estimate_activity: Estimate Infectious Activity from Incidence and Serial...

In jesse-smith/covidModel: COVID-19 Modeling Tools for Shelby County Health Department

Description

Estimate Infectious Activity from Incidence and Serial Interval

Usage

estimate_activity(.data, incid, .t, serial_interval_mean, serial_interval_sd)

## S3 method for class 'data.frame'
estimate_activity(
  .data,
  incid = "trend",
  .t = "collection_date",
  serial_interval_mean = 6,
  serial_interval_sd = 4.17
)

## S3 method for class 'covidmodel_rt'
estimate_activity(
  .data,
  incid = ".incid",
  .t = ".t",
  serial_interval_mean = attr(.data, "serial_interval")[[1L]],
  serial_interval_sd = attr(.data, "serial_interval")[[2L]]
)

Arguments

.data	Daily incidence data in data frame or covidmodel_rt format
incid	Character. The column containing incidence data
.t	Character. The time column.
serial_interval_mean	Numeric. The average of the serial interval.
serial_interval_sd	Numeric. The standard deviation of the serial interval.

jesse-smith/covidModel documentation built on Feb. 21, 2022, 3:23 p.m.