From zemlys at gmail.com  Tue Jun 30 09:20:09 2009
From: zemlys at gmail.com (zemlys at gmail.com)
Date: Tue, 30 Jun 2009 09:20:09 +0200 (CEST)
Subject: [Rd] bug in nlme package function predict.lmList (PR#13788)
Message-ID: <20090630072009.AB048282EFCB@mail.pubhealth.ku.dk>

Full_Name: Vaidotas Zemlys
Version: 2.9.0
OS: Ubuntu 8.10
Submission from: (NULL) (213.197.173.50)


Steps to reproduce the bug:

library(nlme)
data(Oxboys)
qm=lmList(height~age|Subject,data=Oxboys)
grid=with(Oxboys,expand.grid(age=seq(min(age),max(age),length=50),Subject=levels(Subject)))

res <- predict(qm,grid,se=TRUE)
Erreur dans if (pool) { : l'argument est de longueur nulle

res <- predict(qm,grid,se=TRUE,pool=TRUE)
Erreur dans sprintf(gettext(fmt, domain = domain), ...) : 
  objet 'form' introuvable

The result: predicting does not work, when new data is supplied. 

The problem is in the function predict.lmList. When argument newdata is not
NULL, argument subset is set to TRUE, and following code gets executed:

####Start of the relevant code snippet
 if (!is.null(subset)) {
        if (any(is.na(match(subset, names(object))))) {
            stop("Non-existent group requested in \"subset\".")
        }
        oclass <- class(object)
        oatt <- attr(object, "call")
        object <- object[subset]
        attr(object, "call") <- oatt
        class(object) <- oclass
        if (is.null(newdata)) {
            myData <- myData[subset]
        }
    }
#####End of relevant code snippet

Only attribute call is saved from original object, but the following code
assumes that attributes groupsForm and pool are present, and when they are not
found, error is produced. The problem with missing pool attribute can be worked
arround by supplying it directly. But it is not possible to do that with
attribute groupsForm. 

The patch which fixes this problem :

--- lmList.R	2008-02-11 16:05:14.000000000 +0200
+++ lmListnew.R	2009-06-30 09:49:21.000000000 +0300
@@ -853,9 +853,10 @@ predict.lmList <-
       stop("Non-existent group requested in \"subset\".")
     }
     oclass <- class(object)
-    oatt <- attr(object, "call")
+    oatt <- attributes(object)[c("call","groupsForm","pool")]
     object <- object[subset]
-    attr(object, "call") <- oatt
+    oatt <- c(attributes(object),oatt)
+    attributes(object) <- oatt
     class(object) <- oclass
     if(is.null(newdata)) {
       myData <- myData[subset]

I did not do extensive tests, but it works with previous example and my own
datasets.
Here is the relevant information about R and nlme on my system:
> R.version
               _                           
platform       i486-pc-linux-gnu           
arch           i486                        
os             linux-gnu                   
system         i486, linux-gnu             
status                                     
major          2                           
minor          9.0                         
year           2009                        
month          04                          
day            17                          
svn rev        48333                       
language       R                           
version.string R version 2.9.0 (2009-04-17)

> packageDescription("nlme")
Package: nlme
Version: 3.1-92
Date: 2009-05-22
Priority: recommended
Title: Linear and Nonlinear Mixed Effects Models
Author: Jose Pinheiro <Jose.Pinheiro at pharma.novartis.com>, Douglas
        Bates <bates at stat.wisc.edu>, Saikat DebRoy
        <saikat at stat.wisc.edu>, Deepayan Sarkar
        <Deepayan.Sarkar at R-project.org>, the R Core team.
Maintainer: R-core <R-core at R-project.org>
Description: Fit and compare Gaussian linear and nonlinear
        mixed-effects models.
Depends: graphics, stats, R (>= 2.4.0)
Imports: lattice
LazyLoad: yes
LazyData: yes
License: GPL (>= 2)
Packaged: 2009-05-23 16:39:47 UTC; ripley
Repository: CRAN
Date/Publication: 2009-05-24 08:46:01
Built: R 2.9.0; i486-pc-linux-gnu; 2009-06-30 06:00:47 UTC; unix

I did update.packages() before testing and reporting the bug. 

I hope that this is correct place to report bug on package of R. 

Vaidotas Zemlys



[Rd] bug in nlme package function predict.lmList (PR#13788)
zemlys at gmail.com