def create_population(self, ind_type, logging=True):
"""
Create a population according to specified age and household size
distributions.
"""
self.P = Pop_HH(ind_type, logging)
self.P.gen_hh_age_structured_pop(self.params['pop_size'], self.hh_comp,
self.age_dist,
self.params['age_cutoffs'], self.rng)
self.P.allocate_couples()
self.P.print_population_summary()
def create_population(self, ind_type, logging=True):
"""
Create a population according to specified age and household size
distributions.
"""
self.P = Pop_HH(ind_type, logging)
self.P.gen_hh_age_structured_pop(self.params['pop_size'], self.hh_comp,
self.age_dist, self.params['age_cutoffs'], self.rng)
self.P.allocate_couples()
self.P.print_population_summary()
class Simulation(object):
def __init__(self, params, ind_type=Individual, create_pop=True):
# convert ConfigObj to dictionary to store params
self.params = dict(params)
self.params_adj = {}
self.rng = Random(self.params['seed'])
self.load_demographic_data()
if create_pop:
self.create_population(ind_type, params['logging'])
# for storing general data
self.max_hh = 50 # maximum possible hh size
self.pop_size = []
self.age_dist = []
self.hh_size_dist = []
self.hh_size_dist_counts = []
self.hh_size_avg = []
self.hh_count = []
self.fam_types = []
self.start_time = None
self.end_time = None
def create_population(self, ind_type, logging=True):
"""
Create a population according to specified age and household size
distributions.
"""
self.P = Pop_HH(ind_type, logging)
self.P.gen_hh_age_structured_pop(self.params['pop_size'], self.hh_comp,
self.age_dist,
self.params['age_cutoffs'], self.rng)
self.P.allocate_couples()
self.P.print_population_summary()
def parse_age_rates(self, filename, factor, final):
"""
Parse an age-year-rate table to produce a dictionary, keyed by age,
with each entry being a list of annual rates (by year).
Setting final to 'True' appends an age 100 rate of >1 (e.g., to
ensure everyone dies!
"""
dat = load_age_rates(filename)
rates = {}
for line in dat:
rates[line[0]] = [x * factor for x in line[1:]]
if final:
rates[101] = [100 for x in dat[0][1:]] # everybody dies...
return rates
def load_demographic_data(self):
"""
Load data on age-specific demographic processes (mortality/fertility)
and adjust event probabilities according to time-step.
"""
# load household size distribution and age distribution
self.hh_comp = load_probs(
os.path.join(self.params['resource_prefix'],
self.params['hh_composition']), False)
self.params['age_cutoffs'] = [int(x)
for x in self.hh_comp[0][1:][0]] # yuk!
self.age_dist = load_probs(
os.path.join(self.params['resource_prefix'],
self.params['age_distribution']))
annual_factor = self.params['t_dur'] / 365.0
# load and scale MORTALITY rates
self.death_rates = {}
self.death_rates[0] = self.parse_age_rates(
os.path.join(self.params['resource_prefix'],
self.params['death_rates_m']), annual_factor, True)
self.death_rates[1] = self.parse_age_rates(
os.path.join(self.params['resource_prefix'],
self.params['death_rates_f']), annual_factor, True)
### load FERTILITY age probs (don't require scaling) for closed pops
self.fertility_age_probs = load_prob_tables(
os.path.join(self.params['resource_prefix'],
self.params['fertility_age_probs']))
self.fertility_parity_probs = load_probs_new(
os.path.join(self.params['resource_prefix'],
self.params['fertility_parity_probs']))
### load and scale leav/couple/divorce and growth rates
if self.params['dyn_rates']:
# rates will be a list of annual values
self.params['leaving_probs'] = load_prob_list(
