Configuration#
Lineage and locus configuration classes.
- class LineageConfig(n: int | Dict[str, int] | List[int] | ndarray)[source]#
Bases:
objectClass to hold the configuration for the number of lineages.
- __init__(n: int | Dict[str, int] | List[int] | ndarray)[source]#
Initialize the population configuration.
- Parameters:
n (
Union[int,Dict[str,int],List[int],ndarray]) – Number of lineages. Either a single integer if only one population, or a list of integers or dictionary with population names as keys and number of lineages as values for multiple populations. By default, the populations are named ‘pop_0’, ‘pop_1’, etc.
-
lineages:
ndarray# Number of lineages per deme.
-
n:
int# Total number of lineages.
-
n_pops:
int# Number of populations.
-
pop_names:
List[str]# Names of populations.
- property lineage_dict: Dict[str, int]#
Get a dictionary with the number of lineages per population.
- Returns:
Number of lineages per population.
- class LocusConfig(n: int = 1, n_unlinked: int = 0, recombination_rate: float = 0)[source]#
Bases:
objectClass to hold the configuration of the number of loci and with how many independent loci to start.
- __init__(n: int = 1, n_unlinked: int = 0, recombination_rate: float = 0)[source]#
Initialize the locus configuration.
- Parameters:
n (
int) – Number of loci. Either 1 or 2.n_unlinked (
int) – Number of lineages that are initially unlinked between loci. Defaults to 0 meaning that all lineages are initially linked between loci so that the loci are completely linked.recombination_rate (
float) – Recombination rate between loci.
-
n:
int# Number of loci.
-
n_unlinked:
int# Number of loci to start with.
-
recombination_rate:
float# Recombination rate.