[R-sig-ME] spatial covariance structure in glmmTMB

[Alice Domalik]

I did look at the vignette, and the notation wasn't clear to me. 
If, for example, I wanted to add a spatial gaussian, would I write my model as: 

m1<-glmmTMB(count~gau(coordinates) + waterdepth + temperature + chl.conc + (1|individual), family=list(family="truncated_nbinom1", link="log"), data=mydata) ? 

It also isn't clear to me if spatial coordinates need to be in a particular format. 


From: "Mollie Brooks" <mollieebrooks at gmail.com> 
To: "Alice Domalik" <adomalik at sfu.ca> 
Cc: r-sig-mixed-models at r-project.org, "Kasper Kristensen" <kaskr at dtu.dk> 
Sent: Monday, October 9, 2017 6:42:48 AM 
Subject: Re: [R-sig-ME] spatial covariance structure in glmmTMB 

Hi Alice, 
Have you looked at the vignette on covariance structures? There's a section on spatial correlations. 

[ https://cran.r-project.org/web/packages/glmmTMB/vignettes/covstruct.html | https://cran.r-project.org/web/packages/glmmTMB/vignettes/covstruct.html ] 

cheers, 
Mollie 

On Mon, Oct 9, 2017 at 3:22 PM, Alice Domalik < [ mailto:adomalik at sfu.ca | adomalik at sfu.ca ] > wrote: 


Dear list, 

I am fitting mixed effects models using the package glmmTMB to investigate habitat use. 
My current model has the form m1<-glmmTMB(count~waterdepth + temperature + chl.conc + (1|individual), family=list(family="truncated_nbinom1", link="log"), data=mydata) 
I would like to add a spatial covariance structure based on geographic coordinates (mydata$x and mydata$y). 
However, I do not know how to modify my model formula to include a spatial covariance structure. Does anyone have example code to show how this is done? 

Any help would be much appreciated! 



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