[R] Passing data to aov

[Bryan Hanson]

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