conduct_replicate: Handles simulating replicates within 'projections'
In mrc-ide/squire: SEIR transmission model of COVID-19

conduct_replicate

R Documentation

Handles simulating replicates within `projections`

Description

Handles simulating replicates within projections

Usage

conduct_replicate(
  x,
  r = NULL,
  t_steps = NULL,
  R0 = NULL,
  R0_change = NULL,
  tt_R0 = NULL,
  contact_matrix_set = NULL,
  contact_matrix_set_change = NULL,
  tt_contact_matrix = NULL,
  hosp_bed_capacity = NULL,
  hosp_bed_capacity_change = NULL,
  tt_hosp_beds = NULL,
  ICU_bed_capacity = NULL,
  ICU_bed_capacity_change = NULL,
  tt_ICU_beds = NULL,
  model_user_args = NULL
)

Arguments

`x`	Simulation replicate number
`r`	Output of `pmcmc` or `calibrate`
`t_steps`	List of time steps to be run for each replicate
`R0`	Numeric vector for R0 from t = 0 in the calibration. E.g. `R0 = c(2, 1)`. Default = NULL, which will use `R0_change` to alter R0 if provided.
`R0_change`	Numeric vector for relative changes in R0 relative to the final R0 used in the calibration (i.e. at t = 0 in the calibration) E.g. `R0 = c(0.8, 0.5)`. Default = NULL, which will use `R0` to parameterise changes in R0 if provided.
`tt_R0`	Change time points for R0
`contact_matrix_set`	Contact matrices used in simulation. Default = NULL, which will use `contact_matrix_set_change` to alter the contact matrix if provided.
`contact_matrix_set_change`	Numeric vector for relative changes in the contact matrix realtive to the final contact matrix used in the calibration (i.e. at t = 0 in the calibration). E.g. `contact_matrix_set_change = c(0.8, 0.5)`. Default = NULL, which will use `contact_matrix_set` to parameterise changes in contact matrices if if provided.
`tt_contact_matrix`	Time change points for matrix change. Default = 0
`hosp_bed_capacity`	Numeric vector for hospital bed capacity from t = 0 in the calibration. Default = NULL, which will use `hosp_bed_capacity_change` to alter hosp_bed_capacity if provided.
`hosp_bed_capacity_change`	Numeric vector for relative changes in hospital bed capacity relative to the final hospital bed capacity used in the calibration (i.e. at t = 0 in the calibration). E.g. `hosp_bed_capacity_change = c(0.8, 0.5)`. Default = NULL, which will use `hosp_bed_capacity` to parameterise changes in hospital bed capacity if provided.
`tt_hosp_beds`	Change time points for hosp_bed_capacity
`ICU_bed_capacity`	Numeric vector for ICU bed capacity from t = 0 in the calibration. Default = NULL, which will use `ICU_bed_capacity_change` to alter ICU_bed_capacity if provided.
`ICU_bed_capacity_change`	Numeric vector for relative changes in ICU bed capacity relative to the final ICU bed capacity used in the calibration (i.e. at t = 0 in the calibration). E.g. `ICU_bed_capacity_change = c(0.8, 0.5)`. Default = NULL, which will use `ICU_bed_capacity` to parameterise changes in ICU bed capacity if provided.
`tt_ICU_beds`	Change time points for ICU_bed_capacity
`model_user_args`	List of other parameters to be passed to the model to be run. Default = NULL. An example would be: `list( list( "prob_severe" = runif(17), "tt_dur_get_ox_survive" = c(0, 10), "gamma_get_ox_survive" = 0.2), list( "prob_severe" = runif(17), "tt_dur_get_mv_survive" = c(0, 5), "gamma_get_mv_survive" = 0.1) )` The list should be the same length as the number of replicates in the simulations. Each list element should then be a list with elements named to match the arguments expected by the odin model with `r`. Above would be suitable to set the model parameters for a simulation with 2 replicates. You do not have to have the same arguments in each list.