well

by the point that i am understanding, you are trying to calculate repetitive data using R.

for that you can calculate them separately and then import them to R.

if you have further questions i am at disposal.

regards. 

Can you use a mixed effects logistic model?

If so, the glmer function in the lme4 package can do this.

See the following, and search for "glmer" :

http://www.ats.ucla.edu/stat/r/dae/melogit.htm