In the field of biology we often have >1 samples. For instance I can conduct two (but not many) experiments (replicates) each on a number of animals (n1, n2). The aim of the experiment is to estimate the proportion of the animals which prefer a certain habitat area. And I could estimate from each sample the proportion of those animals staying in that area: p1 and p2. Therefore, the sample mean of the proportion is: mean(p1,p2). My question is: based on these two samples, how shall I present the confidence intervals of the sample proportions? Shall I present two CIs or is there anyway to compute one CI just based on these two samples?
Animals have correlated intra-group behavior, so I can not simply combine these two samples into one and then use one of the standard method to compute CI. On the other hand, if I have a large number of samples, I could compute the CI directly from these samples.
The method I could think of is to conduct bootstrapping 500 times from sample 1 and 500 times from sample 2, and then compute the CI from these 1000 random samples.
Do you have any nice suggestions? Thanks