Hello,
not sure if you are looking to run the GLM/GAMs individually but in one
run, or as a community composition type model to test main
drivers/correlates of combined species occurrences. If the latter, another
option is a GLMM with species having random slope to allow responses to
differ. For this, you would need to stack the occurrence matrix into a
?long? format (a row for the presence/absence of each species in each plot
with corresponding predictor variables and a field for species).
Response Species Temp Pptn
0 Sp1 30 1000
1 Sp2 30 1000
1 Sp3 30 1000
In lme4, something like:
lmer(Response ~ Temp + Pptn + (1 + Temp + Pptn|Species),
family=binomial(link="logit"), data)
An example with R code in the Appendix:
http://dx.doi.org/10.1111/jvs.12111
Greg
--
Dr Greg Guerin
Postdoctoral Fellow
School of Biological Sciences, Faculty of Science
The University of Adelaide
CRICOS Provider Number 00123M
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Message: 1
Date: Tue, 10 Feb 2015 09:28:14 -0700
From: Tim Meehan <tmeeha at gmail.com>
To: Rajendra Mohan panda <rmp.iit.kgp at gmail.com>
Cc: "r-sig-ecology at r-project.org" <r-sig-ecology at r-project.org>
Subject: Re: [R-sig-eco] Using multiple species data for gam
Message-ID:
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CAMTWOzpv58RRX2ocgTCpXh1EPAcxzkSCGKHvdUsaytGhCJH8MQ at mail.gmail.com>
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If you want to do this in a glm framework, you might look into the mvabund
package:
http://cran.r-project.org/web/packages/mvabund/mvabund.pdf
I've never used it with anything approaching 1000 species, though.
On Tue, Feb 10, 2015 at 2:41 AM, Rajendra Mohan panda
<rmp.iit.kgp at gmail.com
Dear All
I have >1000 species with presence and absence (0 or 1) values and with
seven corresponding predictor variables. If I can run gam/glm for the
data
using all species data simultaneously vs predictors. Data are arranged
in
columns against their GPS locations (see below). I know it is possible
to
do separately for each species.
Your kind response is highly appreciated.
Sites Sp1 Sp2 Sp3 Alt Temp Pptn Ft
1A 0 1 1 20 30 1000 Evergreen
With Best Regards
Rajendra M Panda
School of Water Resources
Indian Institute of Technology Kharagpur, India
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