[R] A question regarding stratified bootstrap

[qiana@biostat.umn.edu]

Dear experts,
I am asking for help with a question regarding to stratified bootstrap. How
shall I implement my stratified bootstrap in boot() using boot package in R?

My dataset is a longitudinal dataset (3 measurements per person at year
1, 4 and 7) composed of multiple clinic centers and multiple participants
within each clinic. It has missing values.

I want to do a bootstrap to find the standard errors and confidence
intervals for my variance components. My model is a mixed model with
random clinic and random participant within clinic.

I thought two methods to do bootstrap:
(1) bootstrap data; however, I have problem specifying the second
parameter for my statistic function, shall I use indices, weight or
frequency and how shall I relate to my dataset.
(2) bootstrap residuals; however, the dataset has multiple measurements
and missing values. I am wondering how to construct a new data frame
containing the residuals and fitted values.

Your help will be highly appreciated!
Sincerely yours,
Qian