Description Usage Arguments Value Author(s) Examples
These functions are used to compute reproduction numbers and derive
incidence curves from outbreaker's ouptput (functions outbreaker
and
outbreaker.parallel
). They all rely on the entire outbreak having
been sampled.
get.R
derive distributions of
individual effective reproduction numbers.
get.Rt
derives
effective reproduction numbers averaged for each time step.
get.incid
derives incidence curves for each time step.
1 2 3 4 5 6 7 | get.Rt(x, burnin = 20000, plot = TRUE, type = c("boxplot", "lines"),
lines = FALSE, fill.col = "gold", lines.col = transp("grey"), ...)
get.R(x, burnin = 20000, ...)
get.incid(x, burnin = 20000, plot = TRUE, type = c("boxplot", "lines"),
lines = FALSE, fill.col = "gold", lines.col = transp("grey"), ...)
|
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. |
plot |
a logical indicating whether a plot should be displayed. |
type |
a character indicating the type of plot to be used. |
lines |
a logical indicating whether individual lines should be added to the plot. |
fill.col |
the color to be used for the boxplot. |
lines.col |
the color to be used to the lines. |
... |
further arguments to be passed to other functions. |
These functions return a data.frame
containing the plotted
information.
Thibaut Jombart t.jombart@imperial.ac.uk
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## load data
data(fakeOutbreak)
attach(fakeOutbreak)
## individual R
barplot(table(get.R(res)), main="Individual effective reproduction numbers")
## R(t)
get.Rt(res)
## incidence
get.incid(res)
detach(fakeOutbreak)
|
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