os.path.join(self.params['resource_prefix'],
self.params['leaving_prob_file']))
self.params['couple_probs'] = load_prob_list(
os.path.join(self.params['resource_prefix'],
self.params['couple_prob_file']))
self.params['divorce_probs'] = load_prob_list(
os.path.join(self.params['resource_prefix'],
self.params['divorce_prob_file']))
self.params['growth_rates'] = load_prob_list(
os.path.join(self.params['resource_prefix'],
self.params['growth_rate_file']))
self.params['imm_rates'] = load_prob_list(
os.path.join(self.params['resource_prefix'],
self.params['imm_rate_file']))
self.params_adj['leaving_probs'] = [
adjust_prob(x, self.params['t_dur'])
for x in self.params['leaving_probs']
]
self.params_adj['couple_probs'] = [
adjust_prob(x, self.params['t_dur'])
for x in self.params['couple_probs']
]
self.params_adj['divorce_probs'] = [
adjust_prob(x, self.params['t_dur'])
for x in self.params['divorce_probs']
]
self.params_adj['growth_rates'] = [
adjust_prob(x, self.params['t_dur'])
for x in self.params['growth_rates']
]
self.params_adj['imm_rates'] = [
adjust_prob(x, self.params['t_dur'])
for x in self.params['imm_rates']
]
self.dyn_years = min(
len(self.death_rates[0][0]) - 1,
len(self.fertility_age_probs) - 1,
len(self.params_adj['leaving_probs']) - 1,
len(self.params_adj['couple_probs']) - 1,
len(self.params_adj['divorce_probs']) - 1,
len(self.params_adj['growth_rates']) - 1)
else:
# adjust demographic event probabilities according to time step
self.params_adj['couple_probs'] = [
adjust_prob(self.params['couple_prob'], self.params['t_dur'])
]
self.params_adj['leaving_probs'] = [
adjust_prob(self.params['leaving_prob'], self.params['t_dur'])
]
self.params_adj['divorce_probs'] = [
adjust_prob(self.params['divorce_prob'], self.params['t_dur'])
]
self.params_adj['growth_rates'] = [
adjust_prob(self.params['growth_rate'], self.params['t_dur'])
]
self.params_adj['imm_rates'] = [
adjust_prob(self.params['imm_rate'], self.params['t_dur'])
]
def update_individual_demo(self, t, ind, index=0):
"""
Update individual ind; check for death, couple formation, leaving home
or divorce, as possible and appropriate.
"""
death = None
birth = None
couple_prob = self.params_adj['couple_probs'][index]
# if ind.divorced and ind.deps: couple_prob *= 0.5
# DEATH / BIRTH:
if self.rng.random() > exp(-self.death_rates[ind.sex][ind.age][index]):
death = ind
mother = ind
while mother is ind: # make sure dead individual isn't selected as mother!
mother = self.choose_mother(index)
birth = self.update_death_birth(t, ind, mother)
# COUPLE FORMATION:
elif self.params['couple_age'] < ind.age < 60 \
and not ind.partner \
and self.rng.random() < couple_prob:
partner = self.choose_partner(ind)
if partner:
self.P.form_couple(t, ind, partner)
# LEAVING HOME:
elif ind.age > self.params['leaving_age'] \
and ind.with_parents \
and not ind.partner \
and self.rng.random() < self.params_adj['leaving_probs'][index]:
self.P.leave_home(t, ind)
# DIVORCE:
elif self.params['divorce_age'] < ind.age < 50 \
and ind.partner \
and self.rng.random() < self.params_adj['divorce_probs'][index]:
self.P.separate_couple(t, ind)
# ELSE: individual has a quiet year...
return death, birth
def choose_mother(self, index):
"""
Choose a new mother on the basis of fertility rates.
NOTE: there is still a very small possibility (in *very* small
populations) that this will hang due to candidates remaining
forever empty. Should add a check to prevent this and exit gracefully.
