[Biomod-commits] Projection.raster error?

[Wilfried Thuiller]

Dear Jason,

This is indeed surprising. 

I am bit surprised with the following code 

files <- list.files("~/Documents/R/R_data/SD/raster/current", pattern='asc', full.names=T)
CurrentStack <- stack(files[c(1,13,14,15,4,6,7,20)])

Are you sure it works fine? 
Try to make a plot of CurrentStack and print the summary of the rasters. I am surprised you manage to stack these files whereas you do not give the pass to stack. 

In any case, it seems that CurrentStack data are not in the good format. 

Best
Wilfried



Le 8 févr. 2012 à 02:03, jason b mackenzie a écrit :

> 
> All
> 
> 
> I am getting an error (below) using the Projection.raster function. 
> 
> Error in model.frame.default(Terms, newdata, na.action = na.action, xlev = object$xlevels) : 
>   invalid type (list) for variable 'DataF'
> In addition: Warning message:
> 'newdata' had 5711 rows but variable(s) found have 1131 rows
> 
> 
> 
> I thought part of the problem might relate to differences in the naming of my explanatory variables, but they appear to be the same in both my presence-absence site data (='SP.ENV') and my RasterStack (='CurrentStack').
> 
> > colnames(SP.ENV[,4:11])
> [1] "bio_1"      "bio_3"      "bio_4"      "bio_5"      "bio_12"     "bio_14"     "bio_15"     "soil_aws"
> > layerNames(CurrentStack)
> [1] "bio_1"      "bio_3"      "bio_4"      "bio_5"      "bio_12"     "bio_14"     "bio_15"     "soil_aws"
> 
> 
> 
> Also, the row flags noted in the warning message don't correspond with dimensions of either dataset?
> 
> > dim(SP.ENV)
> [1] 1742   75
> > dim(CurrentStack)
> [1] 232 238   8
> 
> 
> 
> Any suggestions? FYI, I am running the latest versions of R (2.14.1) and BIOMOD (1.1.7) and my calls are pasted below.
> 
> 
> 
> Cheers, 
> Jason
> 
> 
> -- 
> 
> Jason MacKenzie, PhD
> Senior Conservation Fellow
> The Nature Conservancy
> 201 Mission Street, 4th Floor
> San Francisco, CA 94105
> jmackenzie at tnc.org
> jasonbmackenzie        [skype]
> 
> 
> 
> 
> 
> 
> 
> 
> library(raster)
> library(BIOMOD)
> 
> setwd("~/Documents/R/R_data/SD/veg4")
> SP.ENV <- read.table("SPENV_veg4.txt",  h=T, sep="\t")
> COORxy <- read.table("CoorXY_veg4.txt", h=T, sep="\t")
> 
> Initial.State(Response=SP.ENV[,12:13], Explanatory=SP.ENV[,4:11], IndependentResponse=NULL, IndependentExplanatory=NULL)
> 					
> Models(GLM=F, TypeGLM="quad", Test="AIC", GAM=T, Spline=4, GBM=T, No.trees=3000, CTA=T, CV.tree=50, ANN=T, CV.ann=3, SRE=T, quant=0.025, FDA=T, MARS=T, RF=T, NbRunEval=3, DataSplit=70, Yweights=NULL, Roc=T, Optimized.Threshold.Roc=T, Kappa=T, TSS=T, KeepPredIndependent=F, VarImport=5, NbRepPA=2, strategy="sre", nb.absences=1000)
> 
> CurrentPred(GLM=F, GAM=T, GBM=T, CTA=T, ANN=T, SRE=T, FDA=T, MARS=T, RF=T, BinRoc=T,  BinKappa=T,  BinTSS=T, FiltRoc=T, FiltKappa=T, FiltTSS=T) 
> 								
> PredictionBestModel(method='all', Bin.trans=T, Filt.trans=T)	
> 		
> files <- list.files("~/Documents/R/R_data/SD/raster/current", pattern='asc', full.names=T)
> CurrentStack <- stack(files[c(1,13,14,15,4,6,7,20)])
> 
> Projection.raster(RasterProj = CurrentStack, Proj.name='CurrentRaster', GLM=F, GAM=T, GBM=T, CTA=T, ANN=T, SRE=T, quant=0.025, FDA=T, MARS=T, RF=T, BinRoc=T, BinKappa=T, BinTSS=T, FiltRoc=T, FiltKappa=T, FiltTSS=T, repetition.model=T, stack.out=T, compress="gzip")
> 
> 
> 
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--------------------------
Dr. Wilfried Thuiller
Laboratoire d'Ecologie Alpine, UMR CNRS 5553
Université Joseph Fourier
BP53, 38041 Grenoble cedex 9, France
tel: +33 (0)4 76 51 44 97
fax: +33 (0)4 76 51 42 79

Email: wilfried.thuiller at ujf-grenoble.fr
Personal website: http://www.will.chez-alice.fr
Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm

ERC Starting Grant TEEMBIO project: http://www.will.chez-alice.fr/Research.html
FP6 European EcoChange project: http://www.ecochange-project.eu







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