kuenm_feval: Evaluation of final Maxent models with independent data

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

Evaluation of final Maxent models with independent data

Description

kuenm_feval evaluates final Maxent models in terms of statistical significance (partial ROC) and omission rates with a user-defined threshold (E).

Usage

kuenm_feval(path, occ.joint, occ.ind, replicates, out.eval, threshold = 5,
            rand.percent = 50, iterations = 500, parallel.proc = FALSE)

Arguments

path	(character) directory in which folders containing final models were created.
occ.joint	(character) the csv file with training and testing occurrences combined, or the file containing occurrences used to create final models; columns must be: species, longitude, latitude.
occ.ind	(character) the name of the csv file with independent occurrences for model evaluation; these occurrences were not used when creating final models; columns as in occ.joint.
replicates	(logical) whether or not final models were created performing replicates.
out.eval	(character) name of the folder where evaluation results will be written.
threshold	(numeric) the percentage of omission error allowed (E), default = 5.
rand.percent	(numeric) the percentage of data to be used for the bootstrapping process when calculating partial ROCs; default = 50.
iterations	(numeric) the number of times that the bootstrap is going to be repeated; default = 500.
parallel.proc	(logical) if TRUE, pROC calculations will be performed in parallel using the available 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 only if models are large RasterLayers or if iterations are more than 5000. Default = FALSE.

Details

This function is used after the creation of final models.

Value

A list with two data.frame objects containing results from the evaluation process, and a folder, in the working directory, containing a csv file with the results from final model evaluation.

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