# 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)
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)
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")
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