[R-sig-eco] Using multiple species data for gam

[Greg Guerin]

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
Œlong¹ 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

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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:
>	<CAMTWOzpv58RRX2ocgTCpXh1EPAcxzkSCGKHvdUsaytGhCJH8MQ at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>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
>> wrote:
>
>> 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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