ecospat.ESM.EnsembleEvaluation {ecospat}R Documentation

Ensemble of Small Models: Evaluation via the Pooling procedure

Description

This function evaluates the Ensemble of Small Models by pooling the different runs of the cross validation as in Collart et al. 2021

Usage

ecospat.ESM.EnsembleEvaluation(ESM.modeling.output,
                               ESM.EnsembleModeling.output,
                               metrics = c("SomersD","AUC","MaxTSS","MaxKappa","Boyce"), 
                               EachSmallModels = FALSE)

Arguments

ESM.modeling.output

a list returned by ecospat.ESM.Modeling

ESM.EnsembleModeling.output

a list returned by ecospat.ESM.EnsembleModeling

metrics

a vector of evaluation metrics chosen among "SomersD", "AUC", "MaxTSS", "MaxKappa", "Boyce"

EachSmallModels

should the individual bivariate models be evaluated by the pooling procedure?

Details

Because a minimum sample size is needed to evaluate models (see Jimenez-Valverde, 2020), this function uses the approach from Collart et al.(2021), which consists to pool the suitability values of the hold-out data (evaluation dataset) across replicates. As the same data point (presence or absence or background point) is presumably sampled in several replicates, the suitability values for each data point is consequently averaged across replicates where they were sampled. This procedure generates a series of independent suitability values with a size approximately equal (as some data points may not have been sampled by chance in any of the n replicates) to that of the number of data point.

Value

a list containing:

ESM.evaluations

a matrix with the evaluation scores for the ESMs based on the different modelling algorithms and based on the consensus across the modelling algorithms (called here "ensemble")

ESM.fit

a matrix of predicted values resulting from the pooling procedure and used to compute the evaluation scores. The column resp is where the species occurs or not

ESM.evaluations.bivariate.models

a list containing a matrix of evaluation scores for each bivariate models (generated only if EachSmallModels = T)

ESM.fit.bivariate.models

a list containing a matrix of of predicted values resulting from the pooling procedure for each bivariate models (generated only if EachSmallModels = T)

Author(s)

Flavien Collart flavien.collart@unil.ch

with contributions of Olivier Broennimann olivier.broennimann@unil.ch

References

Collart, F., Hedenas, L., Broennimann, O., Guisan, A. and Vanderpoorten, A. 2021. Intraspecific differentiation: Implications for niche and distribution modelling. Journal of Biogeography. 48, 415-426. doi: 10.1111/jbi.14009

Jimenez-Valverde, A. 2020. Sample size for the evaluation of presence-absence models. Ecological Indicators. 114, 106289. doi: 10.1016/j.ecolind.2020.106289

See Also

ecospat.ESM.EnsembleModeling


[Package ecospat version 3.3 Index]