"""
candidates = []
while not candidates:
tgt_age = int(
sample_table(self.fertility_age_probs[index], self.rng)[0])
tgt_prev_min = 0
tgt_prev_max = 100
if self.params['use_parity']:
tgt_prev_min = int(
sample_table(
self.fertility_parity_probs[(tgt_age - 15) / 5],
self.rng)[0])
# effectively transform 5 into 5+
tgt_prev_max = tgt_prev_min if tgt_prev_min < 5 else 20
tgt_set = self.P.individuals_by_age(tgt_age, tgt_age)
candidates = [x
for x in tgt_set \
if x.sex == 1 \
and x.can_birth() \
and not x.with_parents \
and tgt_prev_min <= len(x.children) <= tgt_prev_max
]
return self.rng.choice(candidates)
def choose_partner(self, ind):
"""
Choose a partner for i_id, subject to parameter constraints.
:param ind: the first partner in the couple.
:type ind: Individual
:returns: partner if successful, otherwise None.
"""
mean_age = ind.age+self.params['partner_age_diff'] \
if ind.sex == 0 else ind.age-self.params['partner_age_diff']
tgt_age = 0
while tgt_age < self.params['min_partner_age']:
tgt_age = int(
self.rng.gauss(mean_age, self.params['partner_age_sd']))
tgt_set = self.P.individuals_by_age(tgt_age, tgt_age)
candidates = [x \
for x in tgt_set \
if not x.partner \
and x.sex != ind.sex \
and x not in self.P.hh_members(ind)
]
# abort if no eligible partner exists
return None if candidates == [] else self.rng.choice(candidates)
def update_death_birth(self, t, ind, mother):
"""
Replace a dying individual with a newborn. If no individual to die
is passed, only a birth occurs; if no mother is passed, only a death
occurs.
:param t: the current time step.
:type t: int
:param ind: the individual to die.
:type ind: Individual
:returns: the new individual.
"""
if ind:
orphans = self.P.death(t, ind)
self.P.process_orphans(t, orphans, self.params['age_cutoffs'][-2],
self.rng)
if mother:
sex = self.rng.randint(0, 1)
new_ind = self.P.birth(t, self.rng, mother, mother.partner, sex)
return new_ind
return None
def update_all_demo(self, t):
"""
Update population over period of t days.
Returns list of births, deaths, immigrants and birthdays.
"""
birthdays = self.P.age_population(self.params['t_dur'])
deaths = []
births = []
# calculate index for fertility and mortality rates
# basically: use first entry for burn-in, then one entry every
# 'period' years, then use the final entry for any remaining years.
index = min(max(0, (t - (self.params['demo_burn']*365)) /
(self.params['demo_period']*365)), self.dyn_years) \
if self.params['dyn_rates'] else 0
cur_inds = self.P.I.values()
for ind in cur_inds:
death, birth = self.update_individual_demo(t, ind, index)
if death: deaths.append(death)
if birth: births.append(birth)
#population growth
for x in xrange(
int(len(self.P.I) * self.params_adj['growth_rates'][index])):
mother = self.choose_mother(index)
births.append(self.update_death_birth(t, None, mother))
#immigration
imm_count = 0
imm_tgt = int(len(self.P.I) * self.params_adj['imm_rates'][index])
source_hh_ids = []
immigrants = []
while imm_count < imm_tgt:
hh_id = self.rng.choice(self.P.groups['household'].keys())
imm_count += len(self.P.groups['household'][hh_id])
source_hh_ids.append(hh_id)
for hh_id in source_hh_ids:
new_hh_id = self.P.duplicate_household(t, hh_id)
immigrants.extend(self.P.groups['household'][new_hh_id])
return births, deaths, immigrants, birthdays
def record_stats_demo(self, t):
if self.params['record_interval'] <= 0 or t % self.params[
'record_interval'] is not 0:
return
self.pop_size.append(len(self.P.I))
self.age_dist.append(self.P.age_dist(101, 101)[0])
self.hh_size_dist.append(
self.P.group_size_dist('household', self.max_hh)[0])
self.hh_size_dist_counts.append(
self.P.group_size_dist('household', self.max_hh, False)[0])
self.hh_size_avg.append(self.P.group_size_avg('household'))
self.hh_count.append(len(self.P.groups['household']))
self.fam_types.append(self.P.sum_hh_stats_group())
def run(self):
"""
Run simulated population (NB: this probably won't be used, as
external running object may wish to just call update_all itself...)
