setup_importations: Set up importation sims

Description Usage Arguments

View source: R/import_model_source.R

Description

Set up importation sims

Usage

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setup_importations(
  dest = "UT",
  dest_type = c("state"),
  dest_country = "USA",
  dest_aggr_level = c("airport"),
  first_date = ISOdate(2019, 12, 1),
  last_date = Sys.time(),
  output_dir = file.path("output", paste0(paste(dest, collapse = "+"), "_",
    as.Date(Sys.Date()))),
  save_case_data = TRUE,
  get_travel = TRUE,
  n_top_dests = Inf,
  travel_dispersion = 3,
  param_list = list(p_report_source = c(0.05, 0.25), shift_incid_days = -10, delta = 1),
  check_errors = TRUE
)

Arguments

dest

character string, name of destination to simulate importations for

dest_type

character string, options: "airport", "city", "state", "country"

dest_country

optional character string, specify a higher level destination (i.e. dest_0="USA"), default NULL

dest_aggr_level

character string, level to which travel will be aggregated for destination. Includes "airport", "city", "state", "country", "metro" (only available for CA currently)

first_date

Date, first import date

last_date

Date, last import date

output_dir

where output files are saved

save_case_data

Whether to save the JHUCSSE raw data

get_travel

whether to load or pull travel data

n_top_dests

Number of destinations to include, ranked by volume; default (Inf) is all.

travel_dispersion

numeric

param_list

list, with the following elements

  • p_report_source numeric vector of length 2, currently the probability of reporting by source with the first indicating Hubei reporting and second indicating everywhere else (UPDATE WITH THESE https://cmmid.github.io/topics/covid19/severity/global_cfr_estimates.html)

  • shift_incid_days lag from infection to report

  • delta days per time period

check_errors

logical


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