Module dadi.Demographics2D
Two population demographic models.
Expand source code
"""
Two population demographic models.
"""
import numpy
from dadi import Numerics, PhiManip, Integration
from dadi.Spectrum_mod import Spectrum
def snm_2d(notused, ns, pts):
"""
ns = (n1,n2)
Standard neutral model, populations never diverge.
"""
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
fs = Spectrum.from_phi(phi, ns, (xx,xx))
return fs
snm_2d.__param_names__ = []
snm = snm_2d
def bottlegrowth_2d(params, ns, pts):
"""
params = (nuB,nuF,T)
ns = (n1,n2)
Instantanous size change followed by exponential growth with no population
split.
nuB: Ratio of population size after instantanous change to ancient
population size
nuF: Ratio of contempoary to ancient population size
T: Time in the past at which instantaneous change happened and growth began
(in units of 2*Na generations)
n1,n2: Sample sizes of resulting Spectrum
pts: Number of grid points to use in integration.
"""
nuB,nuF,T = params
return bottlegrowth_split_mig((nuB,nuF,0,T,0), ns, pts)
bottlegrowth_2d.__param_names__ = ['nuB', 'nuF', 'T']
bottlegrowth = bottlegrowth_2d
def bottlegrowth_split(params, ns, pts):
"""
params = (nuB,nuF,T,Ts)
ns = (n1,n2)
Instantanous size change followed by exponential growth then split.
nuB: Ratio of population size after instantanous change to ancient
population size
nuF: Ratio of contempoary to ancient population size
T: Time in the past at which instantaneous change happened and growth began
(in units of 2*Na generations)
Ts: Time in the past at which the two populations split.
n1,n2: Sample sizes of resulting Spectrum
pts: Number of grid points to use in integration.
"""
nuB,nuF,T,Ts = params
return bottlegrowth_split_mig((nuB,nuF,0,T,Ts), ns, pts)
bottlegrowth_split.__param_names__ = ['nuB', 'nuF', 'T', 'Ts']
def bottlegrowth_split_mig(params, ns, pts):
"""
params = (nuB,nuF,m,T,Ts)
ns = (n1,n2)
Instantanous size change followed by exponential growth then split with
migration.
nuB: Ratio of population size after instantanous change to ancient
population size
nuF: Ratio of contempoary to ancient population size
m: Migration rate between the two populations (2*Na*m).
T: Time in the past at which instantaneous change happened and growth began
(in units of 2*Na generations)
Ts: Time in the past at which the two populations split.
n1,n2: Sample sizes of resulting Spectrum
pts: Number of grid points to use in integration.
"""
nuB,nuF,m,T,Ts = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
if T >= Ts:
nu_func = lambda t: nuB*numpy.exp(numpy.log(nuF/nuB) * t/T)
phi = Integration.one_pop(phi, xx, T-Ts, nu_func)
phi = PhiManip.phi_1D_to_2D(xx, phi)
nu0 = nu_func(T-Ts)
nu_func = lambda t: nu0*numpy.exp(numpy.log(nuF/nu0) * t/Ts)
phi = Integration.two_pops(phi, xx, Ts, nu_func, nu_func, m12=m, m21=m)
else:
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, Ts-T, 1, 1, m12=m, m21=m)
nu_func = lambda t: nuB*numpy.exp(numpy.log(nuF/nuB) * t/T)
phi = Integration.two_pops(phi, xx, T, nu_func, nu_func, m12=m, m21=m)
fs = Spectrum.from_phi(phi, ns, (xx,xx))
return fs
bottlegrowth_split_mig.__param_names__ = ['nuB', 'nuF', 'm', 'T', 'Ts']
def split_mig(params, ns, pts):
"""
params = (nu1,nu2,T,m)
ns = (n1,n2)
Split into two populations of specifed size, with migration.
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
T: Time in the past of split (in units of 2*Na generations)
m: Migration rate between populations (2*Na*m)
n1,n2: Sample sizes of resulting Spectrum
pts: Number of grid points to use in integration.
"""
nu1,nu2,T,m = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T, nu1, nu2, m12=m, m21=m)
fs = Spectrum.from_phi(phi, ns, (xx,xx))
return fs
split_mig.__param_names__ = ['nu1', 'nu2', 'T', 'm']
def split_mig_mscore(params):
"""
ms core command for split_mig.
