In Hackout2/incidence: Computation and Visualisation of Incidence from Line Lists

# set global chunk options: images will be 7x5 inches
knitr::opts_chunk$set(fig.width=7, fig.height=10, fig.path="figs/")
options(digits = 4)

incidence: Computation and Visualisation of Incidence from Line Lists

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,5000), 3, 
             "x.coord","y.coord", fill.by="gender", 
             zoom=12)

#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")