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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Tests of protracted speciation model/process.
"""
import math
import unittest
import dendropy
from dendropy.model import protractedspeciation
class ProtractedSpeciationCalcs(unittest.TestCase):
def test_expected_duration_of_speciation(self):
refs = [
((0.01, 0.01, 0.0), 69.31471805599453),
((0.01, 0.01, 0.005), 60.96406423356387),
((0.01, 0.01, 0.01), 52.344553381571906),
((0.01, 0.05, 0.0), 18.232155679395458),
((0.01, 0.05, 0.005), 17.03243269197848),
((0.01, 0.05, 0.01), 15.945243534199998),
((0.01, 0.1, 0.0), 9.531017980432493),
((0.01, 0.1, 0.005), 9.151173562881866),
((0.01, 0.1, 0.01), 8.796646443907925),
((0.01, 0.5, 0.0), 1.980262729617973),
((0.01, 0.5, 0.005), 1.9614061471032902),
((0.01, 0.5, 0.01), 1.9428949825831419),
((0.01, 1.0, 0.0), 0.9950330853168092),
((0.01, 1.0, 0.005), 0.9901794650170307),
((0.01, 1.0, 0.01), 0.9853722709707085),
((0.05, 0.01, 0.0), 35.8351893845611),
((0.05, 0.01, 0.025), 34.610696533124994),
((0.05, 0.01, 0.05), 27.67607317551539),
((0.05, 0.05, 0.0), 13.862943611198906),
((0.05, 0.05, 0.025), 12.192812846712773),
((0.05, 0.05, 0.05), 10.46891067631438),
((0.05, 0.1, 0.0), 8.109302162163289),
((0.05, 0.1, 0.025), 7.261356156801292),
((0.05, 0.1, 0.05), 6.4859100952301745),
((0.05, 0.5, 0.0), 1.9062035960864987),
((0.05, 0.5, 0.025), 1.830234712576371),
((0.05, 0.5, 0.05), 1.7593292887815883),
((0.05, 1.0, 0.0), 0.9758032833886409),
((0.05, 1.0, 0.025), 0.9541399331844385),
((0.05, 1.0, 0.05), 0.9333523826096167),
((0.1, 0.01, 0.0), 23.978952727983707),
((0.1, 0.01, 0.05), 25.39055478519575),
((0.1, 0.01, 0.1), 20.28571191298721),
((0.1, 0.05, 0.0), 10.986122886681098),
((0.1, 0.05, 0.05), 9.802581434685468),
((0.1, 0.05, 0.1), 8.109302162163289),
((0.1, 0.1, 0.0), 6.931471805599453),
((0.1, 0.1, 0.05), 6.096406423356386),
((0.1, 0.1, 0.1), 5.23445533815719),
((0.1, 0.5, 0.0), 1.8232155679395459),
((0.1, 0.5, 0.05), 1.7032432691978485),
((0.1, 0.5, 0.1), 1.5945243534199998),
((0.1, 1.0, 0.0), 0.9531017980432493),
((0.1, 1.0, 0.05), 0.9151173562881855),
((0.1, 1.0, 0.1), 0.8796646443907942),
((0.5, 0.01, 0.0), 7.8636512654486515),
((0.5, 0.01, 0.25), 10.29910408256293),
((0.5, 0.01, 0.5), 9.485738357710689),
((0.5, 0.05, 0.0), 4.795790545596741),
((0.5, 0.05, 0.25), 5.07811095703915),
((0.5, 0.05, 0.5), 4.057142382597441),
((0.5, 0.1, 0.0), 3.58351893845611),
((0.5, 0.1, 0.25), 3.4610696533125007),
((0.5, 0.1, 0.5), 2.7676073175515397),
((0.5, 0.5, 0.0), 1.3862943611198906),
((0.5, 0.5, 0.25), 1.219281284671277),
((0.5, 0.5, 0.5), 1.046891067631438),