"""
nu1,nu2,T,m = params
command = "-n 1 %(nu1)f -n 2 %(nu2)f "\
"-ma x %(m12)f %(m21)f x "\
"-ej %(T)f 2 1 -en %(T)f 1 1"
sub_dict = {'nu1':nu1, 'nu2':nu2, 'm12':2*m, 'm21':2*m, 'T': T/2}
return command % sub_dict
split_mig_mscore.__param_names__ = ['nu1', 'nu2', 'T', 'm']
def split_asym_mig(params, ns, pts):
"""
params = (nu1,nu2,T,m12,m21)
ns = (n1,n2)
Split into two populations of specifed size, with asymetric migration .
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
T: Time in the past of split (in units of 2*Na generations)
m12: Migration from pop 2 to pop 1 (2*Na*m12)
m21: Migration from pop 1 to pop 2 (2*Na*m21)
n1,n2: Sample sizes of resulting Spectrum
pts: Number of grid points to use in integration.
"""
nu1,nu2,T,m12,m21 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, T, nu1, nu2, m12=m12, m21=m21)
fs = Spectrum.from_phi(phi, ns, (xx,xx))
return fs
split_asym_mig.__param_names__ = ['nu1', 'nu2', 'T', 'm12', 'm21']
def split_delay_mig(params, ns, pts):
"""
params = (nu1,nu2,Tpre,Tmig,m12,m21)
ns = (n1,n2)
Split into two populations of specifed size, with migration after some time has passed post split.
nu1: Size of population 1 after split.
nu2: Size of population 2 after split.
Tpre: Time in the past after split but before migration (in units of 2*Na generations)
Tmig: Time in the past after migration starts (in units of 2*Na generations)
m12: Migration from pop 2 to pop 1 (2*Na*m12)
m21: Migration from pop 1 to pop 2 (2*Na*m21)
n1,n2: Sample sizes of resulting Spectrum
pts: Number of grid points to use in integration.
"""
nu1,nu2,Tpre,Tmig,m12,m21 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
phi = Integration.two_pops(phi, xx, Tpre, nu1, nu2, m12=0, m21=0)
phi = Integration.two_pops(phi, xx, Tmig, nu1, nu2, m12=m12, m21=m21)
fs = Spectrum.from_phi(phi, ns, (xx,xx))
return fs
split_delay_mig.__param_names__ = ['nu1', 'nu2', 'Tpre', 'Tmig', 'm12', 'm21']
def IM(params, ns, pts):
"""
ns = (n1,n2)
params = (s,nu1,nu2,T,m12,m21)
Isolation-with-migration model with exponential pop growth.
s: Size of pop 1 after split. (Pop 2 has size 1-s.)
nu1: Final size of pop 1.
nu2: Final size of pop 2.
T: Time in the past of split (in units of 2*Na generations)
m12: Migration from pop 2 to pop 1 (2*Na*m12)
m21: Migration from pop 1 to pop 2
n1,n2: Sample sizes of resulting Spectrum
pts: Number of grid points to use in integration.
"""
s,nu1,nu2,T,m12,m21 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = PhiManip.phi_1D_to_2D(xx, phi)
nu1_func = lambda t: s * (nu1/s)**(t/T)
nu2_func = lambda t: (1-s) * (nu2/(1-s))**(t/T)
phi = Integration.two_pops(phi, xx, T, nu1_func, nu2_func,
m12=m12, m21=m21)
fs = Spectrum.from_phi(phi, ns, (xx,xx))
return fs
IM.__param_names__ = ['s', 'nu1', 'nu2', 'T', 'm12', 'm21']
def IM_mscore(params):
"""
ms core command for IM.
"""
s,nu1,nu2,T,m12,m21 = params
alpha1 = numpy.log(nu1/s)/T
alpha2 = numpy.log(nu2/(1-s))/T
command = "-n 1 %(nu1)f -n 2 %(nu2)f "\
"-eg 0 1 %(alpha1)f -eg 0 2 %(alpha2)f "\
"-ma x %(m12)f %(m21)f x "\
"-ej %(T)f 2 1 -en %(T)f 1 1"
sub_dict = {'nu1':nu1, 'nu2':nu2, 'alpha1':2*alpha1, 'alpha2':2*alpha2,
'm12':2*m12, 'm21':2*m21, 'T': T/2}
return command % sub_dict
IM_mscore.__param_names__ = ['s', 'nu1', 'nu2', 'T', 'm12', 'm21']
def IM_pre(params, ns, pts):
"""
params = (nuPre,TPre,s,nu1,nu2,T,m12,m21)
ns = (n1,n2)
Isolation-with-migration model with exponential pop growth and a size change
prior to split.
nuPre: Size after first size change
TPre: Time before split of first size change.
s: Fraction of nuPre that goes to pop1. (Pop 2 has size nuPre*(1-s).)
nu1: Final size of pop 1.
nu2: Final size of pop 2.
