R0_Broken_Time_Sim: R0 Broken Time explicit simulator
In OJWatson/sims4: Epidemic generational simualator

Description Usage Arguments Value Examples

This function starts with a root nucelotide sequence and evolves it via an epidemic time continuous model but fixed offspring always equal to R0. The result can then be used elsehere to generate newick trees and necessary enxus files for BEAUti/BEAST etc.

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R0_Broken_Time_Sim(fasta.file = NULL, seq.length = 1000, N = 1000,
  mu = 1e-04, R0 = 2, Tg = 50, scale = 1, kappa = 2,
  model = "HKY85", I = 1, samples = 10)

`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 10, 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, and parent.id gives the id of the next individual that would be considered for infection.