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SDMtune (version 0.1.0)

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

0.1.0

License

GPL-3

Maintainer

Sergio Vignali

Last Published

June 21st, 2019

Functions in SDMtune (0.1.0)

gridSearch

Grid Search
predict,SDMmodel-method

Predict
maxentTh

MaxEnt Thresholds
predict,Maxent-method

Predict Maxent
trainValTest

Train, Validation and Test datasets
corVar

Print Correlated Variables
plotPA

Plot Presence Absence Map
plotJk

Plot Jackknife Test
train

Train
doJk

Jackknife Test
getSubsample

Get Dataset Subsample
maxentVarImp

Maxent Variable Importance
plotResponse

Plot Response Curve
get_tunable_args

Get Tunable Arguments
plotVarImp

Plot Variable Importance
prepareSWD

Prepare an SWD object
randomSearch

Random Search
SDMtune-class

SDMtune class
confMatrix

Confusion Matrix
condor

Locations of Vultur gryphus.
plot,SDMtune,missing-method

Plot SDMtune object
plotCor

Plot Correlation
thinData

Thin Data
optimizeModel

Optimize Model
modelReport

Model Report
mergeSWD

Merge SWD Objects
plotPred

Plot Prediction
swd2csv

SWD to csv
reduceVar

Reduce Variables
tss

True Skill Statistics
plotROC

Plot ROC curve
varSel

Variable Selection
thresholds

Thresholds
varImp

Variable Importance
Maxent-class

Maxent
Maxnet-class

Maxnet
SDMtune-pkg

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

Sample With Data
SDMmodel-class

SDMmodel
SDMmodel2MaxEnt

SDMmodel2MaxEnt
auc

AUC
SDMmodelCV-class

SDMmodelCV
aicc

AICc