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SDMtune (version 0.2.1)

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.

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Version

Install

install.packages('SDMtune')

Monthly Downloads

516

Version

0.2.1

License

GPL-3

Maintainer

Sergio Vignali

Last Published

December 5th, 2019

Functions in SDMtune (0.2.1)

SDMmodelCV-class

SDMmodelCV
get_tunable_args

Get Tunable Arguments
plotVarImp

Plot Variable Importance
optimizeModel

Optimize Model
plotResponse

Plot Response Curve
old2NewSWD

Convert Old SWD object
getSubsample

Get Dataset Subsample, Deprecated
gridSearch

Grid Search
maxentTh

MaxEnt Thresholds
modelReport

Model Report
old2NewSDMmodel

Convert Old SDMmodel object
plotCor

Plot Correlation
confMatrix

Confusion Matrix
predict,Maxent-method

Predict Maxent
plot,SDMtune,missing-method

Plot SDMtune object
auc

AUC
SWD-class

Sample With Data
swd2csv

SWD to csv
old2NewSDMtune

Convert Old SDMtune object
doJk

Jackknife Test
corVar

Print Correlated Variables
plotJk

Plot Jackknife Test
old2NewSDMmodelCV

Convert Old SDMmodelCV object
thinData

Thin Data
plotPA

Plot Presence Absence Map
virtualSp

Virtual Species
predict,RF-method

Predict RF
thresholds

Thresholds
prepareSWD

Prepare an SWD object
randomFolds

Create Random Folds
predict,ANN-method

Predict ANN
predict,BRT-method

Predict BRT
predict,SDMmodelCV-method

Predict for Cross Validation
predict,SDMmodel-method

Predict
varImp

Variable Importance
train

Train
varSel

Variable Selection
aicc

AICc
maxentVarImp

Maxent Variable Importance
reduceVar

Reduce Variables
plotPred

Plot Prediction
randomSearch

Random Search
tss

True Skill Statistics
mergeSWD

Merge SWD Objects
plotROC

Plot ROC curve
trainValTest

Train, Validation and Test datasets
SDMmodel2MaxEnt

SDMmodel2MaxEnt
RF-class

Random Forest
Maxent-class

Maxent
ANN-class

Artificial Neural Network
BRT-class

Boosted Regression Tree
SDMtune-class

SDMtune class
Maxnet-class

Maxnet
SDMtune-pkg

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

SDMmodel