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

[Ben Bolker]

Did you see the part of the document (sub)titled "Adding coordinate
information" ?  (The example given in the vignette only does a 1-D
example, but it gives instructions that should in principle work for
2-D ...)

On Mon, Oct 9, 2017 at 12:05 PM, Alice Domalik <adomalik at sfu.ca> wrote:
> 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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