((0.5, 1.0, 0.0), 0.8109302162163288),
((0.5, 1.0, 0.25), 0.7261356156801294),
((0.5, 1.0, 0.5), 0.6485910095230177),
((1.0, 0.01, 0.0), 4.61512051684126),
((1.0, 0.01, 0.5), 6.465141234074228),
((1.0, 0.01, 1.0), 6.774422698356164),
((1.0, 0.05, 0.0), 3.044522437723423),
((1.0, 0.05, 0.5), 3.556910942852685),
((1.0, 0.05, 1.0), 2.9389333245105935),
((1.0, 0.1, 0.0), 2.3978952727983707),
((1.0, 0.1, 0.5), 2.539055478519575),
((1.0, 0.1, 1.0), 2.0285711912987203),
((1.0, 0.5, 0.0), 1.0986122886681098),
((1.0, 0.5, 0.5), 0.9802581434685471),
((1.0, 0.5, 1.0), 0.8109302162163288),
((1.0, 1.0, 0.0), 0.6931471805599453),
((1.0, 1.0, 0.5), 0.6096406423356385),
((1.0, 1.0, 1.0), 0.523445533815719),
]
for params, exp_result in refs:
obs_result = protractedspeciation.expected_duration_of_speciation(
speciation_initiation_rate=params[0],
speciation_completion_rate=params[1],
incipient_species_extinction_rate=params[2],
)
self.assertAlmostEqual(obs_result, exp_result)
def test_probability_of_duration_of_speciation(self):
refs = [
((0.01, 0.01, 0.0, 0.8795348619957456), 0.009999226458320016),
((0.01, 0.01, 0.0, 0.14519027181737457), 0.009999978919814594),
((0.01, 0.01, 0.0, 34.684466460885076), 0.008887282087181123),
((0.01, 0.01, 0.0, 63.20061216231189), 0.0068703579303570775),
((0.01, 0.01, 0.005, 0.08536631008065432), 0.012802289144553825),
((0.01, 0.01, 0.005, 0.011137362557058923), 0.01280705070148593),
((0.01, 0.01, 0.005, 76.52294782192368), 0.005405202225298228),
((0.01, 0.01, 0.005, 72.84339288579332), 0.0057297611990511305),
((0.01, 0.01, 0.01, 0.33558726166937963), 0.016125950330407143),
((0.01, 0.01, 0.01, 0.20457203115105108), 0.016147205741964963),
((0.01, 0.01, 0.01, 19.079554492974783), 0.012922829672422163),
((0.01, 0.01, 0.01, 24.68247362845256), 0.011956431293373187),
((0.01, 0.1, 0.0, 0.5935352032024056), 0.09476554969639099),
((0.01, 0.1, 0.0, 0.7003470486083184), 0.09384632919173516),
((0.01, 0.1, 0.0, 81.78775148685204), 1.498228340113515e-05),
((0.01, 0.1, 0.0, 23.412278765465388), 0.009072720079842342),
((0.01, 0.1, 0.005, 0.7792322482865833), 0.09704508143428221),
((0.01, 0.1, 0.005, 0.963289936603788), 0.09533361321027416),
((0.01, 0.1, 0.005, 22.853616783069036), 0.00905378799214888),
((0.01, 0.1, 0.005, 65.4548715141025), 7.09734365226258e-05),
((0.01, 0.1, 0.01, 0.7004511480083776), 0.10172748819395837),
((0.01, 0.1, 0.01, 0.3859718489988695), 0.10501232743022515),
((0.01, 0.1, 0.01, 18.979988804020195), 0.013337248459689992),
((0.01, 0.1, 0.01, 22.757722164422592), 0.0085842630673195),
((0.01, 1.0, 0.0, 0.3130295270193749), 0.7328713233872153),
((0.01, 1.0, 0.0, 0.31154063743324156), 0.7339582420670433),
