default_params_doc: Default parameter documentation
In GenomeAdmixR: Simulate Admixture of Genomes

default_params_doc

R Documentation

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
)

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