On 2012-11-27 14:34, Steve Lianoglou wrote:
Hi,
Comments inline:
On Tue, Nov 27, 2012 at 1:00 PM, Craig P O'Connell
<coconne...@umassd.edu> wrote:
Dear all,
I am having a recurring problem when I attempt to conduct a GLM. Here is
what I am attempting (with fake data):
First, I created a txt file, changed the directory in R (to the proper folder
containing the file) and loaded the file:
#avoid<-read.table("avoid.txt",header=TRUE);avoid
# treatment feeding avoid noavoid
#1 control nofeed 1 357
#2 control feed 2 292
#3 control sat 4 186
#4 proc nofeed 15 291
#5 proc feed 25 288
#6 proc sat 17 140
#7 mag nofeed 87 224
#8 mag feed 34 229
#9 mag sat 46 151
I then try to "attach(avoid)" the data, but continue to get an error message (
The following object(s) are masked _by_ .GlobalEnv :), so to fix this, I do the following:
#newavoid<-avoid
#newavoid (does this do anything?)
It essentially makes a copy of `avoid` to `newavoid` -- what did you
want it to do?
That having been said, a good rule of thumb is to never use `attach`,
so let's avoid it for now.
Lastly, I have several GLM's I wanted to conduct. Please see the following:
#model1<-glm(cbind(avoid, noavoid)~treatment,data=,family=binomial)
#model2=glm(cbind(avoid, noavoid)~feeding, familiy=binomial)
#model3=glm(cbind(avoid, noavoid)~treatment+feeding, familiy=binomial)
`cbind`-ing doesn't make much sense here. What is your target (y)
variable here? are you trying to predict `avoid` or `noavoid` status?
Let's assume you were "predicting" `noavoid` from just `treatment` and
`feeding` (I guess you have more data (rows) than you show), you would
build a model like so:
R> model <- glm(noavoid ~ treatment + feeding, binomial, avoid)
Or to be explicit about the parameters:
R> model <- glm(noavoid ~ treatment + feeding, family=binomial, data=avoid)
It would be greatly appreciated if somebody can help me with my coding, as you
can see I am a novice but doing my best to learn. I figured if I can get
model1 to run, I should be able to figure out the rest of my models.
Since you're just getting started, maybe it would be helpful for
people writing documentation/tutorials/whatever what needs to be
explained better.
For instance, I'm curious why you thought to `cbind` in your first glm
call, which was:
model1<-glm(cbind(avoid, noavoid)~treatment,data=,family=binomial)
What did you think `cbind`-ing was accomplishing for you? Is there an
example somewhere that's doing that as the first parameter to a `glm`
call?
Steve:
re a matrix response: see MASS (the book, 4ed) page 191; also found
in the ch07.R file in the /library/MASS/scripts folder. I seem to
recall that this is mentioned somewhere in the docs, but put my finger
on it now.
One additional comment about the analysis: overdispersion might be
a problem.
Peter Ehlers
[...]
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