I try biomod2 tutorial, buit it does not give the expected output

Question

An error appears in the part where you enter myBiomodEM. Error in BIOMOD_EnsembleModeling.ckeck.args(modeling.output, chosen.modles, : prob.mean, prob.cv, prob.ci, prob.median, committee.averaging and prob.mean.weight arguments must be logical

It usually well, but suddenly an error appears in this part. I'd appreciate it if you could tell me how to solve it.

species <- read.csv(choose.files(),header=T)

species

path = "E:/ecology/tt/Ensemble_tif"
lst <- list.files(path=path,pattern='tif$',full.names = T)


preds <- stack(lst)

suppressWarnings(min(numeric(0), na.rm = TRUE))


SpName <- 'Pinus'
sp <- as.numeric(species[,SpName])
spXY <- species[,c('x','y')]

spExpl <- stack(lst)


myBiomodData <- BIOMOD_FormatingData(resp.var = sp,
                                     expl.var = spExpl,
                                     resp.xy = spXY,
                                     resp.name = SpName)

myBiomodData

plot(myBiomodData)

myBiomodOption <- BIOMOD_ModelingOptions()
myBiomodeloutput <- BIOMOD_Modeling(
  myBiomodData,
  models = c('GLM','CTA','RF','MARS','FDA','GAM','ANN','GBM'),
  models.options = myBiomodOption,
  NbRunEval=10,
  DataSplit=70,
  Yweights = NULL,
  Prevalence= NULL,
  VarImport=7,
  models.eval.meth = c('TSS','ROC'),
  SaveObj = TRUE,
  rescal.all.models = TRUE,
  do.full.models = FALSE,
  modeling.id = paste(SpName,"FirstModeling",sep=""))

myBiomodeloutput

myBiomodModelEval <- get_evaluations(myBiomodeloutput)
myBiomodModelEval

R <- myBiomodModelEval
write.csv(R, file = "E:/ecology/kk/tt/corEnvT.csv")


dimnames(myBiomodModelEval)

get_variables_importance(myBiomodeloutput)

a <- get_variables_importance(myBiomodeloutput)

write.csv(a, file = "E:/ecology/kk/tt/corEnvT.csv")



myBiomodEM <- BIOMOD_EnsembleModeling(
  modeling.output = myBiomodeloutput,
  chosen.models = 'all',
  em.by='all',
  eval.metric = c('TSS'),
  eval.metric.quality.threshold = c(0.8),
  prob.mean = T,
  prob.cv = T,
  prob.ci = T,
  prob.ci.alpha = 0.05,
  prob.median = T,
  committee.averaging = T,
  prob.mean.weight = T,
  prob.mean.weight.decay = 'proportional')


myBiomodEM

get_evaluations(myBiomodEM)

myBiomodProj <- BIOMOD_Projection(
  modeling.output = myBiomodeloutput,
  new.env = spExpl,
  proj.name = 'current',
  selected.models = 'all',
  binary.meth = 'TSS',
  compress = 'xz',
  clamping.mask = T,
  output.format = '.img',
  prob.mean.weight = T,
  prob.mean.weight.decay = 'proportional')

myBiomodProj

myCurrentProj <- get_predictions(myBiomodProj)

myCurrentProj

myBiomodEF <- BIOMOD_EnsembleForecasting(
  EM.output = myBiomodEM,
  projection.output = myBiomodProj)

myBiomodEF

In addition, the result could be exported as a TIF file in the SSDM package, but I wonder whether the completed result is exported as a GIS TIF file within the BIOOD2 package.

I'd really appreciate it if you let me know

I tried to change the code after watching the tutorial, but I don't know what's wrong because it's the same as my code.

I try biomod2 tutorial, buit it does not give the expected output

0 Answers0