knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.align = "center", fig.width = 7, fig.height = 5 )
library(outbreaks) library(incidence2) library(i2extras)
We provide functions to return the peak of the incidence data (grouped or ungrouped), bootstrap from the incidence data, and estimate confidence intervals around a peak.
dat <- fluH7N9_china_2013 x <- incidence(dat, date_index = date_of_onset, groups = gender) bootstrap(x)
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))
Note that the bootstrapping approach used for estimating the peak time makes the following assumptions:
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)
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