[R] Mixed Effects MANOVA

Bert Gunter gunter.berton at gene.com
Thu Apr 3 17:31:40 CEST 2014

This is R-help, not a list that provides statistical help (primarily;
they do intersect at times). Post to the r-sig-mixed-models list
instead. You're likely to do better there anyway for this sort of


Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
H. Gilbert Welch

On Thu, Apr 3, 2014 at 6:29 AM, Nick Negovetich <nj.negovetich at gmail.com> wrote:
> Greetings,
> I have a question regarding data analysis of habitat use of animals.  These
> animals were radio collared and tracked periodically throughout the year.
> When they were sighted/detected, the habitat type was marked.  Our dataset
> recorded the sex of the animal, and we know the data when the surveys were
> performed.  The goal was to address the questions: does habitat use differ
> between the sexes, and does habitat use vary between seasons?  Below is a
> summary table, ignoring seasons.
> dattab <- matrix(c(190,87,206,170,103,23,66,72,53,22),nrow=5,byrow=T)
> rownames(dattab) <- c("Rock","Burrow","Cactus","Brushpile","Other")
> colnames(dattab) <- c("Female","Male")
> dattab
>           Female Male
> Rock         190   87
> Burrow       206  170
> Cactus       103   23
> Brushpile     66   72
> Other         53   22
> We could perform a test of independence, but the problem lies with our
> assumptions.  Because individual animals were tracked through time, each
> animal give a different number of datapoints (min=1, max=126), which
> violates our assumption of independence.  Thus, our sampling unit should be
> at the level of the skunk and analysis should proceed from there.  I'm
> familiar (theory and practice) with linear mixed effect models, but I
> believe that these data call for a mixed effects MANOVA.  Is there such a
> test in R?  Or, would it be better to analyze the data using a standard
> MANOVA where our y1, y2, ... are the percentage of data points within that
> various habitats? My problem with this last analysis is that each skunk will
> carry the same weight even though both could have a large difference in the
> number of data points.  Thanks...
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