Description Usage Arguments Value Examples
This function starts with a root nucelotide sequence and evolves it via an epidemic generational model. The result can then be used elsehere to generate newick trees and necessary enxus files for BEAUti/BEAST etc
1 2 |
fasta.file |
path to a fasta sequence to be used as the root, otherwise random sequence used |
seq.length |
length of root sequence if not specified by fasta.file |
N |
- total popualation size, such that N-I = S |
mu |
- mutation root in base changes per generation time |
R0 |
- basic reproduction number |
Tg |
- mean generation time |
kappa |
- the rate of transitions and transversions |
model |
- substitution model - avaialble so far JC69, HKY85 |
I |
- Initial infected population |
samples |
- 1/samples is equal to the random sample size of tips stored |
Returns a list of 9, with the first 7 lists giving the full infection network. As such res$ID[n] corresponds to res$Time/Parent/IsFather/Offspring/Branch.Length/Sequence/[n]. res$Seq and res$Seq.ID relate to eachother and the value within res$Sequence relates to res$Seq.ID and thus can be used to map a sequence to each individual
1 2 | ## simulate data
TODO(OJ)
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