API

class scriptgenerator.EventList(start_time, end_time=None)

Holds a start and and end time, and a list of events that happens between those times.

class scriptgenerator.MutationTypes(mutation_rate, selection_coeffs, proportions, dominance_coeffs=None)

Holds information about mutations to put into the simulation.

class scriptgenerator.PopulationConfiguration(initial_size, sample_size=None, growth_rate=0)

Holds information about the populations in the simulation. The analogue of msprime.PopulationConfiguration objects.

Variables:
  • initial_size (int) – The number of haploids in the population at the start of the simulation.
  • sample_size – Think – IS THIS NEEDED???
  • growth_rate (float) – The initial growth rate. (GIVEN AS EXPONENT??)
class scriptgenerator.RecentHistory(final_gen, chrom_length, reference_configs, adm_configs, prop, recombination=0, ref_labels=None, adm_label=None, reference_populations=None, admixed_population=None, mutations=None, outfile='recent-history.trees', model_type='WF', scriptfile='recent-history.slim')

An object holding demographic history that can be converted into a SLiM script.

Variables:
  • final_gen (int) – The number of generations to simulate.
  • chrom_length (int) – The number of bases in the simulated segment.
  • reference_configs (slime.PopulationConfiguration) – Configurations of the ancestral populations.
  • adm_configs (slime.PopulationConfiguration) – Configurations of the admixed population.
  • prop (list, dtype=float) – The initial proportion of admixture from each reference population.
  • recombination (float or recombination map (FORMAT?)) – Recombination rate or recombination map.
  • ref_labels –
  • adm_label –
  • reference_populations –
  • admixed_population –
  • mutations –
  • outfile – The filename to which to write the outputted tree sequence.
  • model_type – To be removed.
  • scriptfile – The filename to which to write the SLiM script.
add_continuous_process(new_range, event, early=True)

Adds an event that occurs over an interval of generations. Breaks up existing events if necessary.

add_mass_migration(prop, time)

Specifies a mass migration event from reference populations into admixed population at a specified time. This is like changing the migration rate, but the migration rate is changed to 0 afterwards. # Later: would be useful if it is changed back to original migration rate?

add_migration_rate(rates, time=(2, 'late'))

Specifies rates of migration from references to admixed population.

add_new_single_time(time)

Creates a new code block for the supplied single time.

add_population_parameters_change(paramChanges)

Takes a list of msprime.PopulationParametersChange objects and ‘translates’ them into SLiM commands. https://msprime.readthedocs.io/en/stable/api.html#demographic-events There are two types of changes: exponential growth rate changes and instantaneous population size changes.

find_event_index(time=None, start=False, initialization=False)

Finds the index of the script at which a new event should be inserted.

find_time_index(time)

Finds the index of the script at which a new generation and time should be inserted.