[R-sig-ME] a GlmmTMB advice

Leida Dos Santos |do@@@nto@ @end|ng |rom @mph|b|@n@@org
Wed May 20 17:19:38 CEST 2020

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). There are 19 different specimens, 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’
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
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 would be very grateful for any feedback please:):) Thank
you in advance. :x
*Leida Dos Santos*
*IUCN SSC ASG Programme Officer*
*ldossantos using amphibians.org <ldossantos using amphibians.org>*
*leidamphibian using gmail.com <leidamphibian using gmail.com>*
*http://www.amphibians.org/ <http://www.amphibians.org/>*
*http://www.nzfrogs.org <http://www.nzfrogs.org>*
       *0  0*

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