[R-sig-ME] Binomial glmer with time dependency

[Luca Corlatti]

Dear list member, 
suppose I want to investigate how the success in DNA extraction (binary response 1/0) from, e.g., scats, is affected by the method of sample storage (4 levels: “ethanol”, “silica”, “DMSO” and “lysis”) and the time elapsed from scat deposition (3 levels: “<48h”, "week1”, "week2”). If I collect scats from, e.g, 10 individuals, my dataset will look like:

ID_individual	method	time		DNA_extraction
1			ethanol	<48h	1
1			ethanol	week1	1
1			ethanol	week2	0
1			silica	<48h	1
1			silica	week1	0
1			silica	week2	0
1			DMSO	<48h	1
1			DMSO	week1	1
1			DMSO	week2	1
1			lysis		<48h	1
1			lysis		week1	1
1			lysis		week2	0
2			ethanol	<48h	1
2			ethanol	week1	1
2			ethanol	week2	0
…
10			lysis		<48h	1
10			lysis		week1	1
10			lysis		week2	1

for an overall of 120 records.

A simple model could be:

mod <- glmer(DNA_extraction ~ method*time + (1|ID_individual), family=binomial)

This model should account for pseudoreplication between methods, while different time decays should be corrected for by the “method” variable. 
However, the success in DNA extraction is not independent between 48h, week1 and week2 (e.g. if i fail in 48h, I am likely to fail also in week1 and week 2), and I am not sure how to account for this time dependency.
Any suggestion?
Thanks a lot in advance!
Luca