def set_up_quant_trait_model():
# TODO add neutral variants
N = 1000
demography = np.array([N] * 10 * N, dtype=np.uint32)
rho = 1.
# theta = 100.
# nreps = 500
# mu = theta/(4*N)
r = rho / (4 * N)
GSSmo = fwdpy11.GSSmo([(0, 0, 1), (N, 1, 1)])
a = fwdpy11.Additive(2.0, GSSmo)
p = {
'nregions': [],
'sregions': [fwdpy11.GaussianS(0, 1, 1, 0.25)],
'recregions': [fwdpy11.Region(0, 1, 1)],
'rates': (0.0, 0.025, r),
'gvalue': a,
'prune_selected': False,
'demography': demography
}
params = fwdpy11.ModelParams(**p)
rng = fwdpy11.GSLrng(101 * 45 * 110 * 210)
pop = fwdpy11.DiploidPopulation(N, 1.0)
return params, rng, pop
def runsim(args):
popsizes = np.array([args.popsize] * 20 * args.popsize, dtype=np.int32)
locus_boundaries = [(i, i + 11) for i in range(0, 10 * 11, 11)]
sregions = [fwdpy11.GaussianS(i[0] + 5, i[0] + 6, 1, args.sigma)
for i in locus_boundaries]
recregions = [fwdpy11.PoissonInterval(
*i, args.rho / (4 * args.popsize)) for i in locus_boundaries]
recregions.extend([fwdpy11.BinomialPoint(i[1], 0.5)
for i in locus_boundaries[:-1]])
pop = fwdpy11.DiploidPopulation(args.popsize, locus_boundaries[-1][1])
optima = fwdpy11.GSSmo(
[(0, 0, args.VS), (10 * args.popsize, args.opt, args.VS)])
p = {'nregions': [], # No neutral mutations -- add them later!
'gvalue': fwdpy11.Additive(2.0, optima),
'sregions': sregions,
'recregions': recregions,
'rates': (0.0, args.mu, None),
# Keep mutations at frequency 1 in the pop if they affect fitness.
'prune_selected': False,
'demography': np.array(popsizes, dtype=np.uint32)
}
params = fwdpy11.ModelParams(**p)
rng = fwdpy11.GSLrng(args.seed)
s = Recorder(args.popsize)
fwdpy11.evolvets(rng, pop, params, 100, s,
suppress_table_indexing=True,
track_mutation_counts=True)
return pop
def runsim(args):
popsizes = np.array([args.popsize] * 20 * args.popsize, dtype=np.int32)
pop = fwdpy11.DiploidPopulation(args.popsize, 1.0)
sregions = [fwdpy11.GaussianS(0, 1, 1, args.sigma)]
recregions = [fwdpy11.PoissonInterval(0, 1, args.recrate)]
optima = fwdpy11.GSSmo([(0, 0, args.VS),
(10 * args.popsize, args.opt, args.VS)])
p = {
'nregions': [], # No neutral mutations -- add them later!
'gvalue': fwdpy11.Additive(2.0, optima),
'sregions': sregions,
'recregions': recregions,
'rates': (0.0, args.mu, None),
# Keep mutations at frequency 1 in the pop if they affect fitness.
'prune_selected': False,
'demography': np.array(popsizes, dtype=np.uint32)
}
params = fwdpy11.ModelParams(**p)
rng = fwdpy11.GSLrng(args.seed)
s = Recorder(args.popsize)
fwdpy11.evolvets(rng,
pop,
params,
100,
s,
suppress_table_indexing=True,
track_mutation_counts=True)
return pop
def runsim(args):
"""
Run the simulation and deliver output to files.
"""
pop = fwdpy11.DiploidPopulation(args.popsize, GENOME_LENGTH)
rng = fwdpy11.GSLrng(args.seed)
GSSmo = fwdpy11.GSSmo([(0, 0, args.VS),
(10 * args.popsize, args.opt, args.VS)])
popsizes = [args.popsize
] * (10 * args.popsize + int(args.time * float(args.popsize)))
p = {
'nregions': [], # No neutral mutations -- add them later!
'gvalue': fwdpy11.Additive(2.0, GSSmo),
'sregions': [fwdpy11.GaussianS(0, GENOME_LENGTH, 1, args.sigma)],
'recregions': [fwdpy11.Region(0, GENOME_LENGTH, 1)],
'rates': (0.0, args.mu, args.rho / float(4 * args.popsize)),
# Keep mutations at frequency 1 in the pop if they affect fitness.
'prune_selected': False,
'demography': np.array(popsizes, dtype=np.uint32)
}
params = fwdpy11.ModelParams(**p)
r = Recorder(args.record, args.preserve, args.num_ind)
fwdpy11.evolvets(rng, pop, params, 100, r, suppress_table_indexing=True)
with lzma.open(args.filename, 'wb') as f:
pickle.dump(pop, f)
if args.statfile is not None:
stats = pd.DataFrame(r.data, columns=DATA._fields)
# Write the statistics to an sqlite3 database,
# which can be processed in R via dplyr.
conn = sqlite3.connect(args.statfile)
stats.to_sql('data', conn)
def setUp(self):
self.optima = [(0, 0.0, 1.0), (100, 1.0, 1.0)]
self.g = fwdpy11.GSSmo(self.optima)
def setUp(self):
self.a = fwdpy11.Additive(
2.0, fwdpy11.GSS(0.0, 1.0))
self.b = fwdpy11.Additive(
2.0, fwdpy11.GSSmo([(0, 0.0, 1.0)]))
self.pop = fwdpy11.DiploidPopulation(1000)