coala (version 0.7.2)

locus_trio: Locus Trios

Description

This functions adds a group of three loci to the model that are genetically linked to each other. They are still unlinked to all other loci or locus trios in the model. Simulating linked loci that are far apart from each other can be very slow. Please mind that mutation and recombination rates for locus trios are rates per trio and not per locus, i.e. they account for mutations that occur on the tree loci and the sequences in-between them together.

Usage

locus_trio(
  locus_length = c(left = 1000, middle = 1000, right = 1000),
  distance = c(left_middle = 500, middle_right = 500),
  number = 1
)

Arguments

locus_length

An integer vector of length 3, giving the length of each of the three loci (left, middle and right).

distance

A vector of two, giving the distance between left and middle, and middle an right locus, in base pairs.

number

The number of loci to add.

See Also

For adding unlinked loci: locus

Examples

# A model with one locus trio
coal_model(25) +
  locus_trio(locus_length=c(1250, 1017, 980), distance=c(257, 814))

# Ten identical locus trios:
coal_model(25) +
  locus_trio(locus_length=c(1250, 1017, 980), distance=c(257, 814), number = 10)

# Two different ones:
coal_model(25) +
  locus_trio(locus_length=c(1000, 500, 900), distance=c(200, 400)) +
  locus_trio(locus_length=c(700, 500, 800), distance=c(350, 150))