T: Time in the past of split (in units of 2*Na generations)
m12: Migration from pop 2 to pop 1 (2*Na*m12)
m21: Migration from pop 1 to pop 2
n1,n2: Sample sizes of resulting Spectrum
pts: Number of grid points to use in integration.
"""
nuPre,TPre,s,nu1,nu2,T,m12,m21 = params
xx = Numerics.default_grid(pts)
phi = PhiManip.phi_1D(xx)
phi = Integration.one_pop(phi, xx, TPre, nu=nuPre)
phi = PhiManip.phi_1D_to_2D(xx, phi)
nu1_0 = nuPre*s
nu2_0 = nuPre*(1-s)
nu1_func = lambda t: nu1_0 * (nu1/nu1_0)**(t/T)
nu2_func = lambda t: nu2_0 * (nu2/nu2_0)**(t/T)
phi = Integration.two_pops(phi, xx, T, nu1_func, nu2_func,
m12=m12, m21=m21)
fs = Spectrum.from_phi(phi, ns, (xx,xx))
return fs
IM_pre.__param_names__ = ['nuPre', 'TPre', 's', 'nu1', 'nu2', 'T', 'm12', 'm21']
def IM_pre_mscore(params):
"""
ms core command for IM_pre.
"""
nuPre,TPre,s,nu1,nu2,T,m12,m21 = params
nu1_0 = nuPre*s
nu2_0 = nuPre*(1-s)
alpha1 = numpy.log(nu1/nu1_0)/T
alpha2 = numpy.log(nu2/nu2_0)/T
command = "-n 1 %(nu1)f -n 2 %(nu2)f "\
"-eg 0 1 %(alpha1)f -eg 0 2 %(alpha2)f "\
"-ma x %(m12)f %(m21)f x "\
"-ej %(T)f 2 1 -en %(T)f 1 %(nuP)f "\
"-en %(TP)f 1 1"
sub_dict = {'nu1':nu1, 'nu2':nu2, 'alpha1':2*alpha1, 'alpha2':2*alpha2,
'm12':2*m12, 'm21':2*m21, 'T': T/2, 'nuP':nuPre, 'TP':(T+TPre)/2}
return command % sub_dict
IM_pre_mscore.__param_names__ = ['nuPre', 'TPre', 's', 'nu1', 'nu2', 'T', 'm12', 'm21']Functions
def IM(params, ns, pts)-
ns = (n1,n2) params = (s,nu1,nu2,T,m12,m21)
Isolation-with-migration model with exponential pop growth.
s: Size of pop 1 after split. (Pop 2 has size 1-s.) nu1: Final size of pop 1. nu2: Final size of pop 2. T: Time in the past of split (in units of 2Na generations) m12: Migration from pop 2 to pop 1 (2Na*m12) m21: Migration from pop 1 to pop 2 n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
Expand source code
def IM(params, ns, pts): """ ns = (n1,n2) params = (s,nu1,nu2,T,m12,m21) Isolation-with-migration model with exponential pop growth. s: Size of pop 1 after split. (Pop 2 has size 1-s.) nu1: Final size of pop 1. nu2: Final size of pop 2. T: Time in the past of split (in units of 2*Na generations) m12: Migration from pop 2 to pop 1 (2*Na*m12) m21: Migration from pop 1 to pop 2 n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ s,nu1,nu2,T,m12,m21 = params xx = Numerics.default_grid(pts) phi = PhiManip.phi_1D(xx) phi = PhiManip.phi_1D_to_2D(xx, phi) nu1_func = lambda t: s * (nu1/s)**(t/T) nu2_func = lambda t: (1-s) * (nu2/(1-s))**(t/T) phi = Integration.two_pops(phi, xx, T, nu1_func, nu2_func, m12=m12, m21=m21) fs = Spectrum.from_phi(phi, ns, (xx,xx)) return fs def IM_mscore(params)-
ms core command for IM.
