[R-sig-ME] Spatial correlation in glmmTMB

[André Pardal]

Sorry, forgot to paste the error i get:

dens.exp = glmmTMB(density_cht ~ wf_log + exp(pos + 0|group2) +
(1|subregion/location), data=density2, REML=T, family = nbinom1,
ziformula=~0) ##full

Warning message:
In fitTMB(TMBStruc) :
Model convergence problem; non-positive-definite Hessian matrix. See
vignette('troubleshooting')
> summary(dens.exp)
Error in solve.default(as.matrix(Qm)): system is computationally singular:
reciprocal condition number = 2.67616e-135

On Mon, 22 Jul 2019 at 12:23, André Pardal <andre.pardal.souza using gmail.com>
wrote:

> Hello,
>
> Thank you all for the comments. Actually, there is a misspelling in my
> first email and sorry for not explaining properly. I will try below:
>
> I collected data in 62 locations along a large spatial scale (> 500 km).
> And I surely have replication inside each location.
> First I performed a model selection for identifying the best random
> structure than the fixed structure. The final best model is as below.
>
> m1 = glmmTMB(density ~ wave_exposure + (1|subregion/location), data=
> mydata, family= nbinom1, ziformula= ~0)
>
> The term (1|subregion/location) is the random effect of subregion and
> location (and location is nested in subregion)
>
> When I try to account for spatial correlation a have the following model:
>
> m1.spatial = glmmTMB(density ~ wave_exposure + (1|subregion/location) +
> exp(pos +0|group), data= mydata, family= nbinom1, ziformula= ~0)
>
> The term exp(pos +0|group) refers to the spatial correlation. exp =
> exponential covariance structure; pos = numFactor putting spatial
> coordinates together; group = a dummy factor (mydata$group <- factor(rep(1,
> nrow(mydata))))
>
> I already tried to create a jitter for spatial coordinates, since some
> packages do not work if the distance between two coordinates is zero.
> I also tried changing the dummy factor to be a repetition from 1 to 62
> (since I have 62 locations).
>
> Actually, most of times the model not even runs and cracks my R.
>
> Well, I guess I will try spaMM.
>
>
> Thanks a lot.
>
> Andre.
>
>
>
>
> On Fri, 19 Jul 2019 at 09:47, Francois Rousset <
> francois.rousset using umontpellier.fr> wrote:
>
>> Dear André,
>>
>> I saw your question on R-sig-ME. I am not sure I fully understand syntax
>> in "wave_exposure + (1|location) exp(pos + 0|group)" so I hesitate to reply
>> through R-sig-ME. However, perhaps you should try the spaMM package by
>>
>> library("spaMM")
>>
>> m1 <-  fitme(density ~ wave_exposure + Matern(1|easting+northing), data=
>> mydata, family= negbin())
>>
>> Let me know whether this is useful.
>> F.
>>
>> -------- Message transféré --------
>> Sujet : [R-sig-ME] Spatial correlation in glmmTMB
>> Date : Wed, 17 Jul 2019 18:15:39 +0100
>> De : André Pardal <andre.pardal.souza using gmail.com>
>> <andre.pardal.souza using gmail.com>
>> Pour : r-sig-mixed-models using r-project.org
>>
>> Hello,
>>
>> I would like to ask for help on how to account for spatial correlation in
>> glmmTMB package.
>>
>> According to the help page (
>> https://cran.r-project.org/web/packages/glmmTMB/vignettes/covstruct.html
>> ),
>> I need to create a numFactor object grouping coordinates and a dummy
>> grouping factor.
>>
>> mydata$pos <- numFactor(mydata$easting, mydata$northing)## spatial
>> coordinates
>> mydata$group <- factor(rep(1, nrow(mydata)))## dummy factor
>>
>> Regarding to the dummy variable, I have 62 locations in my dataframe. The
>> dummy variable should be 1 for all observations, or go from 1 to 62?
>> (Actually I have tried both possibilities. First one give me convergence
>> problems, second one cracks my R).
>>
>> I have been trying to run the following negative binomial mixed model:
>>
>> m1 = glmmTMB(density ~ wave_exposure + (1|location) exp(pos + 0|group),
>> data= mydata, family= nbinom1, ziformula= ~0) ##
>>
>> I also tried different covariance structures (gau and mat), but no success
>> so far.
>>
>> Any ideas or suggestions here?
>>
>> Thank you in advance!
>>
>> Andre.
>>
>> --
>> Visiting PhD student
>> School of Ocean Sciences
>> Bangor University
>> Menai Bridge, Anglesey, UK
>>
>> 	[[alternative HTML version deleted]]
>>
>> _______________________________________________R-sig-mixed-models using r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>
>>
>
> --
> M. Sc. André Luiz Pardal-Souza
> Doutorando em Evolução e Diversidade
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC (UFABC)
> Currículo Lattes <http://lattes.cnpq.br/6271009643657143>
>
> Visiting PhD student
> School of Ocean Sciences
> Bangor University
> Menai Bridge, Anglesey, UK
>


-- 
M. Sc. André Luiz Pardal-Souza
Doutorando em Evolução e Diversidade
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC (UFABC)
Currículo Lattes <http://lattes.cnpq.br/6271009643657143>

Visiting PhD student
School of Ocean Sciences
B​angor University
Menai Bridge, Anglesey, UK​

	[[alternative HTML version deleted]]