The following lists all methods and attributes of haploid_lowd, grouped according to purpose and function. Member functions are shown with the prefix ‘’haploid_lowd.*’‘. If you have initialized for example as pop=haploid_lowd(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_lowd.__init__ | Construct a low-dimensional population with certain parameters. |
| haploid_lowd.copy | Copy population into new instance. |
| haploid_lowd.L | Number of loci (read-only) |
| haploid_lowd.number_of_loci | Number of loci (read-only) |
| haploid_lowd.N | Population size (read-only) |
| haploid_lowd.population_size | Population size (read-only) |
| haploid_lowd.generation | Current generation (read-only) |
| haploid_lowd.carrying_capacity | current carrying capacity of the environment |
| haploid_lowd.circular | is the genome circular? |
| haploid_lowd.outcrossing_rate | outcrossing rate (probability of sexual reproduction per generation) |
| haploid_lowd.recombination_model | Model of recombination to use |
| haploid_lowd.status | Print a status list of the population parameters |
| haploid_lowd.set_wildtype | Initialize population of N individuals with the - allele at all loci (wildtype) |
| haploid_lowd.set_allele_frequencies | Initialize the population in linkage equilibrium with specified allele frequencies. |
| haploid_lowd.set_genotypes | Initialize population with fixed counts for specific genotypes. |
| haploid_lowd.set_fitness_additive | Set an additive fitness landscape. |
| haploid_lowd.set_fitness_function | Set the fitness landscape for individual genotypes. |
| haploid_lowd.set_fitness_coefficients | Set the fitness landscape in Fourier space for individual Fourier coefficients. |
| haploid_lowd.circular | is the genome circular? |
| haploid_lowd.outcrossing_rate | outcrossing rate (probability of sexual reproduction per generation) |
| haploid_lowd.recombination_model | Model of recombination to use |
| haploid_lowd.set_recombination_rates | Set the recombination rate(s). |
| haploid_lowd.get_recombination_rates | Get recombination rates. |
| haploid_lowd.set_mutation_rates | Set the mutation rate(s). |
| haploid_lowd.get_mutation_rates | Get one or several mutation rates. |
| haploid_lowd.evolve | Evolve for some generations |
| haploid_lowd.evolve_deterministic | Evolve for some generations deterministically (skips the resampling) |
| haploid_lowd.evolve_norec | Evolve for some generations without recombination |
| haploid_lowd.random_genomes | Get random genomes according sampled from the population. |
| haploid_lowd.get_allele_frequency | Get the frequency of the + allele |
| haploid_lowd.get_allele_frequencies | Get the frequencies of all + alleles |
| haploid_lowd.get_genotype_frequency | Get the frequency of a genotype |
| haploid_lowd.get_genotype_frequencies | Get the frequency of each genotype. |
| haploid_lowd.get_pair_frequency | Get the frequency of genotypes with the + allele at both loci. |
| haploid_lowd.get_chi | Get chi of an allele in the -/+ basis |
| haploid_lowd.get_chi2 | Get \(\chi_{ij}\) |
| haploid_lowd.get_LD | Get linkage disequilibrium |
| haploid_lowd.get_moment | Get moment of two alleles in the -/+ basis |
| haploid_lowd.allele_entropy | get the allele entropy of the population |
| haploid_lowd.genotype_entropy | Get the genotype entropy of the population .. |
| haploid_lowd.get_fitness | Get fitness values of a genotype |
| haploid_lowd.get_fitnesses | Get the fitness of all possible genotypes. |
| haploid_lowd.get_fitness_statistics | haploid_lowd_get_fitness_statistics(haploid_lowd self) -> stat |
| haploid_lowd.get_fitness_histogram | Get the histogram of the fitness of a sample from the population. |
| haploid_lowd.plot_fitness_histogram | Plot the histogram of the fitness of a sample from the population. |
| haploid_lowd.get_divergence_statistics | Get the mean and variance of the divergence of a population sample – same as mean and variance of allele frequencies. |
| haploid_lowd.get_diversity_statistics | Get the mean and variance of the diversity of a population sample |
| haploid_lowd.get_divergence_histogram | Get the histogram of the divergence of a population sample. |
| haploid_lowd.get_diversity_histogram | Get the histogram of the diversity in a sample from the population. |
| haploid_lowd.plot_divergence_histogram | Plot the histogram of the divergence of a population sample. |
| haploid_lowd.plot_diversity_histogram | Plot the histogram of the diversity of a population sample. |