covid_estimate_repro: Fit EpiEstim::estimate_R to covid19 data

In CBDRH/COVIDreconnoitR: Pulls and Analyses COVID data

Description

This fits EpiEstim::estimate_R, with config values mean_si = 4.7 and std_si = 2.9 from https://doi.org/10.1101/2020.02.03.20019497 It assumes that the data is in the format provided by covid_prepare_estimate_repro.

Usage

covid_estimate_repro(
  covid_data_prepared,
  estimate_method = "parametric_si",
  si_sample = NULL,
  config = list(mean_si = 4.7, std_si = 2.9)
)

Arguments

covid_data_prepared	data is in the format provided by covid_prepare_estimate_repro, with columns "dates" and "I", where "dates" contains data of class "Date", and "I" contains cases.
estimate_method	default is "parametric_si"
si_sample	SI samples. Default is NULL.
config	named list of values to pass to EpiEstim::make_config. Default is mean_si = 4.7, and std_si = 2.9.

Value

estimated reproductive number

CBDRH/COVIDreconnoitR documentation built on May 28, 2020, 6:15 a.m.