API reference

The Python API has one canonical path per name, reached through each level's package — there are no top-level re-exports. A run always starts from a simulate_* entry point and returns a *Result object that carries the true history behind the dataset.

from zombi2 import species, genomes
from zombi2.params import Global, PerCopy, PerLineage

result = species.simulate_species_tree(birth=1.0, death=0.3, n_extant=20, seed=1)

The reference is generated from the source docstrings, one page per level, in the same order as the user guide.

The entry points

Every run starts here. The genome level has three resolutions — family ⊂ ordered ⊂ nucleotide — with one entry point each, so the resolution is chosen by which function you call.

Level	Entry point	Returns	Guide
Species	simulate_species_tree	SpeciesResult	Species trees
Genomes · family	simulate_genomes_family	FamilyGenomesResult	Genomes I
Genomes · ordered	simulate_genomes_ordered	OrderedGenomesResult	Genomes II
Genomes · nucleotide	simulate_genomes_nucleotide	NucleotideGenomesResult	Genomes III
Sequences	simulate_sequences	SequencesResult	Sequences
Traits · continuous	simulate_continuous	TraitsResult	Traits
Traits · discrete	simulate_discrete	TraitsResult	Traits
Traits · several at once	simulate_traits	one TraitsResult per name	Traits
Two levels at once	joint.simulate	JointResult	Joint runs

Every result writes its outputs with .write(directory); which files that leaves is catalogued in output files.

The supporting pieces

These are shared across levels rather than owned by one.

Page	What it holds
zombi2.params	the rate grammar — scopes (PerCopy, PerLineage, Global, …), the verbs chained onto them (scaled_by, set_by, weighted_by, and the two shortcuts varying_among, changing_at), the drivers they take (Random, TotalDiversity, Time, Clade, a filename) and the mappings the link carries (Table, Curve, Scalar, Between), the notation shared by the Python API, the CLI and a --params file
zombi2.tree	trees — Tree, Node, prune, read_newick, and the tree-shape helpers. Its own module, documented on the species page because that is the level that grows one

The menus inside a level

Two levels offer a fixed set of choices. Each is owned by that level and documented as a section of its page, not as a module of its own.

Section	What it holds
Who receives a transfer	the transfer-recipient rules — Distance, Clades, Between
The substitution-model menu	the substitution models — jc69 · k80 · hky85 · gtr, and the protein models poisson · jtt · dayhoff · wag · lg

Reading a run back

A run written to disk is read back with the zombi2 tools commands rather than through this API — see tools.