[R] Model building using lmer
Luciano La Sala
luciano_la_sala at yahoo.com
Wed Dec 17 15:46:55 CET 2008
Dear R-experts,
Quite new to R on this end, but learning fast (I hope).
I am running version 2.7.1 on Windows Vista. I have small dataset
which consists of:
# NestID: nest indicator for each chicken. Siblings sharing the same nest have the same nest indicator.
# Chick: chick indicator consisting of a unique ID for each single chick.
# Year: 1, 2.
# ClutchSize: 1-, 2- , 3-eggs.
# HO: hatching order within each clutch (1, 2, 3 [first, second and third-hatched chick]).
# SibComp: sibling competence: present/ absent (0, 1)
# Death2: death at two days post-hatch (0, 1)
# Death10: death at ten days post-hatch (0, 1)
So a subset of my dataset looks something like this:
NestID Chick Year ClutchSize HO Hatching SibComp Death2 Death10
1 1 1 1 1 1 1 1 1
2 2 1 1 1 1 1 0 0
3 3 1 1 1 0 0 0 0
4 4 1 1 1 1 0 1 0
4 5 1 2 2 0 1 0 1
5 6 1 2 1 1 0 0 0
5 7 1 2 2 0 0 0 0
6 8 2 3 1 1 1 0 0
6 9 2 3 2 1 0 1 0
6 10 2 3 3 0 1 0 0
7 11 2 3 1 0 0 0 1
7 11 2 3 2 0 0 0 0
7 11 2 3 3 1 1 1 1
............
In order to account for lack of independence at the nest level (many chicks are siblings), I'd like to run a GLMM with random slopes and intercepts for nests.
Using lmer, my model for survival at 10 days, for example, would read as follows (or not!):
> model <- lmer(Death10 ~ HO + ClutchSize + SibComp + Year + (1|NestID), family=binomial, 1)
> summary(model)
>From what I understand, the model above includes only random intercepts for NestID. So at this point my question is how do I make this model into one which includes both random intercepts and slopes for NestID?
Look forward to receiving your input. Thank you all for your time!
Luciano
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