Expand source code
def IM_mscore(params): """ ms core command for IM. """ s,nu1,nu2,T,m12,m21 = params alpha1 = numpy.log(nu1/s)/T alpha2 = numpy.log(nu2/(1-s))/T command = "-n 1 %(nu1)f -n 2 %(nu2)f "\ "-eg 0 1 %(alpha1)f -eg 0 2 %(alpha2)f "\ "-ma x %(m12)f %(m21)f x "\ "-ej %(T)f 2 1 -en %(T)f 1 1" sub_dict = {'nu1':nu1, 'nu2':nu2, 'alpha1':2*alpha1, 'alpha2':2*alpha2, 'm12':2*m12, 'm21':2*m21, 'T': T/2} return command % sub_dict def IM_pre(params, ns, pts)-
params = (nuPre,TPre,s,nu1,nu2,T,m12,m21) ns = (n1,n2)
Isolation-with-migration model with exponential pop growth and a size change prior to split.
nuPre: Size after first size change TPre: Time before split of first size change. s: Fraction of nuPre that goes to pop1. (Pop 2 has size nuPre(1-s).) nu1: Final size of pop 1. nu2: Final size of pop 2. T: Time in the past of split (in units of 2Na generations) m12: Migration from pop 2 to pop 1 (2Nam12) m21: Migration from pop 1 to pop 2 n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
Expand source code
def IM_pre(params, ns, pts): """ params = (nuPre,TPre,s,nu1,nu2,T,m12,m21) ns = (n1,n2) Isolation-with-migration model with exponential pop growth and a size change prior to split. nuPre: Size after first size change TPre: Time before split of first size change. s: Fraction of nuPre that goes to pop1. (Pop 2 has size nuPre*(1-s).) nu1: Final size of pop 1. nu2: Final size of pop 2. T: Time in the past of split (in units of 2*Na generations) m12: Migration from pop 2 to pop 1 (2*Na*m12) m21: Migration from pop 1 to pop 2 n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ nuPre,TPre,s,nu1,nu2,T,m12,m21 = params xx = Numerics.default_grid(pts) phi = PhiManip.phi_1D(xx) phi = Integration.one_pop(phi, xx, TPre, nu=nuPre) phi = PhiManip.phi_1D_to_2D(xx, phi) nu1_0 = nuPre*s nu2_0 = nuPre*(1-s) nu1_func = lambda t: nu1_0 * (nu1/nu1_0)**(t/T) nu2_func = lambda t: nu2_0 * (nu2/nu2_0)**(t/T) phi = Integration.two_pops(phi, xx, T, nu1_func, nu2_func, m12=m12, m21=m21) fs = Spectrum.from_phi(phi, ns, (xx,xx)) return fs def IM_pre_mscore(params)-
ms core command for IM_pre.
Expand source code
def IM_pre_mscore(params): """ ms core command for IM_pre. """ nuPre,TPre,s,nu1,nu2,T,m12,m21 = params nu1_0 = nuPre*s nu2_0 = nuPre*(1-s) alpha1 = numpy.log(nu1/nu1_0)/T alpha2 = numpy.log(nu2/nu2_0)/T command = "-n 1 %(nu1)f -n 2 %(nu2)f "\ "-eg 0 1 %(alpha1)f -eg 0 2 %(alpha2)f "\ "-ma x %(m12)f %(m21)f x "\ "-ej %(T)f 2 1 -en %(T)f 1 %(nuP)f "\ "-en %(TP)f 1 1" sub_dict = {'nu1':nu1, 'nu2':nu2, 'alpha1':2*alpha1, 'alpha2':2*alpha2, 'm12':2*m12, 'm21':2*m21, 'T': T/2, 'nuP':nuPre, 'TP':(T+TPre)/2} return command % sub_dict def bottlegrowth(params, ns, pts)-
params = (nuB,nuF,T) ns = (n1,n2)
Instantanous size change followed by exponential growth with no population split.
nuB: Ratio of population size after instantanous change to ancient population size nuF: Ratio of contempoary to ancient population size T: Time in the past at which instantaneous change happened and growth began (in units of 2*Na generations) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
Expand source code
def bottlegrowth_2d(params, ns, pts): """ params = (nuB,nuF,T) ns = (n1,n2) Instantanous size change followed by exponential growth with no population split. nuB: Ratio of population size after instantanous change to ancient population size nuF: Ratio of contempoary to ancient population size T: Time in the past at which instantaneous change happened and growth began (in units of 2*Na generations) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ nuB,nuF,T = params return bottlegrowth_split_mig((nuB,nuF,0,T,0), ns, pts) def bottlegrowth_2d(params, ns, pts)-
params = (nuB,nuF,T) ns = (n1,n2)
Instantanous size change followed by exponential growth with no population split.
