def test_calc_relat(self):
relat_sim = HamadryasSim()
relat_pop = HamaPopulation()
group = HamadryasGroup(1)
relat_pop.groupsdict[1] = group
self.setup(relat_sim, relat_pop, group)
output = relatedness.main(relat_pop, relat_sim.parent_dict)
self.assertTrue(output)
def test_half_sib(self):
relat_sim = HamadryasSim()
relat_pop = HamaPopulation()
group = HamadryasGroup(1)
relat_pop.groupsdict[1] = group
self.setup(relat_sim, relat_pop, group)
R = relatedness.calc_relatedness(
[relat_pop.dict[4], relat_pop.dict[5]], relat_sim.parent_dict)
self.assertEqual(R, 0.25)
def test_full_grandniece(self):
relat_sim = HamadryasSim()
relat_pop = HamaPopulation()
group = HamadryasGroup(1)
relat_pop.groupsdict[1] = group
self.setup(relat_sim, relat_pop, group)
R = relatedness.calc_relatedness(
[relat_pop.dict[9], relat_pop.dict[15]], relat_sim.parent_dict)
self.assertEqual(R, 0.125)
def setup(self, OMU1clan, OMU1band, OMU2clan, OMU2band):
recog_sim = HamadryasSim()
recog_pop = HamaPopulation()
if OMU1band == OMU2band:
group1 = HamadryasGroup(OMU1band)
recog_pop.groupsdict[OMU1band] = group1
group2 = group1
else:
group1 = HamadryasGroup(OMU1band)
recog_pop.groupsdict[OMU1band] = group1
group2 = HamadryasGroup(OMU2band)
recog_pop.groupsdict[OMU2band] = group2
HamadryasSeed.addagenttoseed(OMU1band, group1, recog_pop, 'm', None,
None, 10.0, recog_sim)
recog_pop.dict[1].clanID = OMU1clan
group1.leadermales.add(recog_pop.dict[1].index)
HamadryasSeed.addagenttoseed(OMU1band, group1, recog_pop, 'f', 7, 8,
10.0, recog_sim)
HamadryasDispersal.add_female_to_omu(recog_pop.dict[1],
recog_pop.dict[2], recog_pop,
recog_sim)
HamadryasSeed.addagenttoseed(OMU2band, group2, recog_pop, 'm', None,
None, 10.0, recog_sim)
recog_pop.dict[3].clanID = OMU2clan
group2.leadermales.add(recog_pop.dict[1].index)
HamadryasSeed.addagenttoseed(OMU2band, group2, recog_pop, 'f', None,
None, 10.0, recog_sim)
HamadryasDispersal.add_female_to_omu(recog_pop.dict[3],
recog_pop.dict[4], recog_pop,
recog_sim)
HamadryasSeed.addagenttoseed(1, recog_pop.groupsdict[1], recog_pop,
'f', 7, 8, 10.0, recog_sim)
recog_pop.dict[5].clanID = 1
return recog_pop
def setup_rhp(self):
hama_rhp_pop = HamaPopulation()
hama_rhp_group = HamadryasGroup(1)
hama_rhp_pop.groupsdict[1] = hama_rhp_group
hamadryas_sim = HamadryasSim()
HamadryasSeed.addagenttoseed(1, hama_rhp_group, hama_rhp_pop, 'm',
None, None, 10, hamadryas_sim)
HamadryasSeed.addagenttoseed(1, hama_rhp_group, hama_rhp_pop, 'm',
None, None, 10, hamadryas_sim)
HamadryasSeed.addagenttoseed(1, hama_rhp_group, hama_rhp_pop, 'm',
None, None, 13.5, hamadryas_sim)
HamadryasSeed.addagenttoseed(1, hama_rhp_group, hama_rhp_pop, 'm',
None, None, 13.5, hamadryas_sim)
hama_rhp_pop.dict[1].rhp = '1'
hama_rhp_pop.dict[2].rhp = '2'
hama_rhp_pop.dict[3].rhp = '3'
hama_rhp_pop.dict[4].rhp = '4'
return hama_rhp_pop
def makeseed(groupindex, population, sim):
group = HamadryasGroup(groupindex)
# make adult males
for i in range(0, 13):
HamadryasSeed.addagenttoseed(
groupindex, group, population, 'm', None, None,
(float(random.randrange(12.0, 40.0)) / 2.0), sim)
# make some leaders, fols, and sols, and give clans and OMUs
for j in range(0, len(group.agents)):
male = population.dict[group.agents[j]]
male.dispersed = True
if j < 3:
male.clanID = 1 + groupindex
if j == 0 or j == 2:
male.maleState = MaleState.lea
male.OMUID = male.index
group.leadermales.add(male.index)
else:
male.maleState = MaleState.fol
male.OMUID = group.agents[j - 1]
population.dict[group.agents[j - 1]].malefols.append(
male.index)
elif j < 8:
male.clanID = 2 + groupindex
if j == 3 or j == 5 or j == 6:
male.maleState = MaleState.lea
male.OMUID = male.index
group.leadermales.add(male.index)
elif j == 4:
male.maleState = MaleState.fol
male.OMUID = group.agents[j - 1]
population.dict[group.agents[j - 1]].malefols.append(
male.index)
else:
male.maleState = MaleState.sol
male.OMUID = None
else:
male.clanID = 3 + groupindex
if j < 11:
male.maleState = MaleState.lea
male.OMUID = male.index
group.leadermales.add(male.index)
elif j == 11:
male.maleState = MaleState.fol
male.OMUID = group.agents[j - 1]
population.dict[group.agents[j - 1]].malefols.append(
male.index)
else:
male.maleState = MaleState.sol
male.OMUID = None
for k in range(0, 23):
HamadryasSeed.addagenttoseed(
groupindex, group, population, 'f', None, None,
(float(random.randrange(10.0, 40.0)) / 2.0), sim)
for l in range(0, 15):
HamadryasSeed.addagenttoseed(
groupindex, group, population, 'f', None, None,
(float(random.randrange(0.0, 10.0)) / 2.0), sim)
for m in range(0, 14):
HamadryasSeed.addagenttoseed(
groupindex, group, population, 'm', None, None,
(float(random.randrange(0.0, 11.0)) / 2.0), sim)
assert len(group.leadermales) == 8
population.groupsdict[groupindex] = group
return population