library(BactDating) library(ape) set.seed(0)
A ClonalFrameML output can be read using:
t=loadCFML(prefix='cfml-output')
A Gubbins output can be read using:
t=loadGubbins(prefix='gubbins-output')
Instead, for the purpose of making this vignette self-contained, we will simulate an output from a recombination analysis.
This is just an object of class phylo
, unrooted and with the added field unrec
representing the proportion that is unrecombined for each branch.
dates=1990:2010 truetree=simcoaltree(dates) t=unroot(simobsphy(truetree)) t$unrec=runif(length(t$edge.length)) plot(t) axisPhylo(backward = F) edgelabels(round(100*t$unrec))
We run BactDating as follows:
res=bactdate(t,dates,useRec=T) plot(res,'treeCI')
We can compare with the correct tree:
plot(truetree) axisPhylo(backward = F)
We can see what the MCMC traces look like:
plot(res,'trace')
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