def __init__(self, grid, occam=2.0):
# test = Hypothesis('testGrid')
self.grid = grid
self.hypotheses = None
self.occam = occam
self.primitives = list()
self.primitives = [self.And, self.Or, self.Then]
self.objects = grid.objects.keys()
self.space = [self.primitives, self.objects]
# Uniform pDistribution for sampling across objects and primitivres
self.pPrim = np.zeros(len(self.primitives))
self.pPrim = uniform.pdf(self.pPrim)
self.pPrim /= self.pPrim.sum()
self.pObj = np.zeros(len(self.objects))
self.pObj = uniform.pdf(self.pObj)
self.pObj /= self.pObj.sum()
self.p = [self.pPrim, self.pObj]
self.primCount = 0
self.primHypotheses = list()
self.setBetaDistribution()
def p(s1, s2, w, b):
prior_s1 = uniform.pdf(s2, loc=0.5, scale=4.5)
prior_s2 = uniform.pdf(s1, loc=0.5, scale=4.5)
prior_w = uniform.pdf(w, loc=0., scale=2.)
prior_b = uniform.pdf(b, loc=0., scale=2.)
likl = np.prod(norm.pdf(y, loc=x * w + b, scale=[s1, s2]))
return prior_s1 * prior_s2 * prior_w * prior_b * likl
def test_system_ode_solver(self):
# example taken from the paper Hobson Klimmek 2015
UNIFORM_SUPP = [[-1., 1.],
[-2.,
2.]] # UNIFORM_SUPP[0][0] <= UNIFORM_SUPP[1][0] <= UNIFORM_SUPP[1][1] <= UNIFORM_SUPP[1][0]
density_1 = lambda tt: uniform.pdf(tt,
loc=UNIFORM_SUPP[0][0],
scale=UNIFORM_SUPP[0][1] - UNIFORM_SUPP[0][0])
density_2 = lambda tt: uniform.pdf(tt,
loc=UNIFORM_SUPP[1][0],
scale=UNIFORM_SUPP[1][1] - UNIFORM_SUPP[1][0])
def density_mu(tt):
return density_1(tt)
def density_nu(tt):
return density_2(tt)
def density_eta(tt):
return np.maximum(density_mu(tt) - density_nu(tt), 0)
def density_gamma(tt):
return np.maximum(density_nu(tt) - density_mu(tt), 0)
def p_dash_open_formula(tt, xx, yy):
return (tt - yy) / (yy - xx) * density_eta(tt) / density_gamma(xx)
def q_dash_open_formula(tt, xx, yy):
return (xx - tt) / (yy - xx) * density_eta(tt) / density_gamma(yy)
tt = np.linspace(-1 * 0.999, 0.5, 1000)
starting_points = [[1.99, -1.01], [1.01, -1.99]]
# forward equation
empirical = diff_eq.system_ODE_solver(tt, starting_points[0],
[p_dash_open_formula, q_dash_open_formula],
left_or_right="left")
q, p = zip(*empirical)
p = function_iterable.replace_nans_numpy(np.array(p))
q = function_iterable.replace_nans_numpy(np.array(q))
true_p = lambda tt: -1 / 2 * (np.sqrt(12. - 3. * tt * tt) + tt)
true_q = lambda tt: 1 / 2 * (np.sqrt(12. - 3. * tt * tt) - tt)
error = np.mean(np.abs(function_iterable.replace_nans_numpy(p) - true_p(tt)))
error += np.mean(np.abs(function_iterable.replace_nans_numpy(q) - true_q(tt)))
# backward equation
tt = np.linspace(-0.5, 1 * 0.999, 2000)
# forward equation
empirical = diff_eq.system_ODE_solver(tt, starting_points[1],
[p_dash_open_formula, q_dash_open_formula],
left_or_right="left")
q, p = zip(*empirical)
p = function_iterable.replace_nans_numpy(np.array(p))
q = function_iterable.replace_nans_numpy(np.array(q))
error += np.mean(function_iterable.replace_nans_numpy(p) - true_p(tt))
error += np.mean(function_iterable.replace_nans_numpy(q) - true_q(tt))
assert error < 0.1
def pdf(self, X):
"""
generates random samples from the uniform prior, for 3 parameters.
param:
Ndata, number of samples
left, left boundary
right, right boundary
output:
theta, random samples of size (Ndata,3)
"""
left = np.log(self.left)
right = np.log(self.right)
# left = loc
# right = loc + scale
loc = left
scale = right - left
k0 = uniform.pdf(X[:, 0], loc=loc[0], scale=scale[0])
k1 = uniform.pdf(X[:, 1], loc=loc[1], scale=scale[1])
k2 = uniform.pdf(X[:, 2], loc=loc[2], scale=scale[2])
theta = np.vstack((k0, k1, k2)).T
return np.prod(theta, axis=1)
def indiv_MHRW(self, theta, cov, epsilon, prev_gen_sample, prev_gen_eta):
'''
Return the Metropolis Hastings Random Walk Kernel updates of the thetas=(phi, eta, tau)
theta: (array-like) the prior to simulate the population from
cov: ((3,3)-array): The covariance matrix of the thetas previously computed
epsilon (float): The tolerance level of the current iteration
prev_gen_sample (array-like): A sample previously generated
prev_gen_eta (array-like): The eta associated to that sample
-------------------------------------------------------------------------
returns (array-like): the updated or not theta
'''
new_theta = theta + np.random.multivariate_normal([0, 0, 0], (
(2.38**2) / 3) * cov) # Has dimensionality is 3
new_theta = new_theta / new_theta.sum(
) # reparametrization on the real line. Is it the right way to do it ?
new_pop, fail_to_gen_pop = self.simulate_population(theta,
verbose=False)
if fail_to_gen_pop == False:
new_sample = np.random.choice(new_pop,
self.sample_size,
replace=True)
new_gen_eta = self.compute_eta(new_sample)
indicatrices_ratio = int(
self.compute_rho(new_gen_eta) < epsilon) / int(
self.compute_rho(prev_gen_eta) < epsilon)
proposal_ratio = 1 # random walk proposal is symetric then the ratio of q(theta*,theta)/q(theta,theta*)=1
new_priors = np.array([
gamma.pdf(x=new_theta[0], a=0.1),
uniform.pdf(x=new_theta[1], loc=0, scale=theta[0]),
truncnorm.pdf(x=new_theta[2],
a=0,
b=10**10,
loc=0.198,
scale=0.067352)
])
old_priors = np.array([
gamma.pdf(x=theta[0], a=0.1),
uniform.pdf(x=theta[1], loc=0, scale=theta[0]),
truncnorm.pdf(x=theta[2],
a=0,
b=10**10,
loc=0.198,
scale=0.067352)
])
acceptance_probas = np.minimum(
np.ones(len(theta)),
indicatrices_ratio * proposal_ratio * new_priors / old_priors)
unif_draws = uniform.rvs(size=len(theta))
new_theta_accepted = unif_draws <= acceptance_probas
final_theta = np.where(new_theta_accepted, new_theta, theta)
else:
final_theta = theta
return final_theta # Might return acceptance probas
def __init__(self, grid, occam=2.0):
# test = Hypothesis('testGrid')
self.grid = grid
self.hypotheses = None
self.occam = occam
self.primitives = list()
self.primitives = [self.And,self.Or,self.Then]
self.objects = grid.objects.keys()
self.space = [self.primitives, self.objects]
# Uniform pDistribution for sampling across objects and primitivres
self.pPrim = np.zeros(len(self.primitives))
self.pPrim = uniform.pdf(self.pPrim)
self.pPrim /= self.pPrim.sum()
self.pObj = np.zeros(len(self.objects))
self.pObj = uniform.pdf(self.pObj)
self.pObj /= self.pObj.sum()
self.p = [self.pPrim,self.pObj]
self.primCount = 0
self.primHypotheses = list()
self.setBetaDistribution()
def unif():
"""
均匀分布函数
"""
x = np.arange(-0.01, 2.01, 0.01)
y = uniform.pdf(x, loc=0.0, scale=1.0)
y1 = uniform.pdf(x, loc=0.0, scale=2.0)
return x, y, y1
def pdf(self, x: Tuple[float]):
"""Find the PDF for a certain x value.
Args:
x (float): The value for which the PDF is needed.
"""
return uniform.pdf(x[0], loc=self.x_lower_bound, scale=self.x_upper_bound - self.x_lower_bound) \
* uniform.pdf(x[1], loc=self.y_lower_bound, scale=self.y_upper_bound - self.y_lower_bound)
def model_priors(enableInteriorViscosity):
kLink_prior = lambda sample: uniform.pdf(sample, 10.0, 290.0)
kBend_prior = lambda sample: uniform.pdf(sample, 50.0, 350.0)
viscosityRatio_prior = lambda sample: uniform.pdf(sample, 1.0, 14.0)
if enableInteriorViscosity:
return [kLink_prior, kBend_prior, viscosityRatio_prior]
else:
return [kLink_prior, kBend_prior]
def model_prior(sample, enableInteriorViscosity):
kLink_prior = uniform.pdf(sample[0], 10.0, 290.0)
kBend_prior = uniform.pdf(sample[1], 50.0, 350.0)
if enableInteriorViscosity:
viscosityRatio_prior = uniform.pdf(sample[2], 1.0, 14.0)
return np.prod([kLink_prior, kBend_prior, viscosityRatio_prior])
else:
return np.prod([kLink_prior, kBend_prior])
def inferPosterior(self, state, action):
"""
Uses inference engine to compute posterior probability from the
likelihood and prior (beta distribution).
"""
# Beta Distribution
# self.prior = np.linspace(.01,1.0,101)
# self.prior = beta.pdf(self.prior,1.4,1.4)
# self.prior /= self.prior.sum()
# Shifted Exponential
# self.prior = np.zeros(101)
# for i in range(50):
# self.prior[i + 50] = i * .02
# self.prior[100] = