default_params_doc: Default parameter documentation

Description

This function's purpose is to list all parameter documentation to be inherited by the relevant functions.

Usage

default_params_doc(
  module,
  total_runtime,
  migration,
  select_matrix,
  pop_size,
  multiplicative_selection,
  verbose,
  num_threads,
  morgan,
  markers,
  track_junctions
)

Value

Nothing

Arguments

module

Chosen module to simulate, either created with module_ancestry or module_sequence.

total_runtime

Number of generations

migration

settings associated with migration, should be created with migration_settings

select_matrix

Selection matrix indicating the markers which are under selection. If not provided by the user, the simulation proceeds neutrally. If provided, each row in the matrix should contain five entries:

location of the marker under selection (in Morgan)
fitness of wildtype (aa)
fitness of heterozygote (aA)
fitness of homozygote mutant (AA)
Ancestral type that represents the mutant allele A

pop_size

The number of individuals in the population. If the number is larger than the number of individuals in the input population (if provided), additional individuals are sampled randomly from the input population to reach the intended size.

multiplicative_selection

Default: TRUE. If TRUE, fitness is calculated for multiple markers by multiplying fitness values for each marker. If FALSE, fitness is calculated by adding fitness values for each marker.

verbose

Verbose output if TRUE. Default value is FALSE

num_threads

number of threads. Default is 1. Set to -1 to use all available threads

morgan

Length of the chromosome in Morgan (e.g. the number of crossovers during meiosis)

markers

A vector of locations of markers (relative locations in [0, 1]). If a vector is provided, ancestry at these marker positions is tracked for every generation.

track_junctions

Track the average number of junctions over time if TRUE