nuB: Ratio of population size after instantanous change to ancient population size nuF: Ratio of contempoary to ancient population size T: Time in the past at which instantaneous change happened and growth began (in units of 2*Na generations) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
Expand source code
def bottlegrowth_2d(params, ns, pts): """ params = (nuB,nuF,T) ns = (n1,n2) Instantanous size change followed by exponential growth with no population split. nuB: Ratio of population size after instantanous change to ancient population size nuF: Ratio of contempoary to ancient population size T: Time in the past at which instantaneous change happened and growth began (in units of 2*Na generations) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ nuB,nuF,T = params return bottlegrowth_split_mig((nuB,nuF,0,T,0), ns, pts) def bottlegrowth_split(params, ns, pts)-
params = (nuB,nuF,T,Ts) ns = (n1,n2)
Instantanous size change followed by exponential growth then split.
nuB: Ratio of population size after instantanous change to ancient population size nuF: Ratio of contempoary to ancient population size T: Time in the past at which instantaneous change happened and growth began (in units of 2*Na generations) Ts: Time in the past at which the two populations split. n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
Expand source code
def bottlegrowth_split(params, ns, pts): """ params = (nuB,nuF,T,Ts) ns = (n1,n2) Instantanous size change followed by exponential growth then split. nuB: Ratio of population size after instantanous change to ancient population size nuF: Ratio of contempoary to ancient population size T: Time in the past at which instantaneous change happened and growth began (in units of 2*Na generations) Ts: Time in the past at which the two populations split. n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ nuB,nuF,T,Ts = params return bottlegrowth_split_mig((nuB,nuF,0,T,Ts), ns, pts) def bottlegrowth_split_mig(params, ns, pts)-
params = (nuB,nuF,m,T,Ts) ns = (n1,n2)
Instantanous size change followed by exponential growth then split with migration.
nuB: Ratio of population size after instantanous change to ancient population size nuF: Ratio of contempoary to ancient population size m: Migration rate between the two populations (2Nam). T: Time in the past at which instantaneous change happened and growth began (in units of 2*Na generations) Ts: Time in the past at which the two populations split. n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
Expand source code
def bottlegrowth_split_mig(params, ns, pts): """ params = (nuB,nuF,m,T,Ts) ns = (n1,n2) Instantanous size change followed by exponential growth then split with migration. nuB: Ratio of population size after instantanous change to ancient population size nuF: Ratio of contempoary to ancient population size m: Migration rate between the two populations (2*Na*m). T: Time in the past at which instantaneous change happened and growth began (in units of 2*Na generations) Ts: Time in the past at which the two populations split. n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ nuB,nuF,m,T,Ts = params xx = Numerics.default_grid(pts) phi = PhiManip.phi_1D(xx) if T >= Ts: nu_func = lambda t: nuB*numpy.exp(numpy.log(nuF/nuB) * t/T) phi = Integration.one_pop(phi, xx, T-Ts, nu_func) phi = PhiManip.phi_1D_to_2D(xx, phi) nu0 = nu_func(T-Ts) nu_func = lambda t: nu0*numpy.exp(numpy.log(nuF/nu0) * t/Ts) phi = Integration.two_pops(phi, xx, Ts, nu_func, nu_func, m12=m, m21=m) else: phi = PhiManip.phi_1D_to_2D(xx, phi) phi = Integration.two_pops(phi, xx, Ts-T, 1, 1, m12=m, m21=m) nu_func = lambda t: nuB*numpy.exp(numpy.log(nuF/nuB) * t/T) phi = Integration.two_pops(phi, xx, T, nu_func, nu_func, m12=m, m21=m) fs = Spectrum.from_phi(phi, ns, (xx,xx)) return fs def snm(notused, ns, pts)-
ns = (n1,n2)
Standard neutral model, populations never diverge.
Expand source code
def snm_2d(notused, ns, pts): """ ns = (n1,n2) Standard neutral model, populations never diverge. """ xx = Numerics.default_grid(pts) phi = PhiManip.phi_1D(xx) phi = PhiManip.phi_1D_to_2D(xx, phi) fs = Spectrum.from_phi(phi, ns, (xx,xx)) return fs def snm_2d(notused, ns, pts)-
ns = (n1,n2)
Standard neutral model, populations never diverge.
