We are using transmitting time/depth recorders to measure the diving
behavior of 5 harbor seals in Puget Sound.  For each seal, we have two
seasons, while herring are spawning and after they spawn.  Nested in each
season, we have four times of day (labeled period).  We are interested in
whether there is an effect of “season” (spawn / non-spawn), “period”
(morning, day, evening, night) on the “Modal Depth Bin” of harbor seals, or
an interaction between these two factors.

Below is the code that we think is correct.  Does anyone think the model is
specified incorrectly, and if so what do they recommend (and why)?
Thanks very much for your time.

-Austen Thomas

Biology Department
Western Washington University
Biology Building BI 315
Mail Stop 9160
Bellingham, WA 98225-9160



For lme4 package
summary(d)
lmer(MDB~Season*Period+(1|Seal/Season/Period), data=d, REML=F)->fit10
summary(fit10)
lmer(MDB~Season+Period+(1|Seal/Season/Period), data=d, REML=F)->fit11
lmer(MDB~Season+(1|Seal/Season/Period), data=d, REML=F)->fit12
lmer(MDB~1+(1|Seal/Season/Period), data=d, REML=F)->fit13
anova(fit10, fit11, fit12, fit13)

for the nlme package
lme(MDB~Season*Period, random=~1|Seal/Season/Period, method="ML",
data=d)->fit20
summary(fit20)
lme(MDB~Season+Period, random=~1|Seal/Season/Period, method="ML",
data=d)->fit21
lme(MDB~Season, random=~1|Seal/Season/Period, method="ML", data=d)->fit22
lme(MDB~1, random=~1|Seal/Season/Period, method="ML", data=d)->fit23
anova(fit20, fit21, fit22, fit23)

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