## Not run:
#
# #Run biomod2 to produce a model prediction
# DataSpecies <- read.csv(system.file("external/species/mammals_table.csv", package="biomod2"))
#
# 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")]
# # load the environmental raster layers (could be .img, ArcGIS
# # rasters or any supported format by the raster package)
# # Environmental variables extracted from Worldclim (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"))
#
#
# myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
# expl.var = myExpl,
# resp.xy = myRespXY,
# resp.name = myRespName)
# myBiomodData
# myBiomodOption <- BIOMOD_ModelingOptions()
#
# myBiomodModelOut <- BIOMOD_Modeling(
# myBiomodData,
# models = c('GLM'),
# models.options = myBiomodOption,
# NbRunEval=1,
# DataSplit=80,
# Prevalence=0.5,
# VarImport=3,
# models.eval.meth = c('TSS','ROC'),
# SaveObj = TRUE,
# rescal.all.models = TRUE,
# do.full.models = FALSE,
# modeling.id = paste(myRespName,"FirstModeling",sep=""))
#
# myBiomodModelOut
# myBiomodModelEval <- get_evaluations(myBiomodModelOut)
#
# myBiomodEM <- BIOMOD_EnsembleModeling(
# modeling.output = myBiomodModelOut,
# chosen.models = 'all',
# em.by='all',
# eval.metric = c('TSS'),
# eval.metric.quality.threshold = c(0.7),
# prob.mean = TRUE,
# prob.cv = TRUE,
# prob.ci = TRUE,
# prob.ci.alpha = 0.05,
# prob.median = TRUE,
# committee.averaging = TRUE,
# prob.mean.weight = TRUE,
# prob.mean.weight.decay = 'proportional' )
#
# myBiomodEM
#
# myBiomodProj <- BIOMOD_Projection(
# modeling.output = myBiomodModelOut,
# new.env = myExpl,
# proj.name = 'current',
# selected.models = 'all',
# binary.meth = 'TSS',
# compress = 'xz',
# clamping.mask = FALSE,
# output.format = '.grd')
#
# myBiomodProj
# plot(myBiomodProj, str.grep = 'GLM')
# #
# Pred <-get_predictions(myBiomodProj)
# Sp.occ.xy <- DataSpecies[DataSpecies[,5]==1,2:3]
# Percentage <- 7
#
# binary.model<-ecospat.binary.model (Pred, Sp.occ.xy, Percentage)
# plot(binary.model)
# ## End(Not run)
Run the code above in your browser using DataLab