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SDMtune (version 1.0.0)

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.

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Version

Install

install.packages('SDMtune')

Monthly Downloads

461

Version

1.0.0

License

GPL-3

Maintainer

Sergio Vignali

Last Published

December 10th, 2019

Functions in SDMtune (1.0.0)

auc

AUC
aicc

AICc
mergeSWD

Merge SWD Objects
corVar

Print Correlated Variables
plotCor

Plot Correlation
maxentVarImp

Maxent Variable Importance
BRT-class

Boosted Regression Tree
confMatrix

Confusion Matrix
plot,SDMtune,missing-method

Plot SDMtune object
doJk

Jackknife Test
gridSearch

Grid Search
predict,Maxent-method

Predict Maxent
get_tunable_args

Get Tunable Arguments
maxentTh

MaxEnt Thresholds
plotPred

Plot Prediction
plotROC

Plot ROC curve
plotPA

Plot Presence Absence Map
tss

True Skill Statistics
plotVarImp

Plot Variable Importance
plotResponse

Plot Response Curve
plotJk

Plot Jackknife Test
trainValTest

Train, Validation and Test datasets
thinData

Thin Data
randomFolds

Create Random Folds
addSamplesToBg

Add Samples to Background
modelReport

Model Report
train

Train
varImp

Variable Importance
predict,RF-method

Predict RF
prepareSWD

Prepare an SWD object
swd2csv

SWD to csv
virtualSp

Virtual Species
SWD-class

Sample With Data
thresholds

Thresholds
predict,SDMmodel-method

Predict
optimizeModel

Optimize Model
varSel

Variable Selection
predict,SDMmodelCV-method

Predict for Cross Validation
reduceVar

Reduce Variables
predict,ANN-method

Predict ANN
randomSearch

Random Search
predict,BRT-method

Predict BRT
SDMmodel2MaxEnt

SDMmodel2MaxEnt
Maxent-class

Maxent
SDMmodelCV-class

SDMmodelCV
Maxnet-class

Maxnet
SDMtune-class

SDMtune class
SDMtune-pkg

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

Artificial Neural Network
SDMmodel-class

SDMmodel
RF-class

Random Forest