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	0.48 (0.26, 0.89)	0.019	459	119
lupins	0.34 (0.19, 0.63)	<0.001	453	84
Yard			1337	386
1	Reference		312	94
2	1.01 (0.47, 2.15)	0.99	187	50
3	1.16 (0.54, 2.48)	0.70	295	110
4	0.73 (0.29, 1.85)	0.51	193	47
5	0.92 (0.45, 1.91)	0.83	350	85
Time	0.92 (0.89, 0.96)	<0.001	1337	386