Colonster site, MLE with 4 free parameters (grid search method).
For more info about the method used, see the notebook Inference_Notes.
This notebook has the following external dependencies:
In [1]:
import math
import csv
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy import stats
import seaborn as sns
import yaml
%matplotlib inline
The mathematical model is available in the models Python module (see the notebook Models)
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import models
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profile_data = pd.read_csv('profiles_data/colonster_10Be_profile_data.csv',
index_col='sample',
delim_whitespace=True,
quoting=csv.QUOTE_NONNUMERIC, quotechar='\"',
dtype={'depth': 'f', 'depth_g-cm-2': 'f',
'C': 'f', 'std': 'f'})
profile_data
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In [4]:
with open('profiles_data/colonster_10Be_settings.yaml') as f:
colonster_settings = yaml.load(f)
colonster_settings
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The dataset is stored as a :class:pandas.DataFrame object.
The grid search method is implemented in the gridsearch module (see the notebook Grid-Search for more info).
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import gridsearch
Create a new object for setup and results
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gstest = gridsearch.CosmogenicInferenceGC(description='Colonster 4 parameters')
Set the data
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gstest.set_profile_measured(
profile_data['depth'].values,
profile_data['C'].values,
profile_data['std'].values,
None,
)
Set the model
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def C_10Be_colonster(depth, erosion, exposure,
density, inheritance):
"""
10Be colonster
"""
return models.C_10Be(depth, erosion, exposure,
density, inheritance,
P_0=colonster_settings['P_0'])
gstest.set_profile_model(C_10Be_colonster)
Define the parameters to fit and their search ranges / steps. The order must be the same than the order of the arguments of the function used for the model!
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gstest.set_parameter(
'erosion_rate',
[0., 0.5e-3, 70j],
stats.uniform(loc=0, scale=0.5e-3).pdf
)
gstest.set_parameter(
'exposure_time',
[0., 3e6, 130j],
stats.uniform(loc=0, scale=3e6).pdf
)
gstest.set_parameter(
'soil_density',
[1.6, 2.6, 70j],
stats.uniform(loc=1.6, scale=2.6).pdf
)
gstest.set_parameter(
'inheritance',
[0, 1e5, 60j],
stats.uniform(loc=0, scale=1e5).pdf
)
Grid search setup summary
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print gstest.setup_summary()
Perform Maximum likelihood estimation on the search grid
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gstest.compute_mle()
Get the MLE (i.e., the parameter values at the maximum likelihood), in the same order than the definition of the parameters
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gstest.mle
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Plot the profile log-likelihood for each parameter. The blue lines represent the difference between the profile log-likelihood and the maximum log-likelihood, The intersections between the blue line and the black lines define the confidence intervals at the given confidence levels (based on the likelihood ratio test). The red lines indicate the true values.
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%matplotlib inline
def plot_proflike1d(cobj, pname, clevels=[0.68, 0.95, 0.997],
true_val=None, ax=None):
p = cobj.parameters[pname]
pindex = cobj.parameters.keys().index(pname)
x = cobj.grid[pindex].flatten()
proflike = cobj.proflike1d[pindex]
if ax is None:
ax = plt.subplot(111)
difflike = proflike - cobj.maxlike
ax.plot(x, difflike, label='profile loglike')
ccrit = gridsearch.profile_likelihood_crit(
cobj.proflike1d[pindex],
cobj.maxlike,
clevels=clevels
)
ccrit -= cobj.maxlike
for lev, cc in zip(clevels, ccrit):
l = ax.axhline(cc, color='k')
hpos = x.min() + (x.max() + x.min()) * 0.05
ax.text(hpos, cc, str(lev * 100),
size=9, color = l.get_color(),
ha="center", va="center",
bbox=dict(ec='1',fc='1'))
if true_val is not None:
ax.axvline(true_val, color='r')
plt.setp(ax, xlabel=pname,
ylabel='profile log-like - max log-like',
xlim=p['range'][0:2],
ylim=[ccrit[-1], 0.])
