[R-sig-ME] Spatial correlation in glmmTMB

André Pardal @ndre@p@rd@|@@ouz@ @end|ng |rom gm@||@com
Wed Jul 17 19:15:39 CEST 2019


I would like to ask for help on how to account for spatial correlation in
glmmTMB package.

According to the help page (
I need to create a numFactor object grouping coordinates and a dummy
grouping factor.

mydata$pos <- numFactor(mydata$easting, mydata$northing)## spatial
mydata$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!


Visiting PhD student
School of Ocean Sciences
Bangor University
Menai Bridge, Anglesey, UK

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