Outbreak simulation.
Description
Simulate outbreaks of class 'obkData'
(package OutbreakTools), with the outbreak model of phybreak.
Usage
1 2 3 4  sim.phybreak(obsize = 50, popsize = NA, R0 = 1.5, shape.gen = 10,
mean.gen = 1, shape.sample = 10, mean.sample = 1, wh.model = 3,
wh.slope = 1, mu = 1e04, sequence.length = 10000,
output.class = c("list", "obkData"))

Arguments
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 
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. 
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 
Value
The simulation output, either in a list with sequences (class 'phyDat'
) and sampling times (which would be
the observations), and infection times and infectors; or as an object of class 'obkData'
(package OutbreakTools),
containing the outbreak data in the following slots:
 individuals
a
data.frame
with individual labels as row names, a vectorinfector
, and a vectordate
containing the infection times (starting 01012000) dna
an object of class
'obkSequences'
, with SNP data indna
and sampling times inmeta$date
 trees
an object of class
multiphylo
, containing a single tree of classphylo
Author(s)
Don Klinkenberg don@xs4all.nl
References
Klinkenberg et al, on biorXiv.
Examples
1  simulation < sim.phybreak()

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