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biomod2 (version 4.2-5)

OptionsBigboss: Bigboss pre-defined parameter values for single models

Description

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

Usage

OptionsBigboss

Arguments

Format

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

ANN.binary.nnet.nnet

  • size = 5

  • decay = 5

  • 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 = 25)

  • 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 = NULL

  • 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'