coala (version 0.3.0)

feat_selection: Adds positive selection to a model

Description

Adds positive selection to a model

Usage

feat_selection(strength_AA = 0, strength_Aa = 0, strength_aa = 0,
  strength_A = NULL, population = "all", time, start = TRUE,
  start_frequency = 5e-04, Ne = 10000, position = 0.5,
  force_keep = TRUE)

Arguments

strength_AA

The selection strength for the selected homozygote. The parameter is valid for the choosen population and the time further pastwards from either time 0 on if start = TRUE, or from time onwards. The same applies for strength

strength_Aa

The selection strength for the heterozygote.

strength_aa

The selection strength for the recessive homoygote.

strength_A

This sets the strength for the selected allele in an haploid model or a diploid model with additive selection. strength_AA, strength_Aa, strength_aa are ignored when this is argument is given.

population

The population in which the allele is selected. Can either be all for all population, or the number of a population.

time

The time at which the selection starts if start == TRUE (looking forwards in time), or the time at which the selection strength changes if start == FALSE. The new strength applies for to the time period further into the past in t

start

Whether selection should start at this time point. At this time the selected allele is introduced in the population with an initial starting frequency. This must be set to TRUE for exactly one selection feature in the model. The values of

start_frequency

The start frequency at which the selected allele is introduced at time time. If the model has multiple population, this can either be a numeric vector that contains the initial frequency for each population or a single number. In the latter c

Ne

The effective population size that is used for the forward simulations.

position

The position of the selected site, relative to the simulated sequence. Values between 0 and 1 are within the simulated area, while smaller values are to the left of it and larger ones to the right.

force_keep

Whether to restart simulatin in which the selected goes to extinction or not.

Examples

# Positive selection in population 2:
model <- coal_model(c(10, 13), 100) +
  feat_pop_merge(par_range('tau', .1, 2), 2, 1) +
  feat_selection(strength_AA=par_expr(2*s),
                 strength_Aa=par_range('s', 100, 2000),
                 population = 2,
                 time=par_expr(tau))