run_farrington: Run the Farrington early detection algorithm

In EcoGRAPH/epidemiar: epidemiar: Create EPIDEMIA Environmentally-Mediated Disease Forecasts

Description

Run the Farrington early detection algorithm

Usage

run_farrington(
  epi_fc_data,
  quo_groupfield,
  quo_popfield,
  ed_control,
  val_type,
  inc_per,
  groupings,
  report_dates
)

Arguments

epi_fc_data	Internal pass of epidemiological data complete with future forecast values.
quo_groupfield	Quosure of the user given geographic grouping field to run_epidemia().
quo_popfield	Quosure of user-given field containing population values.
ed_control	An extract of report_settings$ed_control - all parameters for early detection algorithm, passed through to that subroutine.
val_type	An extract of report_settings$report_value_type after defaults applies - whether to return epidemiological report values in "incidence" or "cases" (default).
inc_per	An extract of report_settings$report_inc_per after defaults applies - number for what unit of population the incidence should be reported in, e.g. incidence rate per 1000 people. Ignored when report_settings$report_value_type is 'cases'.
groupings	A unique list of the geographic groupings (from groupfield).
report_dates	Internally generated set of report date information: min, max, list of dates for full report, known epidemiological data period, forecast period, and early detection period.

Value

Returns a list of three generated series from the Farrington algorithm: "ed" : early detection alerts (ed period of most recent epi data) "ew" : early warning alerts (forecast/future portion) "thresh" : threshold values per week

EcoGRAPH/epidemiar documentation built on Nov. 13, 2020, 5:31 p.m.