Modified Rt calculation

Merged Chris Jewell requested to merge mod-time-rt into master

Previously, a posterior over the next generation matrix was saved into ngm.nc. In response to SPI'm request for historic Rt, saving the posterior NGM for all timepoints in the analysis resulted in a data structure of [400, 84, 380, 380] or 36GB.

Rt calculation has now been modified to save LAD-level $R_{it}$ as well as national $R_t$ into reproduction_number.nc.

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