"""
timesteps = self.params['years'] * (365 / self.params['t_dur'])
i = 0
while i < timesteps:
t = i * self.params['t_dur']
print i, t
self.update_all_demo(t)
i += 1
class Simulation(object):
def __init__(self, params, ind_type=Individual, create_pop=True):
# convert ConfigObj to dictionary to store params
self.params = dict(params)
self.params_adj={}
self.rng = Random(self.params['seed'])
self.load_demographic_data()
if create_pop:
self.create_population(ind_type, params['logging'])
# for storing general data
self.max_hh = 50 # maximum possible hh size
self.pop_size = []
self.age_dist = []
self.hh_size_dist = []
self.hh_size_dist_counts = []
self.hh_size_avg = []
self.hh_count = []
self.fam_types = []
self.start_time = None
self.end_time = None
def create_population(self, ind_type, logging=True):
"""
Create a population according to specified age and household size
distributions.
"""
self.P = Pop_HH(ind_type, logging)
self.P.gen_hh_age_structured_pop(self.params['pop_size'], self.hh_comp,
self.age_dist, self.params['age_cutoffs'], self.rng)
self.P.allocate_couples()
self.P.print_population_summary()
def parse_age_rates(self, filename, factor, final):
"""
Parse an age-year-rate table to produce a dictionary, keyed by age,
with each entry being a list of annual rates (by year).
Setting final to 'True' appends an age 100 rate of >1 (e.g., to
ensure everyone dies!
"""
dat = load_age_rates(filename)
rates = {}
for line in dat:
rates[line[0]] = [x * factor for x in line[1:]]
if final:
rates[101] = [100 for x in dat[0][1:]] # everybody dies...
return rates
def load_demographic_data(self):
"""
Load data on age-specific demographic processes (mortality/fertility)
and adjust event probabilities according to time-step.
"""
# load household size distribution and age distribution
self.hh_comp = load_probs(os.path.join(self.params['resource_prefix'],
self.params['hh_composition']), False)
self.params['age_cutoffs'] = [int(x) for x in self.hh_comp[0][1:][0]] # yuk!
self.age_dist = load_probs(os.path.join(self.params['resource_prefix'],
self.params['age_distribution']))
annual_factor = self.params['t_dur']/365.0
# load and scale MORTALITY rates
self.death_rates = {}
self.death_rates[0] = self.parse_age_rates(os.path.join(
self.params['resource_prefix'],
self.params['death_rates_m']), annual_factor, True)
self.death_rates[1] = self.parse_age_rates(os.path.join(
self.params['resource_prefix'],
self.params['death_rates_f']), annual_factor, True)
### load FERTILITY age probs (don't require scaling) for closed pops
self.fertility_age_probs = load_prob_tables(os.path.join(
self.params['resource_prefix'],
self.params['fertility_age_probs']))
self.fertility_parity_probs = load_probs_new(os.path.join(
self.params['resource_prefix'],
self.params['fertility_parity_probs']))
### load and scale leav/couple/divorce and growth rates
if self.params['dyn_rates']:
# rates will be a list of annual values
self.params['leaving_probs'] = load_prob_list(os.path.join(
self.params['resource_prefix'], self.params['leaving_prob_file']))
self.params['couple_probs'] = load_prob_list(os.path.join(
self.params['resource_prefix'], self.params['couple_prob_file']))
self.params['divorce_probs'] = load_prob_list(os.path.join(
self.params['resource_prefix'], self.params['divorce_prob_file']))
self.params['growth_rates'] = load_prob_list(os.path.join(
self.params['resource_prefix'], self.params['growth_rate_file']))
self.params['imm_rates'] = load_prob_list(os.path.join(
self.params['resource_prefix'], self.params['imm_rate_file']))
