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About the incidence package

This package provides resources for incidence computation and visualisation based on outbreak line-lists. These resources include:

• get.incidence2: extensions of the OutbreakTools::get.incidence function to allow for doBy statements and conversion to xts/zoo objects
• linelist2xts: takes a linelist in a dataframe and aggregates in flexible fashion using LHSVar ~ RHSVar, with the dates being 'massaged' by a date projection function (e.g. to boil down to monday of the ISO week, start of the month, etc)
• plotIncidence: plot incidence as histograms
• mapIncidence: animate incidence in space and time using maps and time series
• data: Hagelloch 1861 measles outbreak (as obkData object)

Using the incidence package

To install it:

library(devtools)
install_github("Hackout2/incidence")

Examples of the main functions:

## try plotIncidence
library("incidence")
example("plotIncidence")

## try mapIncidence 
head(zombie_outbreak)
mapIncidence(head(zombie_outbreak,20000), 3,
             "x.coord","y.coord", fill.by="gender",
             jitter=0, zoom=15)

#Get the epi curve for the Hagelloch data and visualize using
#the dygraphs package
library("xts")
data("hagelloch.obk")
sts.xts <- inc2xts(get.incidence2(hagelloch.obk, "timeERU", doBy=c("SEX"), add.zero=FALSE))
library("dygraphs")
dg <- dygraph(sts.xts, main = "Hagelloch") %>%
  dyRangeSelector(dateWindow = range(index(sts.xts)))
dg

#Demo of the linelist2xts function
demo("incidence", package="incidence",ask=TRUE)

#Show conversion from linelist to time series animate using 
#the surveillance package.
demo("hagelloch", package="incidence")

Showcase of the incidence package

Sometimes, a collection of pictures motivates more than 1,000 lines of code

Dynamic time series using the dygraphs package: