inst/doc/peak_estimation.R

In i2extras: Functions to Work with 'incidence2' Objects

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center",
  fig.width = 7,
  fig.height = 5
)

## -----------------------------------------------------------------------------
library(outbreaks)
library(incidence2)
library(i2extras) 

## ----bootstrap----------------------------------------------------------------
dat <- fluH7N9_china_2013
x <- incidence(dat, date_index = "date_of_onset", groups = "gender")
bootstrap(x)

## ----findpeak-----------------------------------------------------------------
dat <- fluH7N9_china_2013
x <- incidence(dat, date_index = "date_of_onset", groups = "gender")

# peaks across each group
find_peak(x)

# peak without groupings
find_peak(regroup(x))

## ----estimatepeak-------------------------------------------------------------
dat <- fluH7N9_china_2013
x <- incidence(dat, date_index = "date_of_onset", groups = "province")

# regrouping for overall peak (we suspend progress bar for markdown)
estimate_peak(regroup(x), progress = FALSE)

# across provinces
estimate_peak(x, progress = FALSE)