quetzal Namespace Reference

Simulation of coalescence-based models of molecular evolution. More...

Namespaces
namespace	coalescence
	Simulation of coalescent trees.
namespace	demography
	Simulation, storage and access of spatial demographic quantities.
namespace	expressive
	Mathematical expressions of spatio-temporal quantities.
namespace	format
	Parsers and generators for input/output.
namespace	geography
	Geospatial data formatting and processing.
namespace	mutation
	Update mutational states along a gene genealogy.
namespace	polymorphism
	Generic components for polymorphism analysis.
namespace	sampling
	Sampling schemes for Pseudo-Observed Data generation.
namespace	simulator
	Standard simulators of genetic diversity.
namespace	units
	Compile-time unit quantities for coalescence.
namespace	utils
	Miscellaneous details.

Typedefs
using	haplotype = int

Functions
constexpr std::vector< haplotype >	sample (0, sampling_size)
template<class Graph = quetzal::coalescence::k_ary_tree<boost::no_property, boost::no_property>, class Generator >
auto	get_random_spanning_tree (int n_vertices, int n_edges, Generator &rng)
	Generates a random directed tree.

Variables
int	sampling_size = 10
constexpr auto	L = 100 q_bp
constexpr auto	mu = mutation_rate(10⁻9 q_mutations / q_generation / q_bp)
	assumptions

Detailed Description

Simulation of coalescence-based models of molecular evolution.

• This program is free software; you can redistribute it and/or modify /// it under the terms of the GNU General Public License as published by /// the Free Software Foundation; either version 2 of the License, or /// (at your option) any later version. /// ///

Variable Documentation

assumptions

quetzal::assumptions

Initial value:

=
    {
        panmixia, diploidy, discrete_time, constant_population_size, neutral, non_overlapping_generation_times,
}
 
 
generative_model = {draw, number_of_remaining_lineages, infinite_site_model}
 
summary = {TajimasD}
 
 
auto genealogical_law = gene_genealogy::induce_law_from(assumptions)