Function documentation¶

fwdpy11.
infinite_sites
(rng: fwdpy11._fwdpy11.GSLrng, pop: fwdpy11._fwdpy11.PopulationBase, mu: float) → int¶  Parameters
rng (
fwdpy11.GSLrng
) – Random number generatorpop (
fwdpy11.Population
) – A populationmu (float) – The mutation rate, per haploid genome per generation
 Returns
Number of mutations added
 Return type

fwdpy11.
simplify
(pop: fwdpy11._fwdpy11.PopulationBase, samples: List[int]) → tuple¶ Simplify a TableCollection stored in a Population.
 Parameters
pop – A
fwdpy11.PopulationBase
samples – A list of samples (node indexes).
 Returns
The simplified tables and array mapping input sample IDs to output IDS
 Return type
Note that the samples argument is agnostic with respect to the time of the nodes in the input tables. Thus, you may do things like simplify to a set of “currentlyalive” nodes plus some or all ancient samples by including some node IDs from
fwdpy11.TableCollection.preserved_nodes
.If the input contains ancient samples, and you wish to include them in the output, then you need to include their IDs in the samples argument.
Note
Due to node ID remapping, the metadata corresponding to nodes becomes a bit more difficult to look up. You need to use the output ID map, the original IDs, and the population’s metadata containers.
Deprecated since version 0.3.0: Prefer
fwdpp.simplify_tables()
Changed in version 0.3.0: Ancient samples are no longer kept by default
Changed in version 0.5.0: No longer requires a
MutationVector
argument.

fwdpy11.
simplify_tables
(tables: fwdpy11._fwdpy11.TableCollection, samples: List[int]) → tuple¶ Simplify a TableCollection.
 Parameters
pop (
fwdpy11.TableCollection
) – A table collection.samples – list of samples
 Returns
A simplified TableCollection and an array containing remapped sample ids.
 Return type
New in version 0.3.0.

fwdpy11.
evolvets
(rng, pop, params, simplification_interval, recorder=None, post_simplification_recorder=None, suppress_table_indexing=False, record_gvalue_matrix=False, stopping_criterion=None, track_mutation_counts=False, remove_extinct_variants=True, preserve_first_generation=False, check_demographic_event_timings=True)¶ Evolve a population with tree sequence recording
 Parameters
rng (
fwdpy11.GSLrng
) – random number generatorpop (
fwdpy11.DiploidPopulation
) – A populationparams (
fwdpy11.ModelParams
) – simulation parameterssimplification_interval (int) – Number of generations between simplifications.
recorder (typing.Callable) – (None) A temporal sampler/data recorder.
post_simplification_recorder (typing.Callable) – (None) A temporal sampler
suppress_table_indexing (bool) – (False) Prevents edge table indexing until end of simulation
record_gvalue_matrix (bool) – (False) Whether to record genetic values into
fwdpy11.PopulationBase.genetic_values
.preserve_first_generation (bool) – (False) Whether to record generation 0 as ancient samples. Must be True for tree sequence “recapitation”. See finishwithmsprime.
check_demographic_event_timings (bool) – (True) If
True
, then issue warnings if demographic events will occur prior to the current generation of the population.
The recording of genetic values into
fwdpy11.PopulationBase.genetic_values
is suppressed by default. First, it is redundant withfwdpy11.DiploidMetadata.g
for the common case of mutational effects on a single trait. Second, we save some memory by not tracking these matrices. However, it is useful to track these data for some cases when simulating multivariate mutational effects (pleiotropy).For a detailed description of post_simplification_recorder, see tstimeseries.
Note
If recorder is None, then
fwdpy11.NoAncientSamples
will be used.If post_simplification_recorder is None, then
fwdpy11.RecordNothing
will be used.Changed in version 0.5.2: Added post_simplification_recorder.
Changed in version 0.7.1: Added preserve_first_generation.
Changed in version 0.8.0: Update to refactored ModelParams. Added
check_demographic_event_timings
.

fwdpy11.
exponential_growth_rate
(N0, Nt, time)¶  Parameters
N0 – Population size at onset of size change
Nt – Population size to reach at end of size change
time – Time (in generations) to get from N0 to Nt
 Returns
A list of integers representing population size over time.
New in version 0.6.0.

fwdpy11.
migration_matrix_single_extant_deme
(ndemes, focal_deme)¶ Sets up a migration matrix for a system of ndemes but where only one deme has a size > 0. This is a convenience function for simulations where demes will appear later on and have migration amongst them.
 Parameters
ndemes – The number of demes that will eventually exist.
focal_deme – The index of the initial extant deme.
 Return type
New in version 0.6.0.