Calibrate via particle filter grid search using time series of deaths

calibrate(
  data,
  R0_min,
  R0_max,
  R0_step,
  R0_prior = NULL,
  first_start_date,
  last_start_date,
  day_step,
  Meff_min = 1,
  Meff_max = 1,
  Meff_step = 0.1,
  squire_model = explicit_model(),
  Rt_func = function(R0_change, R0, Meff) {     exp(log(R0) - Meff * (1 - R0_change)) },
  pars_obs = NULL,
  forecast = 0,
  n_particles = 100,
  reporting_fraction = 1,
  treated_deaths_only = FALSE,
  replicates = 100,
  date_R0_change = NULL,
  R0_change = NULL,
  date_ICU_bed_capacity_change = NULL,
  baseline_ICU_bed_capacity = NULL,
  ICU_bed_capacity = NULL,
  date_hosp_bed_capacity_change = NULL,
  baseline_hosp_bed_capacity = NULL,
  hosp_bed_capacity = NULL,
  date_contact_matrix_set_change = NULL,
  baseline_contact_matrix = NULL,
  contact_matrix_set = NULL,
  country = NULL,
  population = NULL,
  dt = 0.1,
  ...
)

Arguments

data	Deaths data to fit to. See `example_deaths.csv` and `particle_filter_data()`
R0_min	Minimum value of R0 in the search
R0_max	Maximum value of R0 in the search
R0_step	Step to increment R0 between min and max
R0_prior	Prior for R0. Default = NULL, which is a flat prior. Should be provided as a list with first argument the distribution function and the second the function arguments (excluding quantiles which are worked out based on R0_min and R0_max), e.g. `list("func" = dnorm, args = list("mean"= 3.5, "sd"= 3))`.
first_start_date	Earliest start date as 'yyyy-mm-dd'
last_start_date	Latest start date as 'yyyy-mm-dd'
day_step	Step to increment date in days
Meff_min	Minimum value of Meff (Movement effect size) in the search. Default = 1, which is the same as `Meff_max`. If `Meff_max` and `Meff_min` are the same then only a 2d grid search is performed based on R0 and start_date
Meff_max	Maximum value of Meff (Movement effect size) in the search. Default = 1, which is the same as `Meff_min`. If `Meff_max` and `Meff_min` are the same then only a 2d grid search is performed based on R0 and start_date
Meff_step	Step to increment Meff (Movement effect size) between min and max. Default = 0.1
squire_model	A squire model. Default = `explicit_SEIR()`
Rt_func	Function for converting R0, Meff and R0_change. Function must have names arguments of R0, Meff and R0_change. Default is linear relationship on the log scale given by `exp(log(R0) - Meff*(1-R0_change))`.
pars_obs	list of parameters to use for the comparison function.
forecast	Number of days to forecast forward. Default = 0
n_particles	Number of particles. Positive Integer. Default = 100
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`
treated_deaths_only	Boolean for whether likelihood is based only on deaths that occur from healthcare systems, i.e. are treated. Default = FALSE, which uses all deaths.
replicates	Replicates to be run. Default = 100
date_R0_change	Calendar dates at which R0_change occurs. Defaut = NULL, i.e. no change in R0
R0_change	Numeric vector for relative changes in R0. Default = NULL, i.e. no change in R0
date_ICU_bed_capacity_change	Calendar dates at which ICU bed capacity changes set in `model_params` change. Defaut = NULL, i.e. no change
baseline_ICU_bed_capacity	The starting number of ICU beds before the epidemic started. Default = NULL, which will use the hospital beds data for the country provided. If no country is provided then this is 3/100 of hospital beds
ICU_bed_capacity	Number of ICU beds at each date specified in `date_ICU_bed_capacity_change`. Must be same length as `date_ICU_bed_capacity_change`.
date_hosp_bed_capacity_change	Calendar dates at which hospital bed capacity changes set in `model_params` change. Defaut = NULL, i.e. no change
baseline_hosp_bed_capacity	The starting number of hospital beds before the epidemic started. Default = NULL, which will use the hospital beds data for the country provided. If no country is provided then this is 5/1000 of the population
hosp_bed_capacity	Number of hospital beds at each date specified in `date_hosp_bed_capacity_change`. Must be same length as `date_hosp_bed_capacity_change`.
date_contact_matrix_set_change	Calendar dates at which the contact matrices set in `model_params` change. Defaut = NULL, i.e. no change
baseline_contact_matrix	The starting contact matrix prior to any changes due to interventions or otherwise. Default = NULL, which will use the contact matrix associated with the coutnry provided.
contact_matrix_set	List of contact matrices to be used from the dates provided in `date_contact_matrix_set_change`.Must be same length as `date_contact_matrix_set_change`
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`
dt	Time Step. Default = 0.1
...	Further aguments for the model parameter function. If using the `explicit_model` (default) this will be `parameters_explicit_SEEIR`.

Value

List of dated squire simulations