haploid_highd_categories.rst

FFPopSim

haploid_highd Overview ===================== The following lists all methods and attributes of haploid_highd, grouped according to purpose and function. Member functions are shown with the prefix haploid_highd.*. If you have initialized for example as pop=haploid_highd(L), the prefix in your program needs to be pop.*.

Note

Clicking on the name of the function will take you to a more detailed explanation listing all arguments.

Initialization, copy, and storage

haploid_highd.__init__ haploid_highd.copy haploid_highd.dump

load_haploid_highd

Attributes

haploid_highd.L haploid_highd.number_of_loci haploid_highd.N haploid_highd.population_size haploid_highd.number_of_traits haploid_highd.generation haploid_highd.participation_ratio haploid_highd.number_of_clones haploid_highd.carrying_capacity haploid_highd.circular haploid_highd.outcrossing_rate haploid_highd.crossover_rate haploid_highd.recombination_model haploid_highd.mutation_rate haploid_highd.trait_weights

Status

haploid_highd.status

Initialize the population

haploid_highd.set_wildtype haploid_highd.set_allele_frequencies haploid_highd.set_genotypes haploid_highd.add_genotype

Set phenotypes and fitness function

haploid_highd.trait_weights haploid_highd.set_trait_additive haploid_highd.add_trait_coefficient haploid_highd.set_random_trait_epistasis haploid_highd.clear_trait haploid_highd.clear_traits

The following methods are shortcuts if you have only one trait and will not work for populations with more than one trait:

haploid_highd.set_fitness_additive haploid_highd.add_fitness_coefficient haploid_highd.set_random_epistasis haploid_highd.clear_fitness

Evolution

haploid_highd.evolve haploid_highd.bottleneck haploid_highd.unique_clones haploid_highd.flip_single_locus haploid_highd.calc_stat

Random Sampling

haploid_highd.random_clone haploid_highd.random_clones haploid_highd.random_genomes

Clone structure and genotypes

haploid_highd.get_clone_size haploid_highd.get_clone_sizes haploid_highd.get_genotype haploid_highd.get_genotypes

Get allele frequencies and linkage disequilibria

haploid_highd.get_allele_frequency haploid_highd.get_allele_frequencies haploid_highd.get_pair_frequency haploid_highd.get_chi haploid_highd.get_LD haploid_highd.get_chi2 haploid_highd.get_moment

Analyze fitness and trait distributions

haploid_highd.calc_stat haploid_highd.get_trait_additive haploid_highd.get_trait_epistasis haploid_highd.get_trait_statistics haploid_highd.get_trait_covariance haploid_highd.get_fitness haploid_highd.get_fitnesses haploid_highd.get_fitness_statistics haploid_highd.get_fitness_histogram haploid_highd.plot_fitness_histogram

Divergence and Diversity

haploid_highd.get_divergence_statistics haploid_highd.get_diversity_statistics haploid_highd.get_divergence_histogram haploid_highd.get_diversity_histogram haploid_highd.plot_divergence_histogram haploid_highd.plot_diversity_histogram

Genealogies and Trees

haploid_highd.track_locus_genealogy haploid_highd.genealogy