kuenm_mmop: Extrapolation risk analysis for multiple comparisons

In manubio13/ku.enm: Detailed development of ecological niche models using Maxent

Extrapolation risk analysis for multiple comparisons

Description

kuenm_mmop calculates mobility-oriented parity (MOP) layers by comparing environmental values between the calibration area and multiple areas or scenarios to which ecological niche models are transferred.

Usage

kuenm_mmop(G.var.dir, M.var.dir, is.swd, sets.var, out.mop, percent = 10,
           comp.each = 2000, parallel = FALSE)

Arguments

G.var.dir	(character) if project is TRUE, name of the directory containing folders names as the sets to be compared (sets.var), which contain subfolders with variables representing the scenarios of projection.
M.var.dir	(character) name of the folder containing either folders with ascii raster layers or csv files (SWD format) representing representing sets of variables used to calibrate the models.
is.swd	(logical) whether model calibration and final models were produced using SWD format.
sets.var	(character) value or vector with the name(s) of the sets of variables from G.var.dir and M.var.dir that are going to be compared to create the MOP(s).
out.mop	(character) name of the folder to which MOP results will be written.
percent	(numeric) percentage of values sampled from the calibration region to calculate the MOP.
comp.each	(numeric) compute distance matrix for a each fixed number of rows (default 2000).
parallel	(logical) option to be passed to the kuenm_mop function (for each independent MOP analyses). If TRUE, calculations will be performed in parallel using n.cores of the computer. This will demand more RAM and almost full use of the CPU; hence, its use is more recommended in high-performance computers. Using this option will speed up the analyses. Default = FALSE.
n.cores	(numeric) number of cores to be used in parallel processing. Default = NULL, in which case all CPU cores on current host - 1 will be used.

Details

This function can be used after selection of parameters that produce the best models (when chosen sets of variables are known), or after producing final models with the function kuenm_mod. In a MOP layer, areas of strict extrapolation are excluded and other values represent how similar areas or scenarios are to environmental conditions in the calibration area. MOP is calculated following Owens et al. (2013; https://doi.org/10.1016/j.ecolmodel.2013.04.011).

Value

A folder containing one or multiple mobility-oriented parity raster layers depending on how many projection areas or scenarios are considered. This results will be organized by the different sets of variables chosen for creating final models. Values of 0 in resultant raster layers represent strict extrapolation.

manubio13/ku.enm documentation built on Jan. 5, 2024, 5:55 a.m.