metric parameter should be Kappa, CCR, TSS, SES, LW, or ROC (see help).")
  }

  # axes.metric
  if (!inherits(axes.metric, "character") || !(axes.metric %in% c("Pearson",
                                                                  "AUC", "Kappa", "omission.rate", "sensitivity", "specificity", "prop.correct"))) {
    stop("axes.metric parameter should be Pearson, AUC, Kappa, omission.rate, sensitivity, specificity or prop.correct (see help).")
  }

  # select
  if (!inherits(select, "logical")) {
    stop("select parameter should be a logical (True or False).")
  }
  if (!inherits(select.metric, "character")) {
    stop("select.metric parameter should be a character.")
  } else {
    for (i in seq_len(length(select.metric))) {
      if (!(select.metric[i] %in% c("AUC", "Kappa", "sensitivity", "specificity",
                                    "prop.correct","calibration"))) {
        stop(paste("select.metric", i, "parameter should be AUC, Kappa, sensitivity, specificity, prop.correct or calibration (see help)."))
      }
    }
  }
  if (!inherits(select.thresh, "numeric")) {
    stop("select.thresh parameter should be a numeric.")
  } else {
    for (i in seq_len(length(select.thresh))) {
      if (select.thresh[i] < 0 || select.thresh[i] > 1) {
        stop(paste("select.thresh", i, "parameter should be a float between 0 and 1."))
      }
    }
  }
  if (length(select.thresh) != length(select.metric)) {
    stop("select.thresh and select.metric parameters should have the same length to correspond (see help).")
  }

  # Verbose, GUI, uncertainty, tmp, MEM and save
  if (!inherits(verbose, "logical")) {
    stop("verbose parameter should be a logical (True or False).")
  }
  if (!inherits(GUI, "logical")) {
    stop("GUI parameter should be a logical (True or False).")
  }
  if (!inherits(uncertainty, "logical")) {
    stop("uncertainty parameter should be a logical (True or False).")
  }
  if (!inherits(tmp, c("logical","character"))) {
    stop("tmp parameter should be a logical (True or False) or character (file path).")
  }
  if (!inherits(save, "logical")) {
    stop("save parameter should be a logical (True or False).")
  }
  if (!inherits(path, "character") && !is.null(path)) {
    stop("path parameter should be a character.")
  }
  if (!inherits(MEM, "logical")) {
    stop("save parameter should be a logical (True or False).")
  }

  # Ensemble
  if (!inherits(weight, "logical")) {
    stop("weight parameter should be a logical (True or False).")
  }
  if (!inherits(ensemble.metric, "character")) {
    stop("ensemble.metric parameter should be a character.")
  } else {
    for (i in seq_len(length(ensemble.metric))) {
      if (!(ensemble.metric[i] %in% c("AUC", "Kappa", "sensitivity",
                                      "specificity", "prop.correct","calibration"))) {
        stop(paste("ensemble.metric", i, "parameter should be AUC, Kappa, sensitivity, specificity, prop.correct or calibration (see help)."))
      }
    }
  }
  if (!inherits(ensemble.thresh, "numeric")) {
    stop("ensemble.thresh parameter should be a numeric.")
  } else {
    for (i in seq_len(length(ensemble.thresh))) {
      if (ensemble.thresh[i] < 0 || ensemble.thresh[i] > 1) {
        stop(paste("ensemble.thresh", i, "parameter should be a float between 0 and 1."))
      }
    }
  }
  if (length(ensemble.thresh) != length(ensemble.metric)) {
    stop("select.thresh and select.metric parameters should have the same length to correspond (see help).")
  }

  # Stacking
  if (!inherits(method, "character") || !(method %in% c("pSSDM", "Bernoulli", "bSSDM",
                                                        "MaximumLikelihood",
                                                        "PRR.MEM", "PRR.pSSDM"))) {
    stop("method parameter should be pSSDM, Bernoulli, bSSDM, MaximumLikelihood, PRR.MEM, or PRR.pSSDM (see help).")
  }
  if (method == "Bernoulli" && !inherits(rep.B, "numeric") && abs(rep.B - round(rep.B)) !=
      0 && rep.B < 1) {
    stop("rep.B parameter should be an integer > 1 (see help).")
  }
  if (!is.null(richness)) {
    warning("Richness check arg to implement !")
  }
  if (!inherits(eval, "logical")) {
    stop("eval parameter should be a logical (True or False).")
  }

  # load.occ and load.var
  if (!inherits(GeoRes, "logical")) {
    stop("GeoRes parameter should be a logical (True or False).")
  }
  if (!inherits(reso, "numeric")) {
    stop("reso parameter should be numeric.")
  }
  if (!inherits(file, "character") && !is.null(file)) {
    stop("file parameter should be characters or NULL")
  }
  if (!inherits(files, "character") && !is.null(files)) {
    stop("files parameter should be characters or NULL")
  }
  if (!is.null(format) && !inherits(format, "character") || (inherits(format,
                                                                      "character") && any(!(format %in% c(".grd", ".tif", ".asc", ".sdat", ".rst",
                                                                                                          ".nc", ".tif", ".envi", ".bil", ".img"))))) {
    stop("format parameter should be .grd, .tif, .asc, .sdat, .rst, .nc, .tif, .envi, .bil or .img")
  }
  if (!inherits(categorical, "character") && !is.null(categorical)) {
    stop("categorical parameter should be characters or NULL")
  }
  if (!inherits(Norm, "logical")) {
    stop("Norm parameter should be a logical (True or False).")
  }

  # save
  if (!inherits(esdm, "Ensemble.SDM")) {
    stop("esdm parameter should be an Ensemble.SDM.")
  }
  if (!inherits(stack, "Stacked.SDM")) {
    stop("stack parameter should be a Stacked.SDM.")
  }

  # Range and Endemism parameters
  if (!is.null(endemism) && length(endemism) > 1) {
    if (!inherits(endemism[1], "character") || !(endemism[1] %in% c("WEI",
                                                                    "CWEI"))) {
      stop("endemism parameter first value should be WEI, or CWEI (see help).")
    }
    if (!inherits(endemism[2], "character") || !(endemism[2] %in% c("NbOcc",
                                                                    "Binary"))) {
      stop("endemism parameter second value should be NbOcc, or Binary (see help).")
    }
  }
  if (!is.null(range)) {
    if (!inherits(range, "numeric") || range < 0) {
      stop("range parameter should be numeric and > 0 (see help).")
    }
  }

  # Cores
  if (!inherits(cores, "numeric") || abs(cores - round(cores)) != 0 || cores <
      0) {
    stop("cores parameter should be an integer > 0 (see help).")
  }
}