((0.01, 1.0, 0.0, 88.07424235690094), 2.3767511877766183e-39),
((0.01, 1.0, 0.0, 50.37034301380811), 8.209658743393956e-23),
((0.01, 1.0, 0.005, 0.9003232000282951), 0.4077827698121026),
((0.01, 1.0, 0.005, 0.12159170357864164), 0.8903084715946127),
((0.01, 1.0, 0.005, 81.55525905558959), 1.1585339262652681e-36),
((0.01, 1.0, 0.005, 72.67637856869439), 9.493325334690782e-33),
((0.01, 1.0, 0.01, 0.6890551804405882), 0.5050883931592011),
((0.01, 1.0, 0.01, 0.9501351410838736), 0.3878984254146435),
((0.01, 1.0, 0.01, 20.649073041437447), 7.368492351424008e-10),
((0.01, 1.0, 0.01, 40.24647761617133), 1.540927018047582e-18),
((0.1, 0.01, 0.0, 0.8113389029985384), 0.01075027226017838),
((0.1, 0.01, 0.0, 0.846887182506354), 0.010784061294478495),
((0.1, 0.01, 0.0, 59.62256474016563), 0.0016681779606101286),
((0.1, 0.01, 0.0, 91.65272435084043), 5.057688899425374e-05),
((0.1, 0.01, 0.05, 0.8760733456577112), 0.018023721654607777),
((0.1, 0.01, 0.05, 0.8409206587355896), 0.01799950113041887),
((0.1, 0.01, 0.05, 51.06343770607376), 0.006125364048638298),
((0.1, 0.01, 0.05, 21.687465805666022), 0.023289784397034694),
((0.1, 0.01, 0.1, 0.4792155173312089), 0.03683021581716226),
((0.1, 0.01, 0.1, 0.7263126839962858), 0.036728414105188914),
((0.1, 0.01, 0.1, 55.892356838488816), 0.002968979103551312),
((0.1, 0.01, 0.1, 81.82838924315757), 0.0005828087031488993),
((0.1, 0.1, 0.0, 0.8258322196685367), 0.09932109002004828),
((0.1, 0.1, 0.0, 0.2824909284607273), 0.09992024131094354),
((0.1, 0.1, 0.0, 53.32752907252014), 9.334034463585915e-06),
((0.1, 0.1, 0.0, 67.44160225894768), 5.548245175549618e-07),
((0.1, 0.1, 0.05, 0.5636100846520368), 0.12412769734346397),
((0.1, 0.1, 0.05, 0.9787149640606224), 0.12081870252730309),
((0.1, 0.1, 0.05, 55.67386202995424), 3.438050746152094e-06),
((0.1, 0.1, 0.05, 43.70942242490415), 4.049995603202447e-05),
((0.1, 0.1, 0.1, 0.3999889157738908), 0.1552139893311176),
((0.1, 0.1, 0.1, 0.6345726544794333), 0.15125759800964952),
((0.1, 0.1, 0.1, 97.62739362247933), 1.0215724557144834e-10),
((0.1, 0.1, 0.1, 24.52730240810091), 0.0012785880221897646),
((0.1, 1.0, 0.0, 0.8115065427563289), 0.4573450980393226),
((0.1, 1.0, 0.0, 0.4516132153221019), 0.6542319875705164),
((0.1, 1.0, 0.0, 40.872089582281994), 3.6075312673974335e-20),
((0.1, 1.0, 0.0, 24.255563803233162), 3.1283987494891642e-12),
((0.1, 1.0, 0.05, 0.3457237938404357), 0.7448748845936354),
((0.1, 1.0, 0.05, 0.576803770523732), 0.5879219371779756),
((0.1, 1.0, 0.05, 83.20031921894818), 7.200169398604266e-42),
((0.1, 1.0, 0.05, 91.43820228760569), 5.9464003697653356e-46),
((0.1, 1.0, 0.1, 0.031986829095719926), 1.057136415593703),
