Module dadi
For examples of dadi's usage, see the examples directory in the source distribution.
Documentation of all methods can be found in doc/api/index.html of the source distribution.
Expand source code
"""
For examples of dadi's usage, see the examples directory in the source
distribution.
Documentation of all methods can be found in doc/api/index.html of the source
distribution.
"""
import logging
logging.basicConfig()
from . import Demographics1D, Demographics2D, Inference, Integration
from . import Misc, Numerics, PhiManip, Spectrum_mod, tridiag
# We do it this way so it's easier to reload.
Spectrum = Spectrum_mod.Spectrum
# Protect import of Plotting in case matplotlib not installed.
try:
from . import Plotting
except ImportError:
pass
# When doing arithmetic with Spectrum objects (which are masked arrays), we
# often have masked values which generate annoying arithmetic warnings. Here
# we tell numpy to ignore such warnings. This puts greater onus on the user to
# check results, but for our use case I think it's the better default.
import numpy
numpy.seterr(all='ignore')
Sub-modules
dadi.DFE
-
Fitting Distributions of Fitness Effects to population genomic data, both single-population and joint.
dadi.Demographics1D
-
Single population demographic models.
dadi.Demographics2D
-
Two population demographic models.
dadi.Godambe
-
Parameter uncertainties and likelihood ratio tests using Godambe information.
dadi.Inference
-
Comparison and optimization of model spectra to data.
dadi.Integration
-
Functions for integrating population frequency spectra.
dadi.Misc
-
Miscellaneous utility functions. Including ms simulation.
dadi.NLopt_mod
dadi.Numerics
-
Numerically useful functions, including extrapolation and default grid.
dadi.PhiManip
-
Manipulating population frequency spectra phi. e.g. population splittings and admixture
dadi.Plotting
-
Routines for Plotting comparisons between model and data …
dadi.Spectrum_mod
-
Contains Spectrum object, which represents frequency spectra.
dadi.Triallele
-
Modeling triallelic data.
dadi.TwoLocus
-
Fitting models to data summarized by pairs of loci, incorporating both allele frequencies and linkage disequilibrium