Broken_Generation_Sim: Fixed Offspring and Generation Time epidemic genetic...
In OJWatson/sims4: Epidemic generational simualator

Description Usage Arguments Details Value Examples

Subset of Generation Sim whereby R0 and Tg never vary

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Broken_Generation_Sim(fasta.file = NULL, seq.length = 1000, N = 1000,
  mu = 1e-04, R0 = 2, Tg = 2, kappa = 2, model = "HKY85", I = 1,
  samples = 10, t.exp = FALSE)

`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
`t.exp`	- boolean determining if timeis treated explicitly, i.e. not via p.mut generation

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.

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.