def plot_proflike1d_all(cobj, n_subplot_cols=2, **kwargs):
n_subplots = len(cobj.parameters)
n_subplot_rows = int(math.ceil(1. *
n_subplots /
n_subplot_cols))
fig, aax = plt.subplots(nrows=n_subplot_rows,
ncols=n_subplot_cols,
**kwargs)
axes = aax.flatten()
fig.text(0.5, 0.975,
"Profile log-like: " + cobj.description,
horizontalalignment='center',
verticalalignment='top')
for i, pname in enumerate(cobj.parameters.keys()):
ax = axes[i]
plot_proflike1d(cobj, pname,
ax=ax)
plt.tight_layout()
plt.subplots_adjust(top=0.93)
plot_proflike1d_all(gstest, figsize=(11, 6))
Show the profile log-likelihood for couples of parameters. Confidence regions are also shown (also based on the likelihood ratio test).
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def plot_proflike2d(cobj, p1p2, ax=None,
cmap='Blues', show_colorbar=True):
pname1, pname2 = p1p2
idim = cobj.parameters.keys().index(pname2)
jdim = cobj.parameters.keys().index(pname1)
if ax is None:
ax = plt.subplot(111)
X, Y = np.meshgrid(cobj.grid[idim].flatten(),
cobj.grid[jdim].flatten())
difflike = cobj.proflike2d[idim][jdim] - cobj.maxlike
ccrit = gridsearch.profile_likelihood_crit(
cobj.proflike2d[idim][jdim],
cobj.maxlike,
clevels=[0.68, 0.95]
)
ccrit -= cobj.maxlike
contours = np.linspace(np.median(difflike),
0,
10)
P2D = ax.contourf(Y, X, difflike,
contours,
cmap=plt.get_cmap(cmap))
ci68 = ax.contour(Y, X, difflike,
[ccrit[0]], colors='w',
linestyles='solid')
plt.clabel(ci68, fontsize=8, inline=True,
fmt='68')
ci95 = ax.contour(Y, X, difflike,
[ccrit[1]], colors=['k'],
linestyles='solid')
plt.clabel(ci95, fontsize=8, inline=True,
fmt='95')
ax.scatter(cobj.mle[jdim], cobj.mle[idim],
marker='*', s=60, c='w')
plt.setp(ax, xlabel=pname1, ylabel=pname2)
if show_colorbar:
plt.colorbar(P2D, ax=ax)
#ax.axhline(true_exposure, color='r')
#ax.axvline(true_erosion, color='r')
fig = plt.figure(figsize=(11, 9))
ax = plt.subplot(321)
plot_proflike2d(gstest, ('erosion_rate', 'exposure_time'), ax=ax)
ax2 = plt.subplot(322)
plot_proflike2d(gstest, ('exposure_time', 'inheritance'), ax=ax2)
ax3 = plt.subplot(323)
plot_proflike2d(gstest, ('erosion_rate', 'inheritance'), ax=ax3)
ax4 = plt.subplot(324)
plot_proflike2d(gstest, ('exposure_time', 'soil_density'), ax=ax4)
ax5 = plt.subplot(325)
plot_proflike2d(gstest, ('erosion_rate', 'soil_density'), ax=ax5)
ax6 = plt.subplot(326)
plot_proflike2d(gstest, ('soil_density', 'inheritance'), ax=ax6)
plt.tight_layout()
Plot the measured concentrations and the predicted profile corresponding to the best fitted data model
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sns.set_context('notebook')
depths = np.linspace(profile_data['depth'].min(),
profile_data['depth'].max(),
100)
Cm_fitted = C_10Be_colonster(depths, *gstest.mle)
plt.figure()
plt.plot(Cm_fitted, -depths, label='best-fitted model')
plt.errorbar(profile_data['C'],
-profile_data['depth'],
xerr=profile_data['std'],
fmt='o', markersize=4,
label='data')
plt.setp(plt.gca(),
xlabel='10Be concentration [atoms g-1]',
ylabel='-1 * depth [cm]',
xlim=[0, None], ylim=[None, 0])
plt.legend(loc='lower right')
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