3.3 Generalized estimating equations model

Below logistic model takes account of repeat observation by cow. Examine different correlation structures. It is of interest to note that (odds of) high protein content in milk appears to decrease as time since calving increases.

Milk <- Milk |> modify_if(is.character, as.factor);
Milk <- Milk |> tidyr::drop_na()
Milk <- droplevels(Milk);
Milk <- Milk |> dplyr::arrange(Yard, Cow, Time);

rm_mvsum(model=geeglm(HP ~ Diet + Yard + Time, id=c(Cow), data=Milk, family=binomial, corstr="ar1"), data=Milk, showN=T, CIwidth=0.95);

	OR(95%CI)	p-value	N	Event
Diet			1337	386
barley	Reference		425	183
barley+lupins	0.46 (0.26, 0.79)	0.005	459	119
lupins	0.31 (0.17, 0.56)	<0.001	453	84
Yard			1337	386
1	Reference		251	66
2	1.27 (0.57, 2.85)	0.56	276	76
3	1.45 (0.75, 2.81)	0.27	272	92
4	1.11 (0.50, 2.47)	0.80	268	87
5	1.10 (0.53, 2.26)	0.80	270	65
Time	0.92 (0.89, 0.95)	<0.001	1337	386