OutbreakTools implements basic tools for the analysis of Disease Outbreaks.
It defines S4 class obkData to store case-base outbreak data. It also provides a function, plotggphy, to visualize such data on the phylogenetic tree.
library(OutbreakTools)
data(FluH1N1pdm2009)
attach(FluH1N1pdm2009)
x <- new("obkData", individuals = individuals, dna = FluH1N1pdm2009$dna,
dna.individualID = samples$individualID, dna.date = samples$date,
trees = FluH1N1pdm2009$trees)
plotggphy(x, ladderize = TRUE, branch.unit = "year",
tip.color = "location", tip.size = 3, tip.alpha = 0.75)
As I mentioned in the post, ggtree for microbiome data, ggtree fits the R ecosystem ...
