get_observed_seasonal_quantities: Compute season onset, peak week, and peak incidence

In reichlab/2017-2018-cdc-flu-contest: code for cdc flu contest 2017-2018

Description

Compute season onset, peak week, and peak incidence

Usage

get_observed_seasonal_quantities(data, season, first_CDC_season_week = 10,
  last_CDC_season_week = 42, onset_baseline, incidence_var, incidence_bins,
  incidence_bin_names)

Arguments

data	a data frame containing at minimum columns named season, season_week and a column with some sort of incidence measure
season	the season to look at
first_CDC_season_week	the first week of the season to use for calculating onset and peak
last_CDC_season_week	the last week of the season to use for calculating onset and peak
onset_baseline	numeric baseline value for determining season onset
incidence_var	a character string naming the variable in the data argument containing a measure of incidence, or an integer index
incidence_bins	a data frame with variables lower and upper defining lower and upper endpoints to use in binning incidence
incidence_bin_names	a character vector with a name for each incidence bin

Value

a list with four entries: 1) observed_onset_week, either an integer between first_CDC_season_week and last_CDC_season_week (inclusive), or "none" 2) observed_peak_week, an integer between first_CDC_season_week and last_CDC_season_week (inclusive) 3) observed_peak_inc, a numeric with the maximum value of the specified incidence measure between first_CDC_season_week and last_CDC_season_week 4) observed_peak_inc_bin, character name of incidence bin for peak incidence

reichlab/2017-2018-cdc-flu-contest documentation built on May 24, 2019, 6:17 a.m.