def test_prior_dates(self):
pgoal_age_mean = 6726.8
pgoal_age_std = 192.94564322687978
pgoal_density_mean = 0.011642671907680679
pgoal_density_std = 0.010893804880746285
dgoal = np.array([77.5, 79.5, 99.5])
dgoal_n = 40
pgoal_n = dgoal_n
chron = read_chron(os.path.join(here, 'MSB2K.csv'))
d_target, p_target = Bacon.prior_dates(chron, **self.mcmc_kws)
np.testing.assert_allclose(d_target[-3:], dgoal)
np.testing.assert_equal(len(d_target), dgoal_n)
np.testing.assert_allclose(np.mean(p_target[-1][:, 0]),
pgoal_age_mean,
atol=7)
np.testing.assert_allclose(np.std(p_target[-1][:, 0]),
pgoal_age_std,
atol=2)
np.testing.assert_equal(len(p_target), pgoal_n)
np.testing.assert_allclose(np.mean(p_target[-1][:, 1]),
pgoal_density_mean,
atol=1e-2)
np.testing.assert_allclose(np.std(p_target[-1][:, 1]),
pgoal_density_std,
atol=1e-2)
def test_run_baconmcmc(self):
testcore_path = path.join(here, 'MSB2K.csv')
c = snek.read_chron(testcore_path)
fullrun_victim = baconwrap.run_baconmcmc(core_labid=c.labid, core_age=c.age, core_error=c.error,
core_depth=c.depth, depth_min=1.5, depth_max=99.5, cc=[1],
cc1='IntCal13', cc2='Marine13', cc3='SHCal13', cc4='ConstCal',
d_r=[0], d_std=[0], t_a=[3], t_b=[4], k=20,
minyr=-1000, maxyr=1e6, th01=4147, th02=4145,
acc_mean=20, acc_shape=1.5, mem_strength=4, mem_mean=0.7)
niter_goal = 3432
nsegs_goal = 20
objective_mean_goal = 218.26212744522144
theta_mean_goal = 4549.6406701631704
w_mean_goal = 0.06277018029195805
x0_mean_goal = 14.487713009032634
xneg1_mean_goal = 15.65397709810606
# Fuzzy to deal with vars across platforms.
np.testing.assert_allclose(len(fullrun_victim['objective']), niter_goal, atol=50)
np.testing.assert_allclose(len(fullrun_victim['w']), niter_goal, atol=50)
np.testing.assert_allclose(len(fullrun_victim['x'][0]), niter_goal, atol=50)
np.testing.assert_allclose(len(fullrun_victim['x'][-1]), niter_goal, atol=50)
self.assertEqual(nsegs_goal, len(fullrun_victim['x']))
np.testing.assert_allclose(fullrun_victim['objective'].mean(), objective_mean_goal, atol=1e-1)
np.testing.assert_allclose(fullrun_victim['theta'].mean(), theta_mean_goal, atol=15)
np.testing.assert_allclose(fullrun_victim['w'].mean(), w_mean_goal, atol=1e-2)
np.testing.assert_allclose(fullrun_victim['x'][0].mean(), x0_mean_goal, atol=2)
np.testing.assert_allclose(fullrun_victim['x'][-1].mean(), xneg1_mean_goal, atol=2)
def test_calibrate_dates(self):
pgoal_age_mean = 6726.8
pgoal_age_std = 192.94564322687978
pgoal_density_mean = 0.011642671907680679
pgoal_density_std = 0.010893804880746285
dgoal = np.array([77.5, 79.5, 99.5])
dgoal_n = 40
pgoal_n = dgoal_n
chron = read_chron(os.path.join(here, 'MSB2K.csv'))
d_r = [0]
d_std = [0]
t_a = [3]
t_b = [4]
cc = [fetch_calibcurve('IntCal13')]
d_target, p_target = calibrate_dates(chron,
calib_curve=cc,
d_r=d_r,
d_std=d_std,
t_a=t_a,
t_b=t_b)
np.testing.assert_allclose(d_target[-3:], dgoal)
np.testing.assert_equal(len(d_target), dgoal_n)
np.testing.assert_allclose(np.mean(p_target[-1][:, 0]),
pgoal_age_mean,
atol=7)
np.testing.assert_allclose(np.std(p_target[-1][:, 0]),
pgoal_age_std,
atol=2)
np.testing.assert_equal(len(p_target), pgoal_n)
np.testing.assert_allclose(np.mean(p_target[-1][:, 1]),
pgoal_density_mean,
atol=1e-2)
np.testing.assert_allclose(np.std(p_target[-1][:, 1]),
pgoal_density_std,
atol=1e-2)
cc3='SHCal13',
cc4='ConstCal',
d_r=[0],
d_std=[0],
t_a=[3],
t_b=[4],
k=20,
minyr=-1000,
maxyr=1e6,
th01=4147,
th02=4145,
acc_mean=20,
acc_shape=1.5,
mem_strength=4,
mem_mean=0.7)
fullrun_agemodel = AgeDepthModel(read_chron(path.join(here, 'MSB2K.csv')),
mcmc_kws=mcmc_kws)
class TestAgeDepth(unittest.TestCase):
def setUp(self):
np.random.seed(123)
self.testdummy = deepcopy(fullrun_agemodel)
def test_init(self):
goal_thick = 4.9
goal_depthrange = (1.5, 99.5)
goal_agemedian_edges = (4552.5750000000007, 6714.1464476499987)
goal_agemedian_025 = (4430.3599999999997, 6582.4278499575012)
goal_agemedian_975 = (4680.6210000000001, 6868.9317877499998)
goal_ageensemble_shape = (99, 3232)
import numpy as np
from snakebacon import read_chron
from snakebacon.mcmc import McmcResults, McmcSetup
here = path.abspath(path.dirname(__file__))
mcmc_kws = dict(depth_min=1.5, depth_max=99.5, cc=[1],
cc1='IntCal13', cc2='Marine13', cc3='SHCal13', cc4='ConstCal',
d_r=[0], d_std=[0], t_a=[3], t_b=[4], k=20,
minyr=-1000, maxyr=1e6, th01=4147, th02=4145,
acc_mean=20, acc_shape=1.5, mem_strength=4, mem_mean=0.7)
fullrun_setup = McmcSetup(read_chron(path.join(here, 'MSB2K.csv')), **mcmc_kws)
fullrun_victim = McmcResults(fullrun_setup)
class TestMcmcResults(unittest.TestCase):
def setUp(self):
self.testdummy = deepcopy(fullrun_victim)
def test_init(self):
niter_goal = 3432
nsegs_goal = 20
objective_mean_goal = 218.26212744522144
theta_mean_goal = 4549.6406701631704
w_mean_goal = 0.06277018029195805
x0_mean_goal = 14.487713009032634
xneg1_mean_goal = 15.65397709810606