Charles,
You should not be treating the classes as numeric (is virginica really
three times setosa?). Q^2 and/or R^2 are not appropriate for classification.
Max
On Sat, Mar 2, 2013 at 5:21 PM, Charles Determan Jr <deter...@umn.edu>wrote:
> I have discovered on of my errors. The timematrix was unnecessary and an
> unfortunate habit I brought from another package. The following provides
> the same R2 values as it should, however, I still don't know how to
> retrieve Q2 values. Any insight would again be appreciated:
>
> library(caret)
> library(pls)
>
> data(iris)
>
> #needed to convert to numeric in order to do regression
> #I don't fully understand this but if I left as a factor I would get an
> error following the summary function
> iris$Species=as.numeric(iris$Species)
> inTrain1=createDataPartition(y=iris$Species,
> p=.75,
> list=FALSE)
>
> training1=iris[inTrain1,]
> testing1=iris[-inTrain1,]
>
> ctrl1=trainControl(method="cv",
> number=10)
>
> plsFit2=train(Species~.,
> data=training1,
> method="pls",
> trControl=ctrl1,
> metric="Rsquared",
> preProc=c("scale"))
>
> data(iris)
> training1=iris[inTrain1,]
> datvars=training1[,1:4]
> dat.sc=scale(datvars)
>
> pls.dat=plsr(as.numeric(training1$Species)~dat.sc,
> ncomp=3, method="oscorespls", data=training1)
>
> x=crossval(pls.dat, segments=10)
>
> summary(x)
> summary(plsFit2)
>
> Regards,
> Charles
>
> On Sat, Mar 2, 2013 at 3:55 PM, Charles Determan Jr <deter...@umn.edu
> >wrote:
>
> > Greetings,
> >
> > I have been exploring the use of the caret package to conduct some plsda
> > modeling. Previously, I have come across methods that result in a R2 and
> > Q2 for the model. Using the 'iris' data set, I wanted to see if I could
> > accomplish this with the caret package. I use the following code:
> >
> > library(caret)
> > data(iris)
> >
> > #needed to convert to numeric in order to do regression
> > #I don't fully understand this but if I left as a factor I would get an
> > error following the summary function
> > iris$Species=as.numeric(iris$Species)
> > inTrain1=createDataPartition(y=iris$Species,
> > p=.75,
> > list=FALSE)
> >
> > training1=iris[inTrain1,]
> > testing1=iris[-inTrain1,]
> >
> > ctrl1=trainControl(method="cv",
> > number=10)
> >
> > plsFit2=train(Species~.,
> > data=training1,
> > method="pls",
> > trControl=ctrl1,
> > metric="Rsquared",
> > preProc=c("scale"))
> >
> > data(iris)
> > training1=iris[inTrain1,]
> > datvars=training1[,1:4]
> > dat.sc=scale(datvars)
> >
> > n=nrow(dat.sc)
> > dat.indices=seq(1,n)
> >
> > timematrix=with(training1,
> > classvec2classmat(Species[dat.indices]))
> >
> > pls.dat=plsr(timematrix ~ dat.sc,
> > ncomp=3, method="oscorespls", data=training1)
> >
> > x=crossval(pls.dat, segments=10)
> >
> > summary(x)
> > summary(plsFit2)
> >
> > I see two different R2 values and I cannot figure out how to get the Q2
> > value. Any insight as to what my errors may be would be appreciated.
> >
> > Regards,
> >
> > --
> > Charles
> >
>
>
>
> --
> Charles Determan
> Integrated Biosciences PhD Student
> University of Minnesota
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> 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.
>
--
Max
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
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.
