fit_spline_rt: Fit squire model using rw splines

In mrc-ide/covid-mortality-ascertainment: Analysis of COVID-19 mortality ascertainment

Description

Fit squire model using rw splines

Usage

fit_spline_rt(
  data,
  country,
  population,
  reporting_fraction,
  n_mcmc = 10000,
  replicates = 100,
  rw_duration = 14,
  hosp_beds = 1e+10,
  icu_beds = 1e+10
)

Arguments

data	Data to fit to. This must be constructed with particle_filter_data
country	Character for country beign simulated. WIll be used to generate population and contact_matrix_set if unprovided. Either country or population and contact_matrix_set must be provided.
population	Population vector (for each age group). Default = NULL, which will cause population to be sourced from country
reporting_fraction	Reporting fraction. Numeric for what proportion of the total deaths the reported deaths represent. E.g. 0.5 results in the model calibrating to twice the deaths provided by data$deaths
n_mcmc	number of mcmc mcmc iterations to perform
replicates	number of trajectories (replicates) to be returned that are being sampled from the posterior probability results produced by run_mcmc_chain to select parameter set. For each parmater set sampled, run particle filter with n_particles and sample 1 trajectory
rw_duration	Random Walk/Spline Duration. Default = 14 days
hosp_beds	General Hospital Beds
icu_beds	ICU Beds

Value

Model fit from [squire:::pmcmc]

mrc-ide/covid-mortality-ascertainment documentation built on Dec. 21, 2021, 10:03 p.m.