I am generating state space models for fish populations in the Florida Everglades. We have a unique sample design that I am trying to incorporate into these models.

Each site has 3 plots with 7 samples collected at each plot. I would like to generate a state space model that has 3 points per time step (mean of each of the three plots). The sample variance is known (calculated from the mean of the 7 samples at each plot). This provides me with 3 sample means and 3 sample variances per time step at each site. I was directed to the paper “Using uncertainty estimates in analyses of population time series”. The code used in that paper is from MATLab.

I was wondering if you would recommend an R package to incorporate this hierarchal sample design. Any help would be greatly appreciated.