Description Usage Arguments Value Examples
Simulate an outbreak
1 2 3 | simulateOutbreak(off.r = 1, off.p = 0.5, neg = 0.25, nSampled = NA,
pi = 0.5, w.shape = 2, w.scale = 1, ws.shape = w.shape,
ws.scale = w.scale, dateStartOutbreak = 2000, dateT = Inf)
|
off.r |
First parameter of the negative binomial distribution for offspring number |
off.p |
Second parameter of the negative binomial distribution for offspring number |
neg |
the within-host effective population size (Ne) timesgeneration duration (g) |
nSampled |
number of sampled infected individuals, or NA for any |
pi |
probability of sampling an infected individual |
w.shape |
Shape parameter of the Gamma probability density function representing the generation time |
w.scale |
Scale parameter of the Gamma probability density function representing the generation time |
ws.shape |
Shape parameter of the Gamma probability density function representing the sampling time |
ws.scale |
Scale parameter of the Gamma probability density function representing the sampling time |
dateStartOutbreak |
Date when index case becomes infected |
dateT |
Date when process stops (this can be Inf for fully simulated outbreaks) |
Combined phylogenetic and transmission tree
1 |
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