((0.1, 1.0, 0.1, 0.5519036055923441), 0.6128084744263474),
((0.1, 1.0, 0.1, 77.67899885507961), 1.554561011597814e-40),
((0.1, 1.0, 0.1, 20.09264881920249), 6.069727719207903e-11),
((1.0, 0.01, 0.0, 0.4446353921382625), 0.015494312486713001),
((1.0, 0.01, 0.0, 0.06884594296267747), 0.01070481974865263),
((1.0, 0.01, 0.0, 45.0622683427891), 1.7484182033029857e-18),
((1.0, 0.01, 0.0, 23.93500942694461), 3.2348325257220874e-09),
((1.0, 0.01, 0.5, 0.07678647673830719), 0.020373520291909725),
((1.0, 0.01, 0.5, 0.3885919433134037), 0.02369988607726227),
((1.0, 0.01, 0.5, 45.11804274928912), 6.08508209809671e-10),
((1.0, 0.01, 0.5, 20.568063200782436), 0.0002670604419545594),
((1.0, 0.01, 1.0, 0.224072444141194), 0.10483702314125201),
((1.0, 0.01, 1.0, 0.5226436349919803), 0.1042922825095739),
((1.0, 0.01, 1.0, 33.02193432605858), 0.0005111539346059228),
((1.0, 0.01, 1.0, 40.74024255784781), 0.00010917936840225393),
((1.0, 0.1, 0.0, 0.8362413301387851), 0.194015289449898),
((1.0, 0.1, 0.0, 0.6926320472771594), 0.17581989725130096),
((1.0, 0.1, 0.0, 92.62429483753988), 6.822494879649729e-44),
((1.0, 0.1, 0.0, 19.625562941290408), 5.095470692858589e-09),
((1.0, 0.1, 0.5, 0.5302925473060789), 0.20894273300712232),
((1.0, 0.1, 0.5, 0.041980900523581485), 0.17708370000687484),
((1.0, 0.1, 0.5, 52.81106500217504), 2.2071314894480564e-17),
((1.0, 0.1, 0.5, 25.460992608253292), 1.7080423876427843e-08),
((1.0, 0.1, 1.0, 0.9296668365468552), 0.31052945846276236),
((1.0, 0.1, 1.0, 0.12145631266764487), 0.36515087675508107),
((1.0, 0.1, 1.0, 50.374060615431524), 1.0868531521448435e-14),
((1.0, 0.1, 1.0, 11.579762731930778), 0.0006666049628160538),
((1.0, 1.0, 0.0, 0.09683251662922314), 0.9906817667603305),
((1.0, 1.0, 0.0, 0.10193348600169332), 0.989681117037441),
((1.0, 1.0, 0.0, 39.66911063337399), 1.3992918064758832e-34),
((1.0, 1.0, 0.0, 13.915328179066181), 3.2761177836735036e-12),
((1.0, 1.0, 0.5, 0.8635504500484475), 0.46002864196564114),
((1.0, 1.0, 0.5, 0.7909190840591199), 0.518603031188729),
((1.0, 1.0, 0.5, 86.89921906556235), 5.226596384633828e-78),
((1.0, 1.0, 0.5, 21.085927006318414), 4.3877525911023785e-19),
((1.0, 1.0, 1.0, 0.6306393480885447), 0.6311458539888442),
((1.0, 1.0, 1.0, 0.041694658805305165), 1.5492998515367982),
((1.0, 1.0, 1.0, 54.275592049617586), 6.057654470628204e-53),
((1.0, 1.0, 1.0, 79.41886144450676), 2.3193926494535927e-77),
]
for params, exp_result in refs:
obs_result = protractedspeciation.probability_of_duration_of_speciation(
tau=params[3],
speciation_initiation_rate=params[0],
speciation_completion_rate=params[1],
incipient_species_extinction_rate=params[2],
)
self.assertAlmostEqual(obs_result, exp_result)
