[R] problem with predict()

[Liaw, Andy]

You still don't get the point.  Please read Peter Dalgaard's reply and the
help page for predict.lm carefully, and try to understand the `Detail'
section.  See the example below:

> n<-100
> p<-10
> y<-rnorm(n)
> xtr<-matrix(rnorm(n*p), n, p)
> xts<- matrix(rnorm(5*p), 5, p)
> myfit<-lm(y~.,data=as.data.frame(xtr))
> length(predict(myfit,as.data.frame(xts)))
[1] 5

Andy


> -----Original Message-----
> From: Czerminski, Ryszard [mailto:ryszard at arqule.com]
> Sent: Friday, June 21, 2002 10:21 AM
> To: 'Liaw, Andy'; Czerminski, Ryszard
> Cc: r-help at stat.math.ethz.ch
> Subject: RE: [R] problem with predict()
> 
> 
> From Liaw, Andy:
> 
> > It's probably easier to do the following:
> > ## Put training data in a data frame.
> > train <- data.frame(y=yr, x=xr)
> > ## Put test data in a data frame.
> > test <- data.frame(y=ys, x=xs)
> > 
> > myfit <- lm(y ~ x, train)
> > test.pred <- predict(myfit, test)
> 
> This looks promissing; however I get an error:
> 
> > train <- data.frame(y=yr, x=xr)
> > test <- data.frame(y=ys, x=xs)
> > myfit <- lm(y ~ x, train)
> Error in eval(expr, envir, enclos) : Object "x" not found
> 
> R
> 
> Ryszard Czerminski   phone: (781)994-0479
> ArQule, Inc.         email:ryszard at arqule.com
> 19 Presidential Way  http://www.arqule.com
> Woburn, MA 01801     fax: (781)994-0679
> 
> 
> -----Original Message-----
> From: Liaw, Andy [mailto:andy_liaw at merck.com]
> Sent: Friday, June 21, 2002 8:34 AM
> To: 'Czerminski, Ryszard'
> Cc: r-help at stat.math.ethz.ch
> Subject: RE: [R] problem with predict()
> 
> 
> The second argument to predict.lm, `newdata', is suppose to 
> be a data frame
> containing variables that were used to fit the model.  Thus 
> if in your lm
> object the predictor is a variable named `xr', the predict 
> method will be
> looking for `xr', and ignored `xs' that you passed in.
> 
> It's probably easier to do the following:
> 
> ## Put training data in a data frame.
> train <- data.frame(y=yr, x=xr)
> ## Put test data in a data frame.
> test <- data.frame(y=ys, x=xs)
> 
> myfit <- lm(y ~ x, train)
> test.pred <- predict(myfit, test)
> 
> Hope this helps,
> Andy
> 
> > -----Original Message-----
> > From: Czerminski, Ryszard [mailto:ryszard at arqule.com]
> > Sent: Friday, June 21, 2002 8:10 AM
> > To: 'Peter Dalgaard BSA'; Czerminski, Ryszard
> > Cc: r-help at stat.math.ethz.ch
> > Subject: RE: [R] problem with predict()
> > 
> > 
> > > Does xs contain a variable called xr?
> > 
> > No - it does not.
> > 
> > I was expecting that if I use model built using
> > (yr,xr) data with 164 cases and 118 variables
> > to predict on a test data (xs) with 35 cases
> > > # dim(xr) = 164 118 ; dim(xs) = 35 118
> > I should get vector of 35 responses from predict(),
> > but I am getting instead 164 responses.
> > > # length(ys) = 35 ; length(ps) = 164
> > 
> > If I go through example provided with help(predict.lm)
> > I get expected number of responses (13).
> > This is however only 1D example.
> > 
> > I am sure I am missing something and probably not using
> > predict() correctly, but I am at loss what it is...
> > 
> > R
> > 
> > Ryszard Czerminski   phone: (781)994-0479
> > ArQule, Inc.         email:ryszard at arqule.com
> > 19 Presidential Way  http://www.arqule.com
> > Woburn, MA 01801     fax: (781)994-0679
> > 
> > 
> > -----Original Message-----
> > From: Peter Dalgaard BSA [mailto:p.dalgaard at biostat.ku.dk]
> > Sent: Thursday, June 20, 2002 5:10 PM
> > To: Czerminski, Ryszard
> > Cc: r-help at stat.math.ethz.ch
> > Subject: Re: [R] problem with predict()
> > 
> > 
> > "Czerminski, Ryszard" <ryszard at arqule.com> writes:
> > 
> > > pr <- predict(model, as.data.frame(xr))
> > > ps <- predict(model, xs)
> > > 
> > > cat("length(yr) =", length(yr), "; length(pr) =", length(pr),"\n")
> > > cat("dim(xr) =", dim(xr), "; dim(xs) =", dim(xs),"\n")
> > > cat("length(ys) =", length(ys), "; length(ps) =", 
> length(ps), "\n")
> > > cat("why length(ps) != length(ys) ???\n")
> > > 
> > > # my output:
> > > #
> > > # length(yr) = 164 ; length(pr) = 164 
> > > # dim(xr) = 164 118 ; dim(xs) = 35 118 
> > > # length(ys) = 35 ; length(ps) = 164 
> > > # why length(ps) != length(ys) ???
> > 
> > Does xs contain a variable called xr?
> > 
> > -- 
> >    O__  ---- Peter Dalgaard             Blegdamsvej 3  
> >   c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
> >  (*) \(*) -- University of Copenhagen   Denmark      Ph: 
> > (+45) 35327918
> > ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: 
> > (+45) 35327907
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