self.params_adj['leaving_probs'] = [adjust_prob(x, self.params['t_dur'])
for x in self.params['leaving_probs']]
self.params_adj['couple_probs'] = [adjust_prob(x, self.params['t_dur'])
for x in self.params['couple_probs']]
self.params_adj['divorce_probs'] = [adjust_prob(x, self.params['t_dur'])
for x in self.params['divorce_probs']]
self.params_adj['growth_rates'] = [adjust_prob(x, self.params['t_dur'])
for x in self.params['growth_rates']]
self.params_adj['imm_rates'] = [adjust_prob(x, self.params['t_dur'])
for x in self.params['imm_rates']]
self.dyn_years = min(len(self.death_rates[0][0])-1, len(self.fertility_age_probs)-1,
len(self.params_adj['leaving_probs'])-1, len(self.params_adj['couple_probs'])-1,
len(self.params_adj['divorce_probs'])-1, len(self.params_adj['growth_rates'])-1)
else:
# adjust demographic event probabilities according to time step
self.params_adj['couple_probs'] = [adjust_prob(
self.params['couple_prob'], self.params['t_dur'])]
self.params_adj['leaving_probs'] = [adjust_prob(
self.params['leaving_prob'], self.params['t_dur'])]
self.params_adj['divorce_probs'] = [adjust_prob(
self.params['divorce_prob'], self.params['t_dur'])]
self.params_adj['growth_rates'] = [adjust_prob(
self.params['growth_rate'], self.params['t_dur'])]
self.params_adj['imm_rates'] = [adjust_prob(
self.params['imm_rate'], self.params['t_dur'])]
def update_individual_demo(self, t, ind, index=0):
"""
Update individual ind; check for death, couple formation, leaving home
or divorce, as possible and appropriate.
"""
death = None; birth = None
couple_prob = self.params_adj['couple_probs'][index]
# if ind.divorced and ind.deps: couple_prob *= 0.5
# DEATH / BIRTH:
if self.rng.random() > exp(-self.death_rates[ind.sex][ind.age][index]):
death = ind
mother = ind
while mother is ind: # make sure dead individual isn't selected as mother!
mother = self.choose_mother(index)
birth = self.update_death_birth(t, ind, mother)
# COUPLE FORMATION:
elif self.params['couple_age'] < ind.age < 60 \
and not ind.partner \
and self.rng.random() < couple_prob:
partner = self.choose_partner(ind)
if partner:
self.P.form_couple(t, ind, partner)
# LEAVING HOME:
elif ind.age > self.params['leaving_age'] \
and ind.with_parents \
and not ind.partner \
and self.rng.random() < self.params_adj['leaving_probs'][index]:
self.P.leave_home(t, ind)
# DIVORCE:
elif self.params['divorce_age'] < ind.age < 50 \
and ind.partner \
and self.rng.random() < self.params_adj['divorce_probs'][index]:
self.P.separate_couple(t, ind)
# ELSE: individual has a quiet year...
return death, birth
def choose_mother(self, index):
"""
Choose a new mother on the basis of fertility rates.
NOTE: there is still a very small possibility (in *very* small
populations) that this will hang due to candidates remaining
forever empty. Should add a check to prevent this and exit gracefully.
"""
candidates = []
while not candidates:
tgt_age = int(sample_table(self.fertility_age_probs[index], self.rng)[0])
tgt_prev_min = 0; tgt_prev_max = 100
if self.params['use_parity']:
tgt_prev_min = int(sample_table(
self.fertility_parity_probs[(tgt_age-15)/5], self.rng)[0])
# effectively transform 5 into 5+
tgt_prev_max = tgt_prev_min if tgt_prev_min < 5 else 20
tgt_set = self.P.individuals_by_age(tgt_age, tgt_age)
candidates = [x
for x in tgt_set \
if x.sex == 1 \
and x.can_birth() \
and not x.with_parents \
and tgt_prev_min <= len(x.children) <= tgt_prev_max
]
return self.rng.choice(candidates)
def choose_partner(self, ind):
"""
Choose a partner for i_id, subject to parameter constraints.
