[Biomod-commits] Projection.raster error?
Wilfried Thuiller
wilfried.thuiller at ujf-grenoble.fr
Fri Feb 10 10:06:07 CET 2012
This error is really weird and I do not see where it comes from then.
Have you tried to identify if it comes from one technique or for all?
Run the Projection.raster just on GLM for instance, and then just on randomForest.
If you do not find, please send me the data offline and we'll try to see.
Le 10 févr. 2012 à 09:21, jason b mackenzie a écrit :
> Hi Wilfried
>
> I got the list.files( ) code for stacking off an earlier post on this list. typically i would use something more like below, but if i compare stacks produced by both approaches, i still get the same maps, vectors or values from functions, such as plots( ), layerNames( ) and setMinMax ( ). the dim ( ) of individual RasterLayers and the RasterStacks appear to be fine?
>
> Any other suggestions what might be wrong with formatting?
>
> I know you're busy, so thanks for the response.
>
> Cheers,
> Jason
>
>
>
> library(raster)
> setwd("/Users/jmackenzie/Documents/R/R_data/SD/raster/current/")
> bio_1 <- raster("bio_1.asc")
> bio_3 <- raster("bio_3.asc")
> bio_4 <- raster("bio_4.asc")
> bio_5 <- raster("bio_5.asc")
> bio_12 <- raster("bio_12.asc")
> bio_14 <- raster("bio_14.asc")
> bio_15 <- raster("bio_15.asc")
> soil_aws5k <- raster("soil_aws5k.asc")
> current <- stack(bio_1, bio_3, bio_4, bio_5, bio_12, bio_14, bio_15, soil_aws5k)
>
>
>
>
> On Feb 10, 2012, at 6:02 PM, Wilfried Thuiller wrote:
>
>> 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
>>
>>
>>
>>
>>
>>
>>
>
>
> --
>
> jason b mackenzie
> 80 banambila street
> aranda, act 2614
>
> 0447 002 629 [mobile]
> jasonbmackenzie [skype]
>
>
>
>
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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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