[R] negative binomial GAMM with variance structures

Meredith Jantzen
Thu, 22 Sep 2011 13:59:39 -0000

Hello,

I am having some difficulty converting my gam code to a correct gamm code, and
I'm really hoping someone will be able to help me.

I was previously using this script for my overdispersed gam data:

M30 <-gam(efuscus~s(mic, k=7) +temp +s(date)+s(For3k, k=7) + pressure+
humidity, family=negbin(c(1,10)), data=efuscus)

My gam.check gave me the attached result.  In order to deal with my
heterogeneity, I need to switch over to a gamm structure and use at least one,
but possibly multiple, variance structures, and I am starting by applying
varPower to my temperature covariate.  (Efuscus is my square root transformed
response variable).

Here is the code I have for the gamm:

K1 <-(efuscus~s(mic, k=7) +temp +s(date)+s(For3k, k=7) + pressure+ humidity+
windspeed + year)
M17.4A <-gamm(K1, method="REML", family=negbin(c(1,10),
data=efuscus, weights=varPower(form=~temp))

With my various versions of the script, the two error messages I have been
getting repeatedly are: Error in eval(expr, envir, enclos) : object
'temp' not found, and Error: unexpected symbol in: "M17.4A
<-gamm(K1, method="REML", family=negbin(c(1,10), data=efuscus,
weights=varPower(form=~temp))"

I know I must be missing something obvious that is causing my script not to
work...I've been looking at both Wood (2006) and Zuur's Mixed Models
book for examples but none of them are completely the same as my situation,
which is causing me to get tripped up.

Am I defining my negative binomial family correctly for the situation?  Do I
need to somehow define the variance term before I apply it?

Thank you very much.  I appreciate your time and patience.
Meredith