Hello ,

I am writing because I would need some advice on the following question. I am working on paternity in a monogamous bird species and I am performing analyses to check whether the probability for a male to be cuckolded (binary variable) depends on his body size, the body size of his female, the degree of genetic relatedness to his female and nest density around his own nest (all continuous variables).
Since I have data for two years (2002 and 2003), I think that the best solution is to conduct a logistic regression for repeated measures.
However, I am a bit worried to use my entire data set. Indeed, a few individuals changed partner between 2002 and 2003 (they divorced or became widowed). For some other pairs, I have data for one year only (the birds did not attempt to breed the other year).
Under these conditions, I am wondering what I should do. 

Shall I use my whole data set? 

Shall I use a subset including only those males for which I have data for both years (in this subset, two males changed female between 2002 and 2003, but no female changed male. If I use pairs as a random variable, I will account for the non-independence of the partners within pairs, but I will have twice two pairs that are not independent from each other since they will have the same male, and these four pairs will only have one year of data)? 

Or shall I use only the pairs for which I have two years of data (in this case, I will only have 13 clusters, vs 55 if I use the whole data set)?

Thank you in advance for your help.

Joël Bried


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