[R] problem with predict()

[Czerminski, Ryszard]

>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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