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SDMtune (version 0.1.1)

Species Distribution Model Selection

Description

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. At the moment only the maximum entropy method is available using the 'Java' implementation, Phillips et al. (2006) , through the 'dismo' package and the 'R' implementation through the 'maxnet' package, Phillips et al. (2017) . 'SDMtune' uses its own script to predict maxent models, resulting in much faster predictions for large datasets compared to native predictions from the use of the 'Java' software. This reduces considerably the computation time when tuning the model using the AICc.

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Version

Install

install.packages('SDMtune')

Monthly Downloads

516

Version

0.1.1

License

GPL-3

Maintainer

Sergio Vignali

Last Published

July 14th, 2019

Functions in SDMtune (0.1.1)

maxentVarImp

Maxent Variable Importance
corVar

Print Correlated Variables
doJk

Jackknife Test
plotJk

Plot Jackknife Test
confMatrix

Confusion Matrix
Maxnet-class

Maxnet
condor

Locations of Vultur gryphus.
plotPA

Plot Presence Absence Map
predict,Maxent-method

Predict Maxent
plotPred

Plot Prediction
predict,SDMmodel-method

Predict
plotROC

Plot ROC curve
maxentTh

MaxEnt Thresholds
gridSearch

Grid Search
plot,SDMtune,missing-method

Plot SDMtune object
mergeSWD

Merge SWD Objects
reduceVar

Reduce Variables
swd2csv

SWD to csv
tss

True Skill Statistics
getSubsample

Get Dataset Subsample
get_tunable_args

Get Tunable Arguments
plotResponse

Plot Response Curve
varImp

Variable Importance
thinData

Thin Data
plotCor

Plot Correlation
thresholds

Thresholds
modelReport

Model Report
varSel

Variable Selection
plotVarImp

Plot Variable Importance
prepareSWD

Prepare an SWD object
optimizeModel

Optimize Model
randomSearch

Random Search
train

Train
trainValTest

Train, Validation and Test datasets
SDMmodelCV-class

SDMmodelCV
SDMtune-pkg

SDMtune: A package for tuning Species Distribution Models.
Maxent-class

Maxent
SDMmodel-class

SDMmodel
aicc

AICc
SDMtune-class

SDMtune class
SDMmodel2MaxEnt

SDMmodel2MaxEnt
SWD-class

Sample With Data
auc

AUC