Description Usage Arguments Value Author(s) References Examples
Simulate outbreaks of class 'phybreakdata'
, with the outbreak model of phybreak.
1 2 3 4 | sim.phybreak(obsize = 50, popsize = NA, samplesperhost = 1, R0 = 1.5,
shape.gen = 10, mean.gen = 1, shape.sample = 10, mean.sample = 1,
additionalsampledelay = 0, wh.model = 3, wh.slope = 1, mu = 1e-04,
sequence.length = 10000, output.class = c("phybreakdata", "obkData"))
|
obsize |
The outbreak size (number of cases) to obtain. If |
popsize |
The population size in which to simulate. If it is not defined (default),
an optimal population size will be chosen based on R0 and obsize. Be aware that choosing a |
samplesperhost |
Number of samples to be taken per host, either a vector or a single number. |
R0 |
The basic reproduction ratio used for simulation. The offspring distribution is Poisson. |
shape.gen |
The shape parameter of the gamma-distributed generation interval. |
mean.gen |
The mean generation interval. |
shape.sample |
The shape parameter of the gamma-distributed sampling interval. |
mean.sample |
The mean sampling interval (for the first sample of each host). |
additionalsampledelay |
Sampling intervals since first sampling times of each host. Values in this vector will be used first for all additional samples of host 1, then of host 2, etc. |
wh.model |
The model for within-host pathogen dynamics (effective pathogen population size = N*gE = actual population size * pathogen generation time), used to simulate coalescence events. Options are:
|
wh.slope |
Within-host increase of effective population size, used if |
mu |
Expected number of mutations per nucleotide per unit of time along each lineage. |
sequence.length |
Number of available nucleotides for mutations. |
output.class |
Class of the simulation output. If package OutbreakTools is available, it is possible to choose
class |
The simulation output, either as an object of class 'phybreakdata'
with sequences (class 'phyDat'
) and
sampling times (which would be the observations), and infection times, infectors, and phylogenetic tree
of class phylo
;
or as an object of class 'obkData'
(package OutbreakTools), containing the outbreak data in the following slots:
a data.frame
with individual labels as row names, a vector infector
,
and a vector date
containing the infection times (starting 01-01-2000)
an object of class 'obkSequences'
, with SNP data in dna
and sampling times
in meta$date
an object of class multiphylo
, containing a single tree of class phylo
Don Klinkenberg don@xs4all.nl
Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.
1 | simulation <- sim.phybreak()
|
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