obs_result = protractedspeciation.log_probability_of_duration_of_speciation(
tau=params[3],
speciation_initiation_rate=params[0],
speciation_completion_rate=params[1],
incipient_species_extinction_rate=params[2],
)
self.assertAlmostEqual(obs_result, math.log(exp_result))
def test_maximum_probability_duration_of_speciation(self):
refs = [
((0.01, 0.0001, 0.0), 455.9574441572374),
((0.01, 0.0001, 0.005), 615.4051920172764),
((0.01, 0.0001, 0.01), 0.0),
((0.01, 0.001, 0.0), 209.32591754491338),
((0.01, 0.001, 0.005), 159.4094017279303),
((0.01, 0.001, 0.01), 0.0),
((0.01, 0.01, 0.0), 0.0),
((0.01, 0.01, 0.005), 0.0),
((0.01, 0.01, 0.01), 0.0),
((0.01, 100.0, 0.0), 0.0),
((0.01, 100.0, 0.005), 0.0),
((0.01, 100.0, 0.01), 0.0),
((0.5, 0.005, 0.0), 9.119148883144735),
((0.5, 0.005, 0.25), 12.308103840345511),
((0.5, 0.005, 0.5), 0.0),
((0.5, 0.05, 0.0), 4.186518350898265),
((0.5, 0.05, 0.25), 3.1881880345586024),
((0.5, 0.05, 0.5), 0.0),
((0.5, 0.5, 0.0), 0.0),
((0.5, 0.5, 0.25), 0.0),
((0.5, 0.5, 0.5), 0.0),
((0.5, 5000.0, 0.0), 0.0),
((0.5, 5000.0, 0.25), 0.0),
((0.5, 5000.0, 0.5), 0.0),
((1.0, 0.01, 0.0), 4.559574441572368),
((1.0, 0.01, 0.5), 6.154051920172756),
((1.0, 0.01, 1.0), 0.0),
((1.0, 0.1, 0.0), 2.0932591754491323),
((1.0, 0.1, 0.5), 1.5940940172793012),
((1.0, 0.1, 1.0), 0.0),
((1.0, 1.0, 0.0), 0.0),
((1.0, 1.0, 0.5), 0.0),
((1.0, 1.0, 1.0), 0.0),
((1.0, 10000.0, 0.0), 0.0),
((1.0, 10000.0, 0.5), 0.0),
((1.0, 10000.0, 1.0), 0.0),
((100, 1.0, 0.0), 0.045595744415723685),
((100, 1.0, 50.0), 0.06154051920172753),
((100, 1.0, 100), 0.0),
((100, 10.0, 0.0), 0.020932591754491324),
((100, 10.0, 50.0), 0.01594094017279301),
((100, 10.0, 100), 0.0),
((100, 100.0, 0.0), 0.0),
((100, 100.0, 50.0), 0.0),
((100, 100.0, 100), 0.0),
((100, 1000000, 0.0), 0.0),
((100, 1000000, 50.0), 0.0),
((100, 1000000, 100), 0.0),
((1000, 10.0, 0.0), 0.004559574441572368),
((1000, 10.0, 500.0), 0.006154051920172753),
((1000, 10.0, 1000), 0.0),
((1000, 100.0, 0.0), 0.0020932591754491327),
((1000, 100.0, 500.0), 0.0015940940172793014),
((1000, 100.0, 1000), 0.0),
((1000, 1000.0, 0.0), 0.0),
((1000, 1000.0, 500.0), 0.0),
((1000, 1000.0, 1000), 0.0),
((1000, 10000000, 0.0), 0.0),
((1000, 10000000, 500.0), 0.0),
((1000, 10000000, 1000), 0.0),
]
for params, exp_result in refs:
obs_result = protractedspeciation.maximum_probability_duration_of_speciation(
speciation_initiation_rate=params[0],
speciation_completion_rate=params[1],
incipient_species_extinction_rate=params[2],
)
self.assertAlmostEqual(obs_result, exp_result)
if __name__ == "__main__":
unittest.main()
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