On 11Oct 2017, at 20:37, Alice Domalik <adomalik at sfu.ca> wrote:
In the end, I was able to run the following model:
m1<-glmmTMB(count~waterdepth + temperature + chl.conc + (1|individual) + gau(coord + 0| group), family=list(family="truncated_nbinom1", link="log"), data=mydata)
Where 'coord' are the spatial coordinates (UTM) represented as a factor, and 'group' is a single level.
group<-factor(rep(1,n))
However, I get the error:
Warning message:
In glmmTMB(count ~ waterdepth + temperature + :
Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
I didn't have this error when I initially ran my model without a covariance structure.
Any advice on how I should move forward?
Thanks!!! Alice
From: "Ben Bolker" <bbolker at gmail.com>
To: "Alice Domalik" <adomalik at sfu.ca>
Cc: "Mollie Brooks" <mollieebrooks at gmail.com>, r-sig-mixed-models at r-project.org, "Kasper Kristensen" <kaskr at dtu.dk>
Sent: Monday, October 9, 2017 3:05:19 PM
Subject: Re: [R-sig-ME] spatial covariance structure in glmmTMB
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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