DecantingPhyloTracker

class DecantingPhyloTracker

Data structure to enable perfect tracking over a fixed-size population with synchronous generations.

Generally less performant than GarbageCollectingPhyloGracker; represents organism records as independent objects (which each require an independent allocations and, on lineage extinction, deletions). Uses a decanting buffer to reduce object creation overhead by only allocating record objects for organisms that produce extant lineages beyond a threshold length.

Does not include organism population loc and trait values in phylogenetic record.

__init__(population_size: int, buffer_size: int = 10, share_common_ancestor: bool = True) → None

Initialize data structure to perfectly track phylogenetic history of a population.

Parameters

population_sizeint

How many locations are available within the tracked fixed-size population?

buffer_sizeint, optional

How many generations should lineages be decanted before creating record objects for organisms with extant lineages?

share_common_ancestorbool, default True

Should a dummy common ancestor be inserted as the first entry in the tracker?

If True, all initial population members will be recorded as children of this dummy ancestor. If False, all initial population members will be recorded as having no parent.

Methods

CompilePhylogeny(progress_wrap=<function DecantingPhyloTracker.<lambda>>) → DataFrame

Generate full phylogenetic record of extant organisms.

Parameters

progress_wrapCallable, default identity function

Wrapper applied around record row iterator; pass tqdm or equivalent to display progress bar for compilation process.

Returns

pandas.DataFrame

Full phylogenetic record of extant organisms alife standard format.

Notes

This operation is non-destructive; further record-keeping may be performed on the tracker object afterwards.

ElapseGeneration(parent_locs: List[int]) → None

Append generational turnover to the phylogenetic record.

Parameters

parent_locsarray_like of int

Parent’s population loc for each population loc.

Position within array corresponds to post-turnover population members’ population positions. Values within array correspond to those members’ parents’ population positions within the pre- turnover population.

__init__(population_size: int, buffer_size: int = 10, share_common_ancestor: bool = True) → None

Initialize data structure to perfectly track phylogenetic history of a population.

Parameters

population_sizeint

How many locations are available within the tracked fixed-size population?

buffer_sizeint, optional

How many generations should lineages be decanted before creating record objects for organisms with extant lineages?

share_common_ancestorbool, default True

Should a dummy common ancestor be inserted as the first entry in the tracker?

If True, all initial population members will be recorded as children of this dummy ancestor. If False, all initial population members will be recorded as having no parent.