[Biomod-commits] Projection.raster error?

[jason b mackenzie]

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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