format_data_simulation: Formating intervention parameters within a database
In SwissTPH/VivaxModelR: Simulation of Plasmodium Vivax dynamics

format_data_simulation

R Documentation

Formating intervention parameters within a database

Description

Helper function to format dataframes

Usage

format_data_simulation(
  df,
  intervention_object,
  delay = FALSE,
  rcd = FALSE,
  mda = FALSE,
  mystart,
  rcd_at_baseline = FALSE,
  maxtime
)

Arguments

`df`	a dataframe containing at least 3 variables : alpha, beta and omega
`intervention_object`	an named list containing the intervention description. It should have the follwing structure: list(intervention_name="string", "alpha.new"=NA, "beta.new"=NA, "omega.new"=NA ) where NA can be replaced by scalars or kepts as such.
`delay`	a boolean indicating if the model including delays in treatment should be used. Default (FALSE) is the model without delay in treatment
`rcd`	a boolean indicating if the model including reactive case detection should be used. Default (FALSE) is the model without RCD
`mda`	a boolean indicating if the model including mass drug administration (MDA) prophylaxis should be used. Default (FALSE) is the model without MDA
`mystart`	an integer indicating the time index of the start of the simulation (this is used to chain interventions appropriately)
`rcd_at_baseline`	a boolean indicating if the model was calibrated using the RCD model (i.e. there is some RCD at baseline already). Default (FALSE) is the model without RCD at baseline
`maxtime`	number of time steps for simulation

Details

If alpha.new is not provided in intervention_object it is equal to alpha. If beta.new is not provided in intervention_object it is equal to beta. If omega.new is not provided in intervention_object it is equal to omega. If rho.new is not provided in intervention_object it is equal to rho