[R-sig-ME] Looking for help to test the effect of a grouping factor in repeated measures

[Léa Fieschi-Méric]

Hello,

I have a dataset to analyse and I am struggling to build my model set and
was wondering if you could advise me please.

The experimental plan is as follows: several species of animals were
observed for a year, but not regularly (some months have many observations,
others have less). *All individuals belonging to the same species were
housed together in the same terrarium* (unequal number of individuals per
species). The response variable is the number of awake individuals per
terrarium (i.e. per species). The year was divided in 3, unequal, periods
as follows: treatment / control / treatment.

I need to determine the effect of the *Period *(treatment / control), of
the *Species* (12 in total), and of their *Interaction *on the *proportion
of awake animals*. I wanted to use a GLMM with a binomial error
distribution. The problem is that I have repeated measures per species, so
I would like to account for that by using Species as a random effect to
avoid pseudoreplication, but I think I need Species to be a fixed effect
because I want to directly test its effect on my response. Therefore, I
wonder if adding the *Date* (as an integer: number of days since the
beginning of the experiment) to the model does control for these repeated
measures (but I can't use it as a random effect because it is continuous,
and it makes my model too complex to converge when integrated as a fixed
effect), or if I should sum the response per month to use *Month* as a
random effect ordered factor. Or if I could just use a linear model without
bothering, like this: y ~ Treatment * Species !
I am stuck here and would like to avoid taking a mathematically
erroneous approach. Could you advise me please?

I was also wondering what I need to do in order to, in a second phase, be
able to conclude exactly which species were sensitive to the treatment and
which were not?

I am looking forward to hearing back from you, and thank you in advance for
your help!

Léa

-- 
*Léa FIESCHI-MERIC*, PhD student

Laboratoire d'Ecologie et de Conservation des Amphibiens (LECA)
Freshwater and OCeanic science Unit of reSearch (FOCUS)
Université de Liège (Belgique)
&
Genetics and Ecology of Amphibians Research Group
Center for Evolutionary Ecology and Ethical Conservation
Laurentian University (Canada)

Tel: (+33) (0)6.59.32.29.15 <+32%204%20366%2050%2077>
E-mail: leafieschimeric using gmail.com

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