model_var_contrib: Evaluation of variable contribution to Maxent final models

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

Evaluation of variable contribution to Maxent final models

Description

model_var_contrib helps to explore variable contribution of Maxent models created as final models with the functions kuenm_mod or kuenm_mod_swd. Variable contribution is measured based on metrics of contribution percentage, permutation importance, and, if existent, a jackknife analysis.

Usage

model_var_contrib(fmod.dir, model_name = NULL, project, ext.type)

Arguments

fmod.dir	(character) the name of the folder in which final models are (e.g., the output folder after using the kuenm_mod) function. It is important to have only the folders containing the models in this directory. It can be only one folder or multiple subfolders containing models for the same species, created with distinct parameter settings. If models were projected, and the distinct types of extrapolation were used, the name of the folders contained in this directory should include a pattern describing the type of extrapolation used (e.g., "EC" for extrapolation and clamping in Maxent).
model_name	(character) pattern to be searched when finding the model of interest. This pattern does not include the pattern of ext.type. By default, NULL, all models are considered.
project	(logical) if TRUE, it is assumed that models were projected to other scenarios (this must be always true if models were produced in SWD format).
ext.type	(character) vector of pattern(s) to be searched in the folders inside fmod.dir that identify the extrapolation type(s) of model projections of interest (e.g., "E", "EC", "NE", or a vector of more than one of them). Ignored if project = FALSE.

Details

When models are created with replicates, the values returned correspond to the average of such replicates.

Value

A list with results of variable contribution, permutation importance, and jackknife results. If multiple models are evaluated, a nested list with results for all models is returned.

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