R/fit_variomodel.R

In MathieuGenu/geffaeR: Generic Function for Abundance Estimation with R

#' Fitting a variogram model.
#'
#' Fitting a variogram model from a "variogram" object.
#'
#' @param variogram Object of class variogram \code{\link[geoR]{variog}}.
#' @param form Shape of the adjusted function. Could be either "matern" or "exponential".
#'
#' @return vario_model : object of class "variomodel" and "variofit, see details on the \code{\link[geoR]{variofit}} page
#'
#' @examples
#' @importFrom geoR variofit
#' @export
fit_variomodel <- function(variogram, form = c("matern", "exponential")) {

  vario_model <- geoR::variofit(variogram,
                                cov.model = form,
                                fix.nugget = FALSE,
                                nugget = mean(variogram$v) / 4,
                                fix.kappa = TRUE,
                                kappa = ifelse(form == "matern", 1.5, 1),
                                weights = "npairs",
                                minimisation.function = "optim",
                                ini.cov.pars = expand.grid(
                                  seq(0, mean(variogram$v)*2, l = 10),
                                  seq(as.numeric(quantile(variogram$u, prob = 0.1)),
                                      as.numeric(quantile(variogram$u, prob = 0.8)),l = 10)
                                ),
                                messages = F)

  return(vario_model = vario_model)
}