opts_list: Return an _opts List per Region

In EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Return an _opts List per Region

Description

Define a list of ⁠_opts()⁠ to pass to regional_epinow() ⁠_opts()⁠ accepting arguments. This is useful when different settings are needed between regions within a single regional_epinow() call. Using opts_list() the defaults can be applied to all regions present with an override passed to regions as necessary (either within opts_list() or externally).

Usage

opts_list(opts, reported_cases, ...)

Arguments

opts	An ⁠_opts()⁠ function call such as rt_opts().
reported_cases	A data frame containing a region variable indicating the target regions.
...	Optional override for region defaults. See the examples for use case.

Value

A named list of options per region which can be passed to the ⁠_opt⁠ accepting arguments of regional_epinow.

See Also

regional_epinow() rt_opts()

Examples

# uses example case vector
cases <- example_confirmed[1:40]
cases <- data.table::rbindlist(list(
  data.table::copy(cases)[, region := "testland"],
  cases[, region := "realland"]
))

# default settings
opts_list(rt_opts(), cases)

# add a weekly random walk in realland
opts_list(rt_opts(), cases, realland = rt_opts(rw = 7))

# add a weekly random walk externally
rt <- opts_list(rt_opts(), cases)
rt$realland$rw <- 7
rt

EpiNow2 documentation built on Oct. 31, 2024, 5:09 p.m.