inst/doc/simulate.R

In TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

## ----echo=F-------------------------------------------------------------------
knitr::opts_chunk$set(fig.width=6, fig.height=4) 

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library(TransPhylo)
set.seed(0)

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neg=100/365
off.r=5
w.shape=10
w.scale=0.1
pi=0.25

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simu <- simulateOutbreak(neg=neg,pi=pi,off.r=off.r,w.shape=w.shape,
                         w.scale=w.scale,dateStartOutbreak=2005,dateT=2008)

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plot(simu)

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ttree<-extractTTree(simu)
plot(ttree)

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plot(ttree,type='detailed',w.shape,w.scale)

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ptree<-extractPTree(simu)
plot(ptree)

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library(ape)
p<-phyloFromPTree(ptree)
plot(p)
axisPhylo(backward = F)

## ----eval=F-------------------------------------------------------------------
#  write.tree(p,'tree.nwk')

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write.tree(p,'')

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dateLastSample(simu)