Bigboss pre-defined parameter values for single models

A BIOMOD.models.options object containing for each single model available in biomod2 the parameter values pre-defined by biomod2 team.

OptionsBigboss

Format

A BIOMOD.models.options object with some changed values :

ANN.binary.nnet.nnet

• size = 5

• decay = 0.1

• trace = FALSE

• rang = 0.1

• maxit = 200

CTA.binary.rpart.rpart

• method = 'class'

• control = list(xval = 5, minbucket = 5, minsplit = 5, cp = 0.001, maxdepth = 10)

• cost = NULL

FDA.binary.mda.fda

• method = 'mars'

GAM.binary.gam.gam

GAM.binary.mgcv.bam

GAM.binary.mgcv.gam

• family = binomial(link = 'logit')

• method = 'GCV.Cp'

• control = list(epsilon = 1e-06, trace = FALSE, maxit = 100)

GBM.binary.gbm.gbm

• n.trees = 2500

• interaction.depth = 7

• n.minobsinnode = 5

• shrinkage = 0.001

• cv.folds = 3

• keep.data = FALSE

• n.cores = 1

GLM.binary.stats.glm

• family = binomial(link = 'logit')

• mustart = 0.5

• control = glm.control(maxit = 50)

MARS.binary.earth.earth

• glm = list(family = binomial(link = 'logit'))

• ncross = 0

• nk = NULL

• penalty = 2

• thresh = 0.001

• nprune = NULL

• pmethod = 'backward'

MAXENT.binary.MAXENT.MAXENT

• path_to_maxent.jar = '.'

RF.binary.randomForest.randomForest

• type = 'classification'

• ntree = 500

• mtry = 2

• strata = factor(c(0, 1))

• sampsize = NULL

• nodesize = 5

• maxnodes = NULL

RFd.binary.randomForest.randomForest

• type = 'classification'

• ntree = 500

• mtry = 2

• strata = factor(c(0, 1))

• sampsize = NULL

• nodesize = 5

• maxnodes = NULL

SRE.binary.biomod2.bm_SRE

• do.extrem = TRUE

XGBOOST.binary.xgboost.xgboost

• params = list(max_depth = 2, eta = 1)

• nthread = 2

• nrounds = 4

• objective = 'binary:logistic'