new_dna: Create the location of a new case

In thibautjombart/quicksim: Quick and simple outbreak simulator

Description

This function creates the DNA sequence for a new case, with or without a known infector. If the infector is missing (NULL, default), the case is imported according to parameters in config.

Usage

new_dna(dna = NULL, generation_time = NULL, ..., config = new_config(...))

Arguments

dna	An optional location of the infector; if provided, it must be a list with the following slots: 'location', 'dna'
generation_time	The number of days separating the dates of infection of the infector, and the infectee. Only needed if the infector is provided.
...	further arguments passed to new_config
config	optionally, a config returned by new_config

Details

We consider that all markers are biallelic, and store only mutations.

Author(s)

Thibaut Jombart [e-mail]

See Also

dist_dna to compute pairwise genetic distances from vectors of mutations.

Examples

## without initial location
x_dna <- new_dna()
x_dna

## drift from this sequence, different nb of generations
new_dna(x_dna, 1L) # 1 generation
new_dna(x_dna, 12L) # 12 generations

## 100 generations, other genetic params
new_dna(x_dna, 100, mutation_rate = 1e-6, genome_length = 2e6)

## illustrate reverse mutations
my_config <- new_config(mutation_rate = 0.1, genome_length = 10)
x <- integer(0)
set.seed(1)
x <- new_dna(x, 5); x
x <- new_dna(x, 5); x
x <- new_dna(x, 5); x
x <- new_dna(x, 5); x
x <- new_dna(x, 5); x

thibautjombart/quicksim documentation built on May 5, 2019, 2:42 a.m.