:param ind: the first partner in the couple.
:type ind: Individual
:returns: partner if successful, otherwise None.
"""
mean_age = ind.age+self.params['partner_age_diff'] \
if ind.sex == 0 else ind.age-self.params['partner_age_diff']
tgt_age = 0
while tgt_age < self.params['min_partner_age']:
tgt_age = int(self.rng.gauss(mean_age, self.params['partner_age_sd']))
tgt_set = self.P.individuals_by_age(tgt_age, tgt_age)
candidates = [x \
for x in tgt_set \
if not x.partner \
and x.sex != ind.sex \
and x not in self.P.hh_members(ind)
]
# abort if no eligible partner exists
return None if candidates == [] else self.rng.choice(candidates)
def update_death_birth(self, t, ind, mother):
"""
Replace a dying individual with a newborn. If no individual to die
is passed, only a birth occurs; if no mother is passed, only a death
occurs.
:param t: the current time step.
:type t: int
:param ind: the individual to die.
:type ind: Individual
:returns: the new individual.
"""
if ind:
orphans = self.P.death(t, ind)
self.P.process_orphans(t, orphans, self.params['age_cutoffs'][-2], self.rng)
if mother:
sex = self.rng.randint(0, 1)
new_ind = self.P.birth(t, self.rng, mother, mother.partner, sex)
return new_ind
return None
def update_all_demo(self, t):
"""
Update population over period of t days.
Returns list of births, deaths, immigrants and birthdays.
"""
birthdays = self.P.age_population(self.params['t_dur'])
deaths = []; births = []
# calculate index for fertility and mortality rates
# basically: use first entry for burn-in, then one entry every
# 'period' years, then use the final entry for any remaining years.
index = min(max(0, (t - (self.params['demo_burn']*365)) /
(self.params['demo_period']*365)), self.dyn_years) \
if self.params['dyn_rates'] else 0
cur_inds = self.P.I.values()
for ind in cur_inds:
death, birth = self.update_individual_demo(t, ind, index)
if death: deaths.append(death)
if birth: births.append(birth)
#population growth
for x in xrange(int(len(self.P.I) * self.params_adj['growth_rates'][index])):
mother = self.choose_mother(index)
births.append(self.update_death_birth(t, None, mother))
#immigration
imm_count = 0
imm_tgt = int(len(self.P.I) * self.params_adj['imm_rates'][index])
source_hh_ids = []
immigrants = []
while imm_count < imm_tgt:
hh_id = self.rng.choice(self.P.groups['household'].keys())
imm_count += len(self.P.groups['household'][hh_id])
source_hh_ids.append(hh_id)
for hh_id in source_hh_ids:
new_hh_id = self.P.duplicate_household(t, hh_id)
immigrants.extend(self.P.groups['household'][new_hh_id])
return births, deaths, immigrants, birthdays
def record_stats_demo(self, t):
if self.params['record_interval'] <= 0 or t%self.params['record_interval'] is not 0:
return
self.pop_size.append(len(self.P.I))
self.age_dist.append(self.P.age_dist(101,101)[0])
self.hh_size_dist.append(self.P.group_size_dist('household', self.max_hh)[0])
self.hh_size_dist_counts.append(self.P.group_size_dist('household',self.max_hh,False)[0])
self.hh_size_avg.append(self.P.group_size_avg('household'))
self.hh_count.append(len(self.P.groups['household']))
self.fam_types.append(self.P.sum_hh_stats_group())
def run(self):
"""
Run simulated population (NB: this probably won't be used, as
external running object may wish to just call update_all itself...)
"""
timesteps = self.params['years'] * (365/self.params['t_dur'])
i = 0
while i < timesteps:
t = i*self.params['t_dur']
print i, t
self.update_all_demo(t)
i += 1