Can't build some models using only one predictor

[pabloriul]

Dear Maya,

I can't get a model using only one predictor for MAXENT.Phillips, MAXENT.Phillips.2 and GBM. Tried using the GuloGulo example as follows:

First attempt was subsetting the stack for one raster

myFiles <- paste0('external/bioclim/current/bio', c(3, 4, 7, 11, 12), '.grd')

myExpl <- raster::stack(system.file(myFiles, package = 'biomod2'))

myExpl <- myExpl[[1]]

Second attempt was loading only one raster

myFiles <- paste0('external/bioclim/current/bio3.grd')

myExpl <- raster(system.file(myFiles, package = 'biomod2'))

Third attempt was stacking the single file

myFiles <- paste0('external/bioclim/current/bio3.grd')

myExpl <- raster::stack(system.file(myFiles, package = 'biomod2'))

Maxent models returns

Model=MAXENT.Phillips (maxnet)
> MAXENT.Phillips modeling...Error in apply(pdata, 1, function(rr) !any(apply(ndata, 1, function(r) identical(r, :
dim(X) must have a positive length
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'predict': object 'model.bm' not found

GBM models returns

GBM modeling...CV: 1
Error in x[i.train, , drop = TRUE][i, , drop = FALSE] :
incorrect number of dimensions
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'predict': object 'model.bm' not found

In both cases they can't find model.bm.

Do you have any idea whats going on?

Thank you

Pablo Riul

[rpatin]

Hello Pablo,
Thank you for reporting the bugs.
I could reproduce the bugs and I think the problems come respectively from maxnet and gbm packages. The three attempt you did at building a single-layer explanatory variables looked all OK.
I tried to correct the bug within the maxnet and gbm packages and created pull-request accordingly, but I do not know when the changes will be accounted for in their respective packages.
Meanwhile you can try to use the forked version of their packages in my repository:
devtools::install_github("rpatin/maxnet")
devtools::install_github("rpatin/gbm")
Let us know if you encounter additional problems with this.
Rémi

[pabloriul]

Dear Rémi,

Thank you very much for your quick reply! Its working fine now.

Cheers,

Pablo

[rpatin]

maxnet was updated so installation can now be done directly from their official repo:
devtools::install_github("mrmaxent/maxnet")