Expand source code
def snm_2d(notused, ns, pts): """ ns = (n1,n2) Standard neutral model, populations never diverge. """ xx = Numerics.default_grid(pts) phi = PhiManip.phi_1D(xx) phi = PhiManip.phi_1D_to_2D(xx, phi) fs = Spectrum.from_phi(phi, ns, (xx,xx)) return fs def split_asym_mig(params, ns, pts)-
params = (nu1,nu2,T,m12,m21) ns = (n1,n2)
Split into two populations of specifed size, with asymetric migration .
nu1: Size of population 1 after split. nu2: Size of population 2 after split. T: Time in the past of split (in units of 2Na generations) m12: Migration from pop 2 to pop 1 (2Nam12) m21: Migration from pop 1 to pop 2 (2Na*m21) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
Expand source code
def split_asym_mig(params, ns, pts): """ params = (nu1,nu2,T,m12,m21) ns = (n1,n2) Split into two populations of specifed size, with asymetric migration . nu1: Size of population 1 after split. nu2: Size of population 2 after split. T: Time in the past of split (in units of 2*Na generations) m12: Migration from pop 2 to pop 1 (2*Na*m12) m21: Migration from pop 1 to pop 2 (2*Na*m21) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ nu1,nu2,T,m12,m21 = params xx = Numerics.default_grid(pts) phi = PhiManip.phi_1D(xx) phi = PhiManip.phi_1D_to_2D(xx, phi) phi = Integration.two_pops(phi, xx, T, nu1, nu2, m12=m12, m21=m21) fs = Spectrum.from_phi(phi, ns, (xx,xx)) return fs def split_delay_mig(params, ns, pts)-
params = (nu1,nu2,Tpre,Tmig,m12,m21) ns = (n1,n2)
Split into two populations of specifed size, with migration after some time has passed post split.
nu1: Size of population 1 after split. nu2: Size of population 2 after split. Tpre: Time in the past after split but before migration (in units of 2Na generations) Tmig: Time in the past after migration starts (in units of 2Na generations) m12: Migration from pop 2 to pop 1 (2Nam12) m21: Migration from pop 1 to pop 2 (2Nam21) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
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def split_delay_mig(params, ns, pts): """ params = (nu1,nu2,Tpre,Tmig,m12,m21) ns = (n1,n2) Split into two populations of specifed size, with migration after some time has passed post split. nu1: Size of population 1 after split. nu2: Size of population 2 after split. Tpre: Time in the past after split but before migration (in units of 2*Na generations) Tmig: Time in the past after migration starts (in units of 2*Na generations) m12: Migration from pop 2 to pop 1 (2*Na*m12) m21: Migration from pop 1 to pop 2 (2*Na*m21) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ nu1,nu2,Tpre,Tmig,m12,m21 = params xx = Numerics.default_grid(pts) phi = PhiManip.phi_1D(xx) phi = PhiManip.phi_1D_to_2D(xx, phi) phi = Integration.two_pops(phi, xx, Tpre, nu1, nu2, m12=0, m21=0) phi = Integration.two_pops(phi, xx, Tmig, nu1, nu2, m12=m12, m21=m21) fs = Spectrum.from_phi(phi, ns, (xx,xx)) return fs def split_mig(params, ns, pts)-
params = (nu1,nu2,T,m) ns = (n1,n2)
Split into two populations of specifed size, with migration.
nu1: Size of population 1 after split. nu2: Size of population 2 after split. T: Time in the past of split (in units of 2Na generations) m: Migration rate between populations (2Na*m) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration.
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def split_mig(params, ns, pts): """ params = (nu1,nu2,T,m) ns = (n1,n2) Split into two populations of specifed size, with migration. nu1: Size of population 1 after split. nu2: Size of population 2 after split. T: Time in the past of split (in units of 2*Na generations) m: Migration rate between populations (2*Na*m) n1,n2: Sample sizes of resulting Spectrum pts: Number of grid points to use in integration. """ nu1,nu2,T,m = params xx = Numerics.default_grid(pts) phi = PhiManip.phi_1D(xx) phi = PhiManip.phi_1D_to_2D(xx, phi) phi = Integration.two_pops(phi, xx, T, nu1, nu2, m12=m, m21=m) fs = Spectrum.from_phi(phi, ns, (xx,xx)) return fs def split_mig_mscore(params)-
ms core command for split_mig.
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def split_mig_mscore(params): """ ms core command for split_mig. """ nu1,nu2,T,m = params command = "-n 1 %(nu1)f -n 2 %(nu2)f "\ "-ma x %(m12)f %(m21)f x "\ "-ej %(T)f 2 1 -en %(T)f 1 1" sub_dict = {'nu1':nu1, 'nu2':nu2, 'm12':2*m, 'm21':2*m, 'T': T/2} return command % sub_dict