[R-sig-ME] glmmTMB warnings and no output Gamma distribution
Willem (Wim) Kaijser
w|||em@k@|j@er @end|ng |rom un|-due@de
Mon Feb 3 10:03:40 CET 2020
Hello, It was suggested to me to place my question in this mailing-list.
I have some problems and lack of knowledge constructing a GLMM with the
glmmTMB package (version 0.2.03). Therefore, I am sorry If the
explanation is not as sufficient as it should be, and want to thank you
in advance for your time.
I try to include both fixed plus random effects and correction for
serial correlation in a GLMM with a Gamma distribution (link =
"inverse"). However, I get several warnings and the processing time is
long, so I prematurely stopped the permutations (see the code below). If
the Gamma distribution, with “log” link, is used in the model containing
only the fixed and random effects; these warnings do not occur.
Including this with the model correcting for serial correlation it does
return a warning, but I can extract the residuals (AIC and BIC are
returned as NA though). This seems like the following issue:
https://github.com/glmmTMB/glmmTMB/issues/329. However, this seems to be
resolved. What might be the issue here (is it my coding)?
############################################################
#Code with only the fixed and random effects with warnings:#
############################################################
mod1 <- glmTMB(Chla ~ pCO2 + (1|River/ID), family = ”Gamma”, data = df)
There were 19 warnings (use warnings() to see them)
Timing stopped at: 33.7 0.08 34.19
Warning messages:
1: In nlminb(start = par, objective = fn, gradient = gr, ... :
NA/NaN function evaluation
#######################################################################################
#Code with both the fixed, random and correction for serial correlation
with warnings:#
#######################################################################################
mod2 <- glmTMB(Chla ~ pCO2 + (1|River/ID) + ar1(1|Month), family =
”Gamma”, data = df)
There were 20 warnings (use warnings() to see them)
Timing stopped at: 24.71 0.08 25.49
Warning messages:
1: In FUN(X[[i]], ...) : AR1 not meaningful with intercept
2: In nlminb(start = par, objective = fn, gradient = gr, ... :
NA/NaN function evaluation
Best regards,
--
Willem (Wim) Kaijser
Fakultät für Biologie
Aquatische Ökologie
Universitätsstr. 5
D-45141 Essen
Room: S05T03B02
Tel: +49.201.183.3113
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