R help - Feb 2019 - Help formulating gamm with repeated measures and spatial autocorrelation using mgcv package

(Also posted on StackExchange but submitting to R-help to reach more potential
experts)I am using the gamm function in the mgcv package in R to specify a model
that predicts abundance with respect to elevation and year based on repeated
measures from several sites. My overarching question is how abundance changes
over elevation, knowing and accounting for the fact that it also changes over
time. GAMM is used because I do not want to restrict the relationship of either
elevation or year with abundance to be linear. I expect the data to be spatially
autocorrelated within years (sites closer together will have more similar values
than sites further apart within each year) and would like to account for this.

I'm having trouble figuring out the proper full formulation of the GAMM.

The variables are: 1) abundance (continuous response) 2) elevation (numeric,
continuous predictor) 3) year (numeric, continuous predictor as we expect a
gradual change in abundance over time) 4) spatial autocorrelation term (based on
the lat/long of the sites where data were collected) 5) site (random factor)

The model formulation I have come up with is:

model<-gamm(abundance ~ s(elevation, bs = "tp")+s(year, bs =
"tp"), correlation=corSpher(form = ~ y+x|year), random=list(site=~1),
data=input.data)

My questions are:

Is the repeated measures nature of the data adequately accounted for here or do
I also need to include year in my random effects (nest site in year)?

Have I properly taken year into account in my spatial autocorrelation term?
Finally, when running this model, I get an error and a warning:Error in
corFactor.corSpatial(object):??Na/NaN/Inf in foreign function call (arg 1)?In
addition: Warning message:?In
min(unlist(attr(object,"covariate"))):?no non-missing arguments to
min, returning InfNot sure why this is happening. If I run the GAMM without the
random effect of site, it does not return the error...

Not sure why this is happening. If I run the GAMM without the random effect of
site, it does not return the error...

Many thanks in advance for any help!


	[[alternative HTML version deleted]]

Crossposting is explicitly advised against in the rhelp posting guide. 
Furthermore, this is the wrong list for this sort of question within the 
r-project hierarchy of mailing lists. I do not believe an answer is 
possible in the absence of the data (and note the request .... some 
would say demand... for reproducible code and data at the end of every 
posting from the Rhelp server). And finally rhelp is a plain text list, 
so posting with html is also deprecated.

Please read the posting guide. I'm just repeating relevant points that 
are already discussed there at greater length and clarity.

David

On 2/26/19 2:36 PM, Julie Lee-Yaw via R-help wrote:
> (Also posted on StackExchange but submitting to R-help to reach more
potential experts)I am using the gamm function in the mgcv package in R to
specify a model that predicts abundance with respect to elevation and year based
on repeated measures from several sites. My overarching question is how
abundance changes over elevation, knowing and accounting for the fact that it
also changes over time. GAMM is used because I do not want to restrict the
relationship of either elevation or year with abundance to be linear. I expect
the data to be spatially autocorrelated within years (sites closer together will
have more similar values than sites further apart within each year) and would
like to account for this.
>
> I'm having trouble figuring out the proper full formulation of the
GAMM.
>
> The variables are: 1) abundance (continuous response) 2) elevation
(numeric, continuous predictor) 3) year (numeric, continuous predictor as we
expect a gradual change in abundance over time) 4) spatial autocorrelation term
(based on the lat/long of the sites where data were collected) 5) site (random
factor)
>
> The model formulation I have come up with is:
>
> model<-gamm(abundance ~ s(elevation, bs = "tp")+s(year, bs =
"tp"), correlation=corSpher(form = ~ y+x|year), random=list(site=~1),
data=input.data)
>
> My questions are:
>
> Is the repeated measures nature of the data adequately accounted for here
or do I also need to include year in my random effects (nest site in year)?
>
> Have I properly taken year into account in my spatial autocorrelation term?
> Finally, when running this model, I get an error and a warning:Error in
corFactor.corSpatial(object):??Na/NaN/Inf in foreign function call (arg 1)?In
addition: Warning message:?In
min(unlist(attr(object,"covariate"))):?no non-missing arguments to
min, returning InfNot sure why this is happening. If I run the GAMM without the
random effect of site, it does not return the error...
>
> Not sure why this is happening. If I run the GAMM without the random effect
of site, it does not return the error...
>
> Many thanks in advance for any help!
>
>
> 	[[alternative HTML version deleted]]
>
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