Made demographics but the totals are off somehow on who is infected and recovered.
Created a scan of all trajectories in a file in order to set up parsing of the data into things we can plot.
ensemble_sum now reads through trajectories in c++. Fast. Doesn't save anything yet, but yowza.
Now calculate prevalence and incidence. Have to save everything to a file.
Now writes summary data to hdf5 file.
The report now has some things. Lots of work
Added a nice little summary to the report.
Fixed the density plot by making it one entry per time interval so that the total count per time interval is correct.
Added diagram