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.
| haploid_highd.__init__ | Construct a high-dimensional population with certain parameters. |
| haploid_highd.copy | Copy population into new instance. |
| haploid_highd.dump | Dump a population to binary file, for later use. |
| load_haploid_highd | Load a population from a compressed pickle file |
| haploid_highd.L | Number of loci (read-only) |
| haploid_highd.number_of_loci | Number of loci (read-only) |
| haploid_highd.N | Population size (read-only) |
| haploid_highd.population_size | Population size (read-only) |
| haploid_highd.number_of_traits | Number of traits (read-only) |
| haploid_highd.generation | Current generation (read-only) |
| haploid_highd.participation_ratio | Participation ratio (read-only) |
| haploid_highd.number_of_clones | Number of non-empty clones (read-only) |
| haploid_highd.carrying_capacity | current carrying capacity of the environment |
| haploid_highd.circular | is the genome circular? |
| haploid_highd.outcrossing_rate | outcrossing rate (probability of sexual reproduction per generation) |
| haploid_highd.crossover_rate | crossover rate (probability of crossover per site per generation) |
| haploid_highd.recombination_model | Model of recombination to use |
| haploid_highd.mutation_rate | mutation rate (per site per generation) |
| haploid_highd.trait_weights | weight of each trait on fitness |
| haploid_highd.status | Print a status list of the population parameters |
| haploid_highd.set_wildtype | Initialize a population of wildtype individuals |
| haploid_highd.set_allele_frequencies | Initialize the population according to the given allele frequencies in linkage equilibrium. |
| haploid_highd.set_genotypes | Initialize population with fixed counts for specific genotypes. |
| haploid_highd.add_genotype | Add new individuals to the population with certain genotypes |
| haploid_highd.trait_weights | weight of each trait on fitness |
| haploid_highd.set_trait_additive | Set the additive part of a trait |
| haploid_highd.add_trait_coefficient | Add a coefficient to the trait landscape. |
| haploid_highd.set_random_trait_epistasis | Set a random epistatic term in the genotype-phenotype map. |
| haploid_highd.clear_trait | Clear a trait landscape. |
| haploid_highd.clear_traits | Clear all trait landscapes |
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 | Shortcut for set_trait_additive when there is only one trait |
| haploid_highd.add_fitness_coefficient | Shortcut for add_trait_coefficient when there is only one trait |
| haploid_highd.set_random_epistasis | Shortcut for set_random_trait_epistasis when there is only one trait |
| haploid_highd.clear_fitness | Shortcut for clear_trait when there is only one trait |
| haploid_highd.evolve | Evolve for some generations. |
| haploid_highd.bottleneck | Make the population undergo a bottleneck |
| haploid_highd.unique_clones | Recompress the clone structure |
| haploid_highd.flip_single_locus | Take a random clone, flip the allele at the selected locus and create a new clone. |
| haploid_highd.calc_stat | Calculate trait and fitness statistics for the population |
| haploid_highd.random_clone | Get a random clone |
| haploid_highd.random_clones | Get random clones |
| haploid_highd.random_genomes | Get a sample of random genomes from the population |
| haploid_highd.get_clone_size | Get the size of a clone |
| haploid_highd.get_clone_sizes | Get the size of all clones. |
| haploid_highd.get_genotype | |
| haploid_highd.get_genotypes | Get all genotypes of the population. |
| haploid_highd.get_allele_frequency | Get the frequency of the + allele at the selected locus |
| haploid_highd.get_allele_frequencies | Get all allele frequencies |
| haploid_highd.get_pair_frequency | Get the joint frequency of two + alleles |
| haploid_highd.get_chi | Get \(\chi_i\) of an allele |
| haploid_highd.get_LD | Get linkage disequilibrium |
| haploid_highd.get_chi2 | Get \(\chi_{ij}\) |
| haploid_highd.get_moment | Get moment of two alleles in the -/+ basis |
| haploid_highd.calc_stat | Calculate trait and fitness statistics for the population |
| haploid_highd.get_trait_additive | Get an array with the additive coefficients of all loci of a trait. |
| haploid_highd.get_trait_epistasis | Get the epistatic terms of the genotype/phenotype map of the chosen trait. |
| haploid_highd.get_trait_statistics | Get the mean and variance of a trait in the population. |
| haploid_highd.get_trait_covariance | Get the covariance of two traits in the population. |
| haploid_highd.get_fitness | Get the fitness of an individual |
| haploid_highd.get_fitnesses | Get the fitness of all clones. |
| haploid_highd.get_fitness_statistics | Get the mean and variance of the fitness in the population. |
| haploid_highd.get_fitness_histogram | Calculate the fitness histogram of a population sample. |
| haploid_highd.plot_fitness_histogram | Plot a distribution of fitness of a population sample. |
| haploid_highd.get_divergence_statistics | Get the mean and variance of the divergence in the population. |
| haploid_highd.get_diversity_statistics | Get the mean and variance of the diversity in the population. |
| haploid_highd.get_divergence_histogram | Get the divergence histogram restricted to those chunks of the genome. |
| haploid_highd.get_diversity_histogram | Get the diversity histogram restricted to those chunks of the genome. |
| haploid_highd.plot_divergence_histogram | Plot the divergence histogram of a population sample. |
| haploid_highd.plot_diversity_histogram | Plot the diversity histogram of a population sample. |
| haploid_highd.track_locus_genealogy | Track the genealogy of some loci. |
| haploid_highd.genealogy | Genealogy of the tracked loci. |