[R] Passing data to aov

Thu Aug 26 17:17:55 CEST 2010

A big thanks David!  Eliminating the env = parent.frame() seems to fix
everything.  I hate it when I'm that close... I included that because from
?as.formula it seemed to be the default, but on re-read, I guess it doesn't
really say that.  In addition, I had included it even though it was the
default as I felt at some point I would have to change it so I wanted it
there as a reminder.  Instead, it led me astray...

Thanks so much! Bryan (coming to you from the R-Inferno today)

On 8/26/10 10:14 AM, "David Winsemius" <dwinsemius at comcast.net> wrote:

> 
> On Aug 26, 2010, at 8:47 AM, Bryan Hanson wrote:
> 
>> 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
> 
> Actually I got a different error (also on a Mac. but with a version
> that is two month later than yours and with quite a smaller number of
> packages loaded):
>> hypTestScores(mylist = td2, score.matrix = td1,
> +    fac = c("f1", "f2"))
> Error in eval(expr, envir, enclos) : object 'scores' not found
> 
> Which went away if I removed the "env=" argument. My guess is that you
> were telling manova to look further up the lexical tree than it should
> have (or that attach() operation messed up the environment somehow):
> 
>> hypTestScores(mylist = td2, score.matrix = td1,
> +    fac = c("f1", "f2"))
>            Df  Pillai approx F num Df den Df Pr(>F)
> f1         1 0.31663  0.61777      3      4 0.6392
> f2         1 0.36652  0.77145      3      4 0.5673
> f1:f2      1 0.15687  0.24808      3      4 0.8593
> Residuals  6
> 
>> detach("mylist") # needed if there is an error
> Error in detach("mylist") : invalid 'name' argument
> 
> You might want to do inside the function something like
> 
> res =try(  your function )
> if (res="try-error") {stop() } else{
>      <process>}
> 
>> 
>> 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
>> 
>> ______________________________________________
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> David Winsemius, MD
> West Hartford, CT
> 