R help - Jan 2009 - problems with extractPrediction in package caret

Hi list,

I´m working on a predictive modeling task using the caret package.
I found the best model parameters using the train() and trainControl() command.
Now I want to evaluate my model and make predictions on a test dataset. I tried
to follow the instructions in the manual and the vignettes but unfortunately I´m
getting an error message I can`t figure out.
Here is my code:
rfControl <- trainControl(method = "oob", returnResamp =
"all", returnData=TRUE, verboseIter = TRUE)
rftrain <- train(x=train_x, y=trainclass, method="rf",
tuneGrid=tuneGrid, tr.control=rfControl)

pred <- predict(rftrain) 
pred	# this works fine
expred <- extractPrediction(rftrain)

Error in models[[1]]$trainingData : 
  $ operator is invalid for atomic vectors

My predictors are 28 numeric attributes and one factor.
I`m working with the latest version of caret and R 2.7.2 on WinXP.

Any advice is very welcome.

Thanks.
TIM


------------------------------------------------------------------------------- 
Dipl.-Geogr. Tim Häring
Sachgebiet Standort und Bodenschutz (SG 2.1)
Bayerische Landesanstalt für Wald und Forstwirtschaft
Am Hochanger 11
D-85354 Freising

Tel.: +49-(0)8161/71-4769
E-Mail: tim.haering@lwf.bayern.de
http://www.lwf.bayern.de




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H?ring, Tim (LWF) wrote:
> Hi list,
> 
> I?m working on a predictive modeling task using the caret package.
> I found the best model parameters using the train() and trainControl()
command. Now I want to evaluate my model and make predictions on a test dataset.
I tried to follow the instructions in the manual and the vignettes but
unfortunately I?m getting an error message I can`t figure out.
> Here is my code:
> rfControl <- trainControl(method = "oob", returnResamp =
"all", returnData=TRUE, verboseIter = TRUE)
> rftrain <- train(x=train_x, y=trainclass, method="rf",
tuneGrid=tuneGrid, tr.control=rfControl)
> 
> pred <- predict(rftrain) 
> pred	# this works fine
> expred <- extractPrediction(rftrain)
> 
> Error in models[[1]]$trainingData : 
>   $ operator is invalid for atomic vectors

I cannot reproduce it (not having your data) and I doubt you are using 
the most recent version which is 3.51.
Anyway, *if* it is a bug, then please report to the package maintainer.

Best,
Uwe Ligges

> My predictors are 28 numeric attributes and one factor.
> I`m working with the latest version of caret and R 2.7.2 on WinXP.
> 
> Any advice is very welcome.
> 
> Thanks.
> TIM
> 
> 
>
-------------------------------------------------------------------------------
> Dipl.-Geogr. Tim H?ring
> Sachgebiet Standort und Bodenschutz (SG 2.1)
> Bayerische Landesanstalt f?r Wald und Forstwirtschaft
> Am Hochanger 11
> D-85354 Freising
> 
> Tel.: +49-(0)8161/71-4769
> E-Mail: tim.haering at lwf.bayern.de
> http://www.lwf.bayern.de
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
> ------------------------------------------------------------------------
> 
> ______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

The issue is the usage of extractPrediction.

   expred <- extractPrediction(rftrain)

should really be

   expred <- extractPrediction(list(rftrain))

Since this function is intended to get predictions across multiple
models, the man file has a description of the first argument to teh
funtion being "a list of objects of the class train."

-- 

Max