[Biomod-commits] Error in model.frame.default - "invalid type (list) for variable" - using BIOMOD

[Chris Hassall]

I have exactly the same problem, both with my own data and with the 
tutorial data.  I have not found a solution or any previous mention of 
this problem.  I have used BIOMOD successfully before on the same 
computer.  I have BIOMOD version 1.1-7.02/r300 and R version 2.15.0 (all 
up to date).

Input code:

------------------------------------------------------------------------
library(BIOMOD)
data(Sp.Env)
LatLong <- Sp.Env[,2:3]
Expl.Var <- Sp.Env[,4:10]
Resp.Var <- Sp.Env[,11:17]
Initial.State(Response = Resp.Var[,1:2], Explanatory = Expl.Var)
Models(GLM = FALSE, TypeGLM = "quad", Test = "AIC", GBM = FALSE, 
No.trees = 3000, GAM = FALSE, CTA = TRUE, CV.tree = 50,
    ANN = FALSE, CV.ann = 2, SRE = FALSE, quant=0.05, FDA = TRUE, MARS = 
FALSE, RF = FALSE, NbRunEval = 2, DataSplit = 80,
    Yweights=NULL, Roc=TRUE, Optimized.Threshold.Roc=TRUE, Kappa=TRUE, 
TSS=TRUE, KeepPredIndependent = FALSE, VarImport=5,
    NbRepPA=2, strategy="circles", coor=LatLong, distance=2, 
nb.absences=1000)
------------------------------------------------------------------------

Output error:

------------------------------------------------------------------------
-----------------------------------
Modelling summary
-----------------------------------
Number of species modelled :            2
Sp281, Sp290

numerical variables :                   Var1, Var2, Var3, Var4, Var5, 
Var6, Var7


number of evaluation repetitions :      2
number of pseudo-absences runs :        2
models selected :                       CTA, FDA
total number of model runs :            24
-----------------------------------


#####                    Sp281                  #####
#####              pseudo-absence run 1                 #####
Model=Classification tree
          50 Fold Cross-Validation
Error in model.frame.default(Terms, newdata, na.action = na.action, xlev 
= attr(object,  :
   invalid type (list) for variable 'Var1'
------------------------------------------------------------------------

Any assistance would be greatly appreciated,

Chris

___________________________________________________

*Dr Christopher Hassall*
Ontario MRI Postdoctoral Fellow
Carleton University
Ottawa, ON,
K1S 5B6 Canada
Tel: 00 1 (613) 520 2600 (ext. 3866)
Fax: 00 1 (613) 520 3539
http://www.christopherhassall.com/
___________________________________________________

On 10/05/2012 4:57 PM, Oscar Javier Ramos wrote:
> Hi,
>
> I'm beginning with BIOMOD.
>
> Just running the example on the "BIOMOD: Tutorial (February 13, 2012)" 
> => data(Sp.Env)",
>
> I got the following error:
>
> ------------------------------
> -----
> Modelling summary
> -----------------------------------
> Number of species modelled :            2
> Sp281, Sp290
>
> numerical variables :                   Var1, Var2
>
>
> number of evaluation repetitions :      3
> number of pseudo-absences runs :        2
> models selected :                       ANN, CTA, GAM, GBM, GLM, MARS, 
> FDA, RF, SRE
> total number of model runs :            144
> -----------------------------------
>
>
> #####                    Sp281                  #####
> #####              pseudo-absence run 1                 #####
> Model=Artificial Neural Network
>          2 Fold Cross Validation + 3 Repetitions
> Calibration and evaluation phase: Nb of cross-validations:  3
>
> Error in model.frame.default(formula = eval(parse(text = 
> paste("Target[Samp$calibration]",  :
>   invalid type (list) for variable 'Var1'
>
>
> Could anyone help me to overcome this problem?
>
>
> Thanks,
>
> Oscar
>
>
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>
> -- 
>
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