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SDMtune

Species Distribution Model Selection

User-friendly framework that enables the training and the evaluation of species distribution models (SDMs). The package implements functions for data driven variable selection and model tuning and includes numerous utilities to display the results. All the functions used to select variables or to tune model hyperparameters have an interactive real-time chart displayed in the 'RStudio' viewer pane during their execution.

Functions (52)

ANN-class

Artificial Neural Network

BRT-class

Boosted Regression Tree

Maxent-class

Maxent

Maxnet-class

Maxnet

RF-class

Random Forest

SDMmodel-class

SDMmodel

SDMmodel2MaxEnt

SDMmodel2MaxEnt

SDMmodelCV-class

SDMmodelCV

SDMtune-class

SDMtune class

SDMtune-package

SDMtune: Species Distribution Model Selection

SWD-class

Sample With Data

addSamplesToBg

Add Samples to Background

aicc

AICc

auc

AUC

checkMaxentInstallation

Check Maxent Installation

confMatrix

Confusion Matrix

corVar

Print Correlated Variables

doJk

Jackknife Test

getTunableArgs

Get Tunable Arguments

gridSearch

Grid Search

maxentTh

MaxEnt Thresholds

maxentVarImp

Maxent Variable Importance

mergeSWD

Merge SWD Objects

modelReport

Model Report

optimizeModel

Optimize Model

plot-methods

Plot SDMtune object

plotCor

Plot Correlation

plotJk

Plot Jackknife Test

plotPA

Plot Presence Absence Map

plotPred

Plot Prediction

plotROC

Plot ROC curve

plotResponse

Plot Response Curve

plotVarImp

Plot Variable Importance

predict-ANN-method

Predict ANN

predict-BRT-method

Predict BRT

predict-Maxent-method

Predict Maxent

predict-RF-method

Predict RF

predict-SDMmodel-method

Predict

predict-SDMmodelCV-method

Predict for Cross Validation

prepareSWD

Prepare an SWD object

randomFolds

Create Random Folds

randomSearch

Random Search

reduceVar

Reduce Variables

swd2csv

SWD to csv

thinData

Thin Data

thresholds

Thresholds

train

Train

trainValTest

Train, Validation and Test datasets

tss

True Skill Statistics

varImp

Variable Importance

varSel

Variable Selection

virtualSp

Virtual Species

SDMtune

Species Distribution Model Selection

v1.1.4

GPL-3

Authors

Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>), Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>), Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>), Conservation Biology - University of Bern [fnd]

Initial release

SDMtune

Functions (52)

SDMtune

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