[R-sig-ME] a GlmmTMB advice

Tue May 26 02:48:54 CEST 2020

 �� No need to apologize (but do, please, keep the mailing� list in the Cc:)

 �� Are you running/planning to run 16 separate abundance analyses?� If 
so, see comments below ...

On 5/25/20 8:40 PM, Leida Dos Santos wrote:
> There are 486 individuals of 16 different species ! Sorry !
>
> Get Outlook for iOS <https://aka.ms/o0ukef>
> ------------------------------------------------------------------------
> *From:* Ben Bolker <bbolker using gmail.com>
> *Sent:* Tuesday, May 26, 2020 1:38:09 AM
> *To:* Leida Dos Santos <ldossantos using amphibians.org>; 
> r-sig-mixed-models using r-project.org <r-sig-mixed-models using r-project.org>
> *Subject:* Re: [R-sig-ME] a GlmmTMB advice
>
> �� [please keep the mailing list in Cc:]
>
> On 5/25/20 8:31 PM, Leida Dos Santos wrote:
>> Thank very much Ben,
>> >There are 19 different specimens<- I mean 19 different species 
>> (specimens in portuguese, I am sorry!)
>
>
> � OK.
>
>>
>> Ben I am concerned because after checking the data carefully, I have 
>> noticed�that some 13 of the 16 different species�there are less than 
>> 10 individuals�per species. Would it be ok to run the Glmm anyways? I 
>> am modelling the abundance as response variable and 
>> predictor�variables year/month (the month of sampling for each year), 
>> species, climate data (tmax, tmin, precipitation, and species life 
>> traits�history (size, habitat, habit, etc).
>
> �� I don't see immediately why this would be a problem with the 
> species-richness analysis.
>
> �� Are you running 19 (or 16, I can't tell how many species there 
> really are) separate abundance analyses?� That's going to be very 
> difficult if you have small numbers of individuals per species.� Also, 
> if you run 19 analyses with 8 covariates each, the chances of getting 
> a lot of false positives/need for some kind of shrinkage or 
> multiple-comparisons correction goes up.� (This is not really a mixed 
> modeling question, more a generic question of what to do with 
> relatively small, noisy ecological data sets ...)
>
>
>>
>> I am sorry for not being able to formulate my questions properly.
>>
>> Kind regards,
>>
>>
>>
>>
>>
>> *Leida Dos Santos*
>> */BSc/**/,QTS,MSc,/**/PhD/*
>> /_**_*IUCN SSC ASG***�Programme *Officer*/
>> /ldossantos using amphibians.org <mailto:ldossantos using amphibians.org>/
>> _leidamphibian using gmail.com <mailto:leidamphibian using gmail.com>_
>> */@anfileida/*
>> */http://www.amphibians.org//*
>> **/http://www.nzfrogs.org/**
>> *0� 0*
>> *����� ( -- )
>> /\(����� )/\
>> ^^� ^^� ^^� ^^
>> **PS: Please consider the environment before printing this E-mail*
>>
>>
>>
>>
>>
>> On Mon, 25 May 2020 at 17:44, Ben Bolker <bbolker using gmail.com 
>> <mailto:bbolker using gmail.com>> wrote:
>>
>>
>>     On 5/20/20 11:19 AM, Leida Dos Santos wrote:
>>     > Hello there, I was wondering if you help. I am still learning
>>     how to work
>>     > with GlmmTMB and I have fitted GlmmTMB before but for
>>     categorical data . I
>>     > currently am working on a paper and have a data set where I am
>>     trying to
>>     > fit a GlmmTMB. I want to show the effect climate data on
>>     species richness
>>     > and abundance . I have fitted the predictor response with
>>     species "Richness
>>     > Index" and another with "abundance ", and predictor variables
>>     "climate
>>     > data" such as tmax, tmin, precipitation (Richness index I
>>     calculated using
>>     > vegan package). I have fitted (site and Month) as random
>>     intercept, because
>>     > the data was collected with no consistency but random days and
>>     month, and
>>     > years (2010-2019).
>>
>>     ��� does the Month variable include both month and year (e.g.
>>     2010.April, 2018.May)?
>>
>>     >� �There are 19 different specimens
>>
>>     ���� Not sure what this means ...
>>
>>     >� �and n= 467. All
>>     > variables are numerical. #Global Model example: Abun_2<-
>>     glmmTMB(Richness ~
>>     > (tmin +ppt1 + tmax1 + tmax2 +tmin2+ ppt2 + Year)^2+ (1|Site/Month),
>>     > data=Main_data, family="nbinom2"). However when I run this
>>     model, I come
>>     > across some warning messages:
>>     >
>>     > "Found more than one class "Matrix" in cache; using the first, from
>>     > namespace 'Matrix'
>>     > Also defined by �arkhe�
>>
>>     ��� This is harmless is in this case (although it seems like a
>>     questionable decision on the part of the arkhe package developers).
>>
>>     > Warning messages:
>>     > _1: In glmmTMB(Abundance ~ (tmin + ppt + tmax2 + tmax + tmin2 +
>>     ppt2 + :
>>     > non-integer counts in a nbinom2 model
>>     > 2: In fitTMB(TMBStruc) :
>>     > Model convergence problem; non-positive-definite Hessian
>>     matrix. See
>>     > vignette('troubleshooting')
>>     > 3: In fitTMB(TMBStruc) :
>>     > Model convergence problem; function evaluation limit reached
>>     without
>>     > convergence (9). See vignette('troubleshooting')".
>>     >
>>     > I checked vignette, but the truth is, this is too advanced for
>>     and I do not
>>     > understand what it is saying:) I would love to have some
>>     feedback with
>>     > regards to the model. Additionally, should I use just count for
>>     Richness
>>     > instead of the Menhinick index for richness? Or should I use a
>>     completely
>>     > different model? I
>>
>>     ��� The main issue here is that it almost never makes sense to use a
>>     count-based model (nbinom1, nbinom2, Poisson) for data that are not
>>     actual counts (i.e. integers).� I'm not going to weigh in on which
>>     index/model you should use; there are long discussions about
>>     that, and
>>     you should decide as much on biological grounds (what question
>>     are you
>>     trying to answer?) as statistical grounds.� As long as the model
>>     converges to a stable answer, and the assumptions of linearity and
>>     homoscedasticity are reasonably well met, you should be OK
>>     statistically.
>>
>>     >� �would be very grateful for any feedback please:):) Thank
>>     > you in advance. :x
>>
>>
>>
>>     > *Leida Dos Santos*
>>     > *BSc**,QTS,MSc,**PhD*
>>     > *IUCN SSC ASG Programme Officer*
>>     > *ldossantos using amphibians.org <mailto:ldossantos using amphibians.org>
>>     <ldossantos using amphibians.org <mailto:ldossantos using amphibians.org>>*
>>     > *leidamphibian using gmail.com <mailto:leidamphibian using gmail.com>
>>     <leidamphibian using gmail.com <mailto:leidamphibian using gmail.com>>*
>>     > *@anfileida*
>>     > *http://www.amphibians.org/ <http://www.amphibians.org/>*
>>     > *http://www.nzfrogs.org <http://www.nzfrogs.org>*
>>     >� � � � �*0� 0*
>>     >
>>     >
>>     >
>>     > *� � � ( -- )� /\(� � � )/\^^� ^^� ^^� ^^**PS: Please consider the
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>>     >
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