- Compiled compare function allowing running on a GPU
- helium_compare: use total daily pharyngitis rate when age-disaggregated unavaliable
- outputt UKHSA-aggregated etiologic fraction from model
- update helium and hydrogen compare to fit to GP scarlet fever incidence, as well as notifiable cases (subject to time-varying under-reporting)
- update helium compare to use Normal for pharyngitis rates and Dirichlet for scarlet fever proportions
- add running and fitting functions for both hydrogen and helium models
- reduce helium age groups to 16, so max group is 75+
- output new model states: prev_A and prev_R, will scale by age
- output new model states: gas_pharyngitis_inc, pharyngitis_inc (all-cause cases)
- when n_group == 19, additionally output: proportion of scarlet fever cases, proportion of all-cause pharyngitis cases, proportion of all-cause pharyngitis or scarlet fever cases in each UKHSA age group
- update model date functions to align with UKHSA epi weeks, which end on Sunday i.e. model week 1 ends on Sun 5 Jan 2014.
- output daily incidence rates (based on 7-day average) for scarlet fever and pharyngitis-or-scarlet-fever
- allow fitting of daily incidence rates by age-groups reported in GP surveillance
- allow time in each compartment to be Erlang distributed
- add pre scarlet fever compartment P (pharyngitis symptoms but no rash)
- remove iGAS compartment - output iGAS cases at observation level
- add time-varying births
- add under-reporting of pharyngitis (p_T)
- allow immigration via negative omega
- add aging between groups
- make all demographic processes deterministic
- add age-structure to model
- add stochastic compartmental model of GAS transmission and pmcmc fitting capabilities via mrc-ide/mcstate.git
- initial setup