tracts.demography.parametrized_demography.ParametrizedDemography#

class ParametrizedDemography(name=None, min_time=1, max_time=inf)#

Bases: BaseParametrizedDemography

A class representing a demographic history for multiple populations of interest, with parametrized migrations from other populations.

name#

The name of the demographic model.

Type:

str

min_time#

The minimum time for the demographic model, in generations. Default is 1 generation ago.

Type:

float

max_time#

The maximum time for the demographic model, in generations. Default is infinity.

Type:

float

logger#

The logger.

Type:

logging.Logger

__init__(name=None, min_time=1, max_time=inf)#

Initializes a ParametrizedDemography object.

Parameters:

  • name (str | None) – The name of the demographic model. Default is None, which will be set to an empty string.

  • min_time (float) – The minimum time for the demographic model, in generations. Default is 1 generation ago.

  • max_time (float) – The maximum time for the demographic model, in generations. Default is infinity.

add_continuous_migration(dest_population, source_population, rate_param, start_param, end_param=None)#

Adds a continuous migration from a source population, parametrized by start_time, end_time, and magnitude.

add_founder_event(dest_population, source_populations, remainder_population, found_time, end_time=None)#

Adds a founder event. A parametrized demography must have exactly one founder event.

Parameters:

  • dest_population (str) – The name of the destination population for the founder event.

  • source_populations (dict[str, str]) – A dictionary where each key is a source population and each value is the name of the parameter defining the migration ratio of each population.

  • remainder_population (str) – The name of the source population for the remaining migrants, such that the total migration ratio adds up to 1.

  • found_time (str) – The name of the parameter defining the time of the founder event.

  • end_time (str) – The name of the parameter defining the end time of the founder event, for continuous founding. If None, the founder event is a pulse founding. Default is None.

Return type:

None

add_pulse_migration(dest_population, source_population, rate_param, time_param)#

Adds a pulse migration from a source population, parametrized by time and rate.

Parameters:

  • dest_population (str) – The name of the destination population for the pulse migration.

  • source_population (str) – The name of the source population for the pulse migration.

  • rate_param (str) – The name of the parameter defining the rate of the pulse migration.

  • time_param (str) – The name of the parameter defining the time of the pulse migration.

execute_migration_events(migration_matrices, params)#

Adds the migration events to the migration matrices.

Parameters:

  • migration_matrices (dict[str, ndarray]) – A dictionary mapping population names to their corresponding migration matrices.

  • params (list[float]) – The list of parameter values.

get_founding_time(population)#

Gets the name of the parameter defining the founding time of a population.

Parameters:

population (str) – The name of the population for which to get the founding time.

Returns:

The name of the parameter defining the founding time of the population.

Return type:

str

get_migration_matrices(params)#

Takes in a list of params equal to the length of model_base_params and returns a \(P \times G\) migration matrix for each population of interest where P is the number of incoming populations and G is the number of generations. If one of the parameters (time or migration) is incorrect, returns an empty matrix.

Parameters:

params (list[float]) – A list of parameter values, where the order of the values corresponds to the order of the parameters in model_base_params.

Returns:

A dictionary mapping population names to their corresponding migration matrices.

Return type:

dict[str, ndarray]

get_random_parameters()#
static load_from_YAML(source)#

Creates an instance of ParametrizedDemography from a YAML file.

Parameters:

source (str | Path) – The path to the YAML file containing the demographic model. See online documentations for details on how to specify demographic models in YAML files.

Returns:

An instance of ParametrizedDemography representing the demographic model specified in the YAML file.

Return type:

ParametrizedDemography