Hi,
First, some toy data would have helped a lot, and that can explain why
you got so few answers...
Second, I have maybe some thoughts about it, not sure if this can help.
The error tells you that the data passed to aov is not a matrix. In your
function, you don't specify explicitly the data object to be used, that
might be a problem. And that object has to be a matrix, it might not be.
Maybe something like:
form<- as.formula(paste("pcs", "~", paste(fac, collapse = "*")),
...
if (length(pcs) == 1) out<- aov(formula = form, data=score.matrix)
That would work if I understood what you're doing (hum...) and if both "pcs"
and "fac" are parts of "score.matrix". But I've always done aov from a
dataframe, which makes sense if you have both numerical variables and factors.
How can you do it from a matrix? Maybe my understanding is limited.
As I said, just some thoughts...
HTH,
Ivan
Le 8/26/2010 14:47, Bryan Hanson a écrit :
> Hello Again Gurus and Lurkers:
>
> I¹m trying to build a very user-friendly function which does aov without
> having the user type in a formula (which would be tedious in this case).
> The idea is to take the response from a PCA score matrix, and the factors
> from a list. A simple example is the function given below, along with test
> data and a sample call to the function.
>
> I'm certainly having trouble understanding the proper ways to work with
> formulas and related items, but I think what I do in the function should
> work (it's built on ideas dug out of the archives). However, when the data
> is passed to aov (directly or via manova), something in the bowels of aov
> complains with the following error:
>
> Error in model.frame.default(formula = form, drop.unused.levels = TRUE) :
> object is not a matrix
>
> To me, the formula looks legitimate, and the variables in the formula are
> all in the environment (I think: The way I am doing this is basically that
> described in ?summary.manova where only a formula is passed, no data
> argument). Based upon reading the archives, the problem might arise with
> one of the deparse statements in aov, but I can't resolve it. It might also
> be one of scoping/environment, but again, this is only an idea.
>
> TIA for any assistance. Bryan
> *************
> Bryan Hanson
> Professor of Chemistry& Biochemistry
> DePauw University, Greencastle IN USA
>
>
> hypTestScores<-
> function(mylist, score.matrix, pcs = 1:3, fac = NULL, ...) {
>
> scores<- score.matrix[,pcs]
> # str(scores) # looks correct to me
> form<- as.formula(paste("scores", "~", paste(fac, collapse = "*")),
> env = parent.frame())
> # str(form) # looks correct to me
> attach(mylist)
> if (length(pcs)> 1) out<- manova(formula = form, ...)
> if (length(pcs) == 1) out<- aov(formula = form, ...)
> print(summary(out))
> detach(mylist)
> invisible(out)
> }
>
> # test data
> td1<- matrix(rnorm(50), ncol = 5) # like PCA scores
> td2<- list(
> f1 = as.factor(sample(c("A", "B"), 10, replace = TRUE)),
> f2 = as.factor(sample(c("C", "D"), 10, replace = TRUE)))
>
> # test call
> hypTestScores(mylist = td2, score.matrix = td1,
> fac = c("f1", "f2"))
> detach("mylist") # needed if there is an error
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] datasets tools grid graphics grDevices utils stats
> [8] methods base
>
> other attached packages:
> [1] faraway_1.0.4 GGally_0.2 xtable_1.5-6
> [4] mvbutils_2.5.1 ggplot2_0.8.8 proto_0.3-8
> [7] reshape_0.8.3 ChemoSpec_1.45 R.utils_1.4.0
> [10] R.oo_1.7.2 R.methodsS3_1.2.0 rgl_0.91
> [13] lattice_0.18-5 mvoutlier_1.4 plyr_1.0.3
> [16] RColorBrewer_1.0-2 chemometrics_0.8 som_0.3-5
> [19] robustbase_0.5-0-1 rpart_3.1-46 pls_2.1-0
> [22] pcaPP_1.8-1 mvtnorm_0.9-9 nnet_7.3-1
> [25] mclust_3.4.4 MASS_7.3-5 lars_0.9-7
> [28] e1071_1.5-23 class_7.3-2
>
> ______________________________________________
> 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.
>
--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. Säugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calan...@uni-hamburg.de
**********
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php
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