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.