Hi all,

I am a Phd student from Brazil and new to Mixed models and R. Recently I
sent a manuscript to Marine Ecology Progress Series and it was declined.
The editor pointed out one problem (there were others but I could solve
them): He/she said that I did not provide confidence intervals for the
random effect and if it could be calculated he/she assumed that would be
too large.

I am looking for environmental drivers influencing whales distribution in
Rio de Janeiro. The study are was divided in 2x2km. Presence-absence of
whales are the response variable.

I searched in R for confidence intervals in GAMM4 but I did not find it. I
could obtain variance and std deviation for the random and fixed effects
Groups Name             Variance            Std.Dev.
 RANDOM (Intercept)  1.4973e+01        3.8694319
 Xr.0   s(DISTCOAST)  4.7361e-02        0.2176263
 Xr     s(DEPTH)          1.9779e-06        0.0014064


Here it is my model.
n3 <- gamm4(OCC_BIN~s(DEPTH)+s(DISTANCE_TO_COAST)+offset(RT),random = ~
(1|RANDOM),correlation=corAR1(),method="ML", family=binomial,data=bryde3)

The OFFSET is the boat route (the number of times the boat searched for
whales in each 2x2km grid)
RANDOM is the individual whale as done in previous studies (Hazen et al
2009 - MEPS - doi:10.3354/meps08108)

Can someone help me, please?
Sincerely,
-- 
Rodrigo Tardin

Doutorando em Ecologia e Conservação - IBRAG - UERJ
Mestre em Biologia Animal - PPGBA - UFRRJ
Especialista em Docência do Ensino Superior - IAVM
Laboratório de Bioacústica e Ecologia de Cetáceos - UFRRJ/ IF/ DCA

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