[R-sig-eco] R-sig-ecology Digest, (80/1): Binomial GLM: Is it the right way?

[Claas Damken]

Dear Ludovico,
"the likelihood of colonizing or becoming extinct" is not a binary response as such. For each of your plant species, you actually can run one of two models : "Species A persists on plot YX or goes extinct" or "Species B colonizes plot xy or is still absent". Otherwise you would ignore that a species can be present during both surveys. 

Also, your "PROB_COL" is not really a probability. It is just the number of species with a certain trait that showed up only during the second survey divided by 24. If you would calculate this for each species separately, you would get a fraction (still not a probability).

To me your data look like it should be analysed with some other method. GLMs are more convincing and easier to interpret/plot if your predictors are continuous (e.g., area, elevation, site age, pH, vegetation cover, etc) and not a factor with 12 levels when you have only 24 plots.

More importantly, don't forget that  the probability of a species colonizing a plot not only depends on which life form that particular species has, but also on how many species with the same life form are the regional species pool, i.e. in the draw.

HTH,

Claas   

Claas Damken, Postdoctoral Fellow
Institute for Biodiversity and Environmental Research
Universiti Brunei Darussalam
Brunei Darussalam
email: c.damken at auckland.ac.nz

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Today's Topics:

   1. Binomial GLM: Is it the right way? (Ludovico Frate)


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Message: 1
Date: Fri, 31 Oct 2014 21:49:26 +0100
From: Ludovico Frate <ludovicofrate at hotmail.it>
To: "r-sig-ecology at r-project.org" <r-sig-ecology at r-project.org>
Subject: [R-sig-eco] Binomial GLM: Is it the right way?
Message-ID: <DUB126-W76C71CD937F919A537C3ECD69A0 at phx.gbl>
Content-Type: text/plain; charset="UTF-8"

Dear List,
I'am trying to fit a GLM with a binomial error distribution but I am a little bit confused about the model.
I have 24 vegetation permanent plots, randomly distributed, sampled two times: 1962 and 2009. I am looking for any changes in vegetation composition and in particular based on plant traits (life forms).For each species, I assessed whether it had colonized (i.e. been in 1962 absent but in 2009 present) or become locally extinct (i.e. been in 1962 present but recently absent) in the plot.I would like to analyze whether a species trait affected the likelihood of colonizing or becoming extinct on a summit.
example: Colonizing species
Traits           TOTAL   COLONIZING      PROB_
COLChF       24              0                       0
ChC              24              1                       0,041666667
ChR              24              11                      0,458333333
ChSC            24              1                       0,041666667
ChS              24              18                      0,75
Ph                24              2                       0,083333333
Geo             24              18                      0,75
HeB             24              1                       0,041666667
HeC             24              36                      1,5
HeR             24              47                      1,958333333
HeS             24              161                     6,708333333
Th                24              28                      1,166666667

Traits is the plant trait analyzed, TOTAL is the number of plots and COLONIZING represents the number of new species found in 2009 per plot, PROB_COL is the probability of colonization (COLONIZING/TOT)
However PROB_COL is >1, so I think that TOTAL should be different (i.e. total number of colonizing species)?
Any suggestions?Thank you,Ludovico

Ludovico
Frate

PhD student (University of Molise - Italy)
Environmetrics Lab
http://www.distat.unimol.it/STAT/environmetrica/organico/collaboratori/ludovico-frate-1
Department of Biosciences and Territory - DiBT
Universit?el Molise.
Contrada Fonte
Lappone,
86090 -  Pesche (IS)
ITALIA.
Cel: ++39
3333767557
Fax: ++39 (0874) 404123
E-mail ludovico.frate at unimol.it
ludovicofrate at hotmail.it


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