biomod2: BIOMOD_cv – R documentation

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BIOMOD_cv

Custom models cross-validation procedure

Description

This function creates a DataSplitTable which could be used to evaluate models in Biomod with repeated k-fold cross-validation (cv) or stratified cv instead of repeated split sample runs

Usage

BIOMOD_cv(
  data,
  k = 5,
  repetition = 5,
  do.full.models = TRUE,
  stratified.cv = FALSE,
  stratify = "both",
  balance = "pres"
)

Arguments

`data`	BIOMOD.formated.data object returned by BIOMOD_FormatingData
`k`	number of bins/partitions for k-fold cv
`repetition`	number of repetitions of k-fold cv (1 if stratified.cv=TRUE)
`do.full.models`	if true, models calibrated and evaluated with the whole dataset are done
`stratified.cv`	logical. run a stratified cv
`stratify`	stratification method of the cv. Could be "x", "y", "both" (default), "block" or the name of a predictor for environmental stratified cv.
`balance`	make balanced particions for "presences" (default) or "absences" (resp. pseudo-absences or background).

Details

Stratified cv could be used to test for model overfitting and for assessing transferability in geographic and environmental space. If balance = "presences" presences are divided (balanced) equally over the particions (e.g. Fig. 1b in Muscarelly et al. 2014). Pseudo-Absences will however be unbalanced over the particions especially if the presences are clumped on an edge of the study area. If balance = "absences" absences (resp. Pseudo-Absences or background) are divided (balanced) as equally as possible for the particions (geographical balanced bins given that absences are spread over the study area equally, approach similar to Fig. 1 in Wenger et Olden 2012). Presences will however be unbalanced over the particians. Be careful: If the presences are clumped on an edge of the study area it is possible that all presences are in one bin.

Value

DataSplitTable matrix with k*repetition (+ 1 for Full models if do.full.models = TRUE) columns for BIOMOD_Modeling function. Stratification "x" and "y" was described in Wenger and Olden 2012. While Stratification "y" uses k partitions along the y-gradient, "x" does the same for the x-gradient and "both" combines them. Stratification "block" was described in Muscarella et al. 2014. For bins of equal number are partitioned (bottom-left, bottom-right, top-left and top-right).

Author(s)

Frank Breiner frank.breiner@wsl.ch

References

Muscarella, R., Galante, P.J., Soley-Guardia, M., Boria, R.A., Kass, J.M., Uriarte, M. & Anderson, R.P. (2014). ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods in Ecology and Evolution, 5, 1198-1205. Wenger, S.J. & Olden, J.D. (2012). Assessing transferability of ecological models: an underappreciated aspect of statistical validation. Methods in Ecology and Evolution, 3, 260-267.

Examples

## Not run: 
# species occurrences
DataSpecies <- read.csv(system.file("external/species/mammals_table.csv",
                                    package="biomod2"))
head(DataSpecies)

the name of studied species
myRespName <- 'GuloGulo'

# the presence/absences data for our species 
myResp <- as.numeric(DataSpecies[,myRespName])

# the XY coordinates of species data
myRespXY <- DataSpecies[,c("X_WGS84","Y_WGS84")]


# Environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
myExpl = stack( system.file( "external/bioclim/current/bio3.grd", 
                             package="biomod2"),
                system.file( "external/bioclim/current/bio4.grd", 
                             package="biomod2"), 
                system.file( "external/bioclim/current/bio7.grd", 
                             package="biomod2"),  
                system.file( "external/bioclim/current/bio11.grd", 
                             package="biomod2"), 
                system.file( "external/bioclim/current/bio12.grd", 
                             package="biomod2"))

# 1. Formatting Data
myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
                                     expl.var = myExpl,
                                     resp.xy = myRespXY,
                                     resp.name = myRespName)

# 2. Defining Models Options using default options.
myBiomodOption <- BIOMOD_ModelingOptions()


# 3. Creating DataSplitTable

DataSplitTable <- BIOMOD_cv(myBiomodData, k=5, rep=2, do.full.models=F)
DataSplitTable.y <- BIOMOD_cv(myBiomodData,stratified.cv=T, stratify="y", k=2)
colnames(DataSplitTable.y)[1:2] <- c("RUN11","RUN12")
DataSplitTable <- cbind(DataSplitTable,DataSplitTable.y)
head(DataSplitTable)

# 4. Doing Modelisation

myBiomodModelOut <- BIOMOD_Modeling( myBiomodData, 
                                     models = c('RF'), 
                                     models.options = myBiomodOption, 
                                     DataSplitTable = DataSplitTable,
                                     VarImport=0, 
                                     models.eval.meth = c('ROC'),
                                     do.full.models=FALSE,
                                     modeling.id="test")

## get cv evaluations
eval <- get_evaluations(myBiomodModelOut,as.data.frame=T)

eval$strat <- NA
eval$strat[grepl("13",eval$Model.name)] <- "Full"
eval$strat[!(grepl("11",eval$Model.name)|
             grepl("12",eval$Model.name)|
             grepl("13",eval$Model.name))] <- "Random"
eval$strat[grepl("11",eval$Model.name)|grepl("12",eval$Model.name)] <- "Strat"

boxplot(eval$Testing.data~ eval$strat, ylab="ROC AUC")

## End(Not run)

biomod2

Ensemble Platform for Species Distribution Modeling

v3.4.6

GPL-2

Authors

Wilfried Thuiller [aut, cre], Damien Georges [aut, cre], Robin Engler [aut], Frank Breiner [aut]

Initial release

2020-02-24