[R] ipred and lda
Philippe Grosjean
phgrosjean at sciviews.org
Fri Jan 9 17:32:46 CET 2004
I got also this problem and I solved it a couple of months ago.
Unfortunatelly, I do not have access to the machine with my code before
monday, so, I cannot give you the exact recipe... I am just recalling from
my poor memory!
If I remember, the problem occured when MASS moved to use namespace, so,
predict.lda was not visible externally any more, something that some ipred
function assumed in the version I used at that time. The solution was to
change the code of ipred to explicitly call the predict.lda function in
MASS, that is, something like:
MASS:::predict.lda
give it a try. Since you use an old version of R (1.7.1), you may face a
similar problem. I suppose the solution is to use latest versions of R, MASS
and ipred.
Best,
Philippe Grosjean
P.S.: Andrea and Thorsten: sorry for not having mentioned this when I got
the problem. I was in a rush,... and then I forgot! But I suppose the latest
version of ipred is OK now, isn't it?
.......................................................<°}))><....
) ) ) ) )
( ( ( ( ( Prof. Philippe Grosjean
\ ___ )
\/ECO\ ( Numerical Ecology of Aquatic Systems
/\___/ ) Mons-Hainaut University, Pentagone
/ ___ /( 8, Av. du Champ de Mars, 7000 Mons, Belgium
/NUM\/ )
\___/\ ( phone: + 32.65.37.34.97, fax: + 32.65.37.33.12
\ ) email: Philippe.Grosjean at umh.ac.be
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-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of Martin Maechler
Sent: Friday, 09 January, 2004 17:14
To: Stefan Böhringer
Cc: R Help
Subject: Re: [R] ipred and lda
>>>>> "Stefan" == Stefan Böhringer <commercial at s-boehringer.de>
>>>>> on 09 Jan 2004 16:46:23 +0100 writes:
Stefan> Dear all, can anybody help me with the program
Stefan> below? The function predict.lda seems to be defined
Stefan> but cannot be used by errortest.
Stefan> The R version is 1.7.1
>> library("MASS");
>> library("ipred");
>>
>> data(iris3);
>> tr <- sample(1:50, 25);
>> train <- rbind(iris3[tr,,1], iris3[tr,,2], iris3[tr,,3]);
>> test <- rbind(iris3[-tr,,1], iris3[-tr,,2], iris3[-tr,,3]);
>> cl <- factor(c(rep("s",25), rep("c",25), rep("v",25)));
>> z <- lda(train, cl);
>> predict(z, test)$class;
>>
>> data.frame(class=cl, train);
>> flowers <- data.frame(class=cl, train);
>> errorest(class ~ ., data=flowers, model=lda, estimator="cv",
>> predict=predict.lda);
Stefan> Error-Message is :
Stefan> Error: Object "predict.lda" not found
predict.lda is not exported from new versions of MASS
since one should use predict( <lda-fit> , ...).
i.e., I presume that
errorest(class ~ ., data=flowers, model=lda, estimator="cv",
predict=predict)
will work.
BTW: Please, remove the ";" at the end of lines.
In S code, they are just plain ugly.
Martin Maechler <maechler at stat.math.ethz.ch> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
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