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 = 1e04,
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 gammadistributed generation interval. 
mean.gen 
The mean generation interval. 
shape.sample 
The shape parameter of the gammadistributed 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 withinhost pathogen dynamics (effective pathogen population size = N*gE = actual population size * pathogen generation time), used to simulate coalescence events. Options are:

wh.slope 
Withinhost 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 01012000)
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 [email protected]
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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