[R] Help with lme
Bert Gunter
gunter.berton at gene.com
Fri Nov 9 18:27:55 CET 2012
Well, you've posted to the wrong list!
First off, you're almost always better off posting to an R SIG list
when one exists in your area of concern,as it does here:
r-sig-mixed-models.
Second, this appears to be primarily a statistics question, and R-help
is not a statistics help list (though, I admit, the intersection is
nonempty, and that may be the case here). For statistics primarily
questions,you should generally post to a statistics help list like
stats.stackexchange.com.
Otherwise, you're fine. :-)
Cheers,
Bert
On Fri, Nov 9, 2012 at 9:15 AM, Annie Hoen <anniehoen at gmail.com> wrote:
> Hi,
>
> This is my first time posting to the list so please forgive any breeches
> of etiquette!
> I am new to mixed-effects modeling.
>
> This is my dataset:
>
> subject treatment day replicate outcome
> 1 1 1 1 0.0
> 1 1 4 1 0.0
> 1 1 8 1 14.5
> 1 1 8 2 15.4
> 2 1 2 1 0.0
> 2 1 4 1 0.0
> 2 1 7 1 12.1
> 2 1 7 2 11.9
> 3 1 2 1 0.0
> 3 1 4 1 0.0
> 3 1 7 1 0.0
> 4 1 2 1 4.2
> 4 1 2 2 5.0
> 4 1 4 1 8.5
> 4 1 4 2 10.0
> 4 1 6 1 16.4
> 4 1 6 2 18.1
> 5 1 2 1 0.0
> 5 1 4 1 0.0
> 5 1 7 1 0.0
> 6 2 2 1 0.0
> 6 2 4 1 9.1
> 6 2 4 2 9.7
> 6 2 7 1 12.6
> 6 2 7 2 10.3
> 7 2 1 1 3.3
> 7 2 1 2 4.8
> 7 2 4 1 6.2
> 7 2 4 2 6.4
> 7 2 7 1 12.9
> 7 2 7 2 13.1
> 8 2 2 1 0.0
> 8 2 4 1 0.0
> 8 2 8 1 0.0
> 9 2 2 1 2.7
> 9 2 2 2 3.2
> 9 2 4 1 5.6
> 9 2 4 2 5.4
> 9 2 8 1 14.9
> 9 2 8 2 14.8
> 10 2 1 1 0.0
> 10 2 4 1 10.7
> 10 2 4 2 11.0
> 10 2 7 1 13.7
> 10 2 7 2 12.9
> 11 2 1 1 0.0
> 11 2 4 1 0.0
> 11 2 7 1 0.0
> 12 2 1 1 0.0
> 12 2 4 1 0.0
> 12 2 7 1 0.0
>
>
> It can be made using this:
>
> subject=c(1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 6,
> 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10,
> 10, 11, 11, 11, 12, 12, 12)
> treatment=c(rep(1, 20), rep(2, 31))
> day=c(1, 4, 8, 8, 2, 4, 7, 7, 2, 4, 7, 2, 2, 4, 4, 6, 6, 2, 4, 7, 2, 4, 4,
> 7, 7, 1, 1, 4, 4, 7, 7, 2, 4, 8, 2, 2, 4, 4, 8, 8, 1, 4, 4, 7, 7, 1, 4, 7,
> 1, 4, 7)
> replicate=c(1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1,
> 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 2, 1, 2, 1,
> 1, 1, 1, 1, 1)
> outcome=c(0, 0, 14.5, 15.4, 0, 0, 12.1, 11.9, 0, 0, 0, 4.2, 5.0, 8.5,
> 10.0, 16.4, 18.1, 0, 0, 0, 0, 9.1, 9.7, 12.6, 10.3, 3.3, 4.8, 6.2, 6.4,
> 12.9, 13.1, 0,0,0, 2.7,3.2, 5.6, 5.4, 14.9, 14.8, 0, 10.7, 11.0, 13.7,
> 12.9, 0, 0, 0, 0, 0, 0)
>
> data<-data.frame(cbind(subject, treatment, day, replicate, outcome))
>
> I have two groups of subjects, each given a different treatment. The
> outcome (growth) was observed post-treatment on each of three days. If
> there was growth, it was measured in duplicate measurements.
>
> There are uneven numbers of subjects in my two treatment groups. Also, the
> outcome was always observed on 3 days, but the exact day of observation is
> not always consistent.
>
> I just want to know the effect of treatment on outcome.
>
> This is the model I've run:
>
> model <- lme(outcome ~ treatment * day, random = list(subject = pdDiag(~
> day)), data = data)
> summary(model)
>
>
> Can any experts out there let me know if I'm doing this right? Thanks!!!
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
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