run_daily_import_model: Run the full simulation of daily importations
In HopkinsIDD/covidImportation: Estimating the Number of Imported COVID-19 Cases

Run the full simulation of daily importations

run_daily_import_model(
  input_data,
  travel_data_monthly,
  travel_data_daily,
  travel_dispersion = 3,
  travel_restrictions = NULL,
  allow_travel_variance = FALSE,
  tr_inf_redux = 0,
  get_detection_time = FALSE,
  param_list = list(incub_mean_log = log(5.89), incub_sd_log = log(1.74),
    inf_period_nohosp_mean = 15, inf_period_nohosp_sd = 5, inf_period_hosp_mean_log =
    1.23, inf_period_hosp_sd_log = 0.79)
)

`input_data`	full importation input data, including case, travel, and population data
`travel_data_monthly`	monthly travel data between sources and destinations
`travel_dispersion`	how evenly the monthly travel should be distributed across days
`travel_restrictions`	data.frame of travel restrictions
`allow_travel_variance`	whether to sample from the travel variance
`tr_inf_redux`	proportion reduction in travel when individuals are infected
`get_detection_time`	logical; return importation detection or not
`n_sim`	number of simulations to run
`meanD_mat`	matrix of mean duration during which infected individuals can travel
`u_origin`	reporting rate, origin
`time_inftodetect`	Time from infection to detection
`incub_mean_log`	log mean incubation period
`incub_sd_log`	log sd of incubation period
`inf_period_hosp_mean_log`	infectious period of hospitalized, log-mean
`inf_period_hosp_sd_log`	infectious period of hospitalized, log-sd
`inf_period_nohosp_mean`	infectious period of non-hospitalized, shape
`inf_period_nohosp_sd`	infectious period of non-hospitalized, scale
`project_name`	project name, if saving in the function
`batch`	run batch, if saving in the function
`version`	run version, if saving in the function
`print_progress`	logical, whether to print the progress of the simulations
`cores`	number of cores for parallel processing
`time_inftotravel`	time from infection to traveling

list consisting of two objects: 1) an array of importations by date, location, and simulation, 2) a dataframe with negative binomial parameters for each location and date

HopkinsIDD/covidImportation documentation built on Sept. 14, 2020, 2:43 p.m.