Description Usage Arguments Value Author(s) Examples
The function get.mu
is used to obtain a distribution of the mutation
rate from outbreaker's ouptput (functions outbreaker
and
outbreaker.parallel
). The mutation rates used in outbreaker's model
are expressed per generation of infection, which can be problematic to
interprete biologically. get.mu
derives classical estimates of the
mutation rate per unit of time, with one value being estimated for each
chain of the MCMC. By default, the mutation rate is expressed in number of
nucleotide changes per unit time and per genome. If genome.size
is
provided, the mutation rate is expressed in number of nucleotide changes per
unit time and per site.
1 |
x |
the output of |
burnin |
an integer indicating the number of steps of the MCMC to be discarded as burnin period. Defaults to 20,000. |
genome.size |
the size of the genome; if not provided, mutation rate will be expressed in number of mutations per unit of time and per genome. |
A vector of mutation rates derived from the MCMC.
Thibaut Jombart t.jombart@imperial.ac.uk
1 2 3 4 5 6 7 8 9 10 11 12 | ## load data
data(fakeOutbreak)
attach(fakeOutbreak)
mu <- get.mu(res, genome.size=ncol(dat$dna))
hist(mu, col="grey",
main="Inferred distribution of mu",
xlab="mutations/site/day")
abline(v=1e-4,lty=2, lwd=4, col="royalblue")
mtext(side=3, "Dashed line = actual value")
detach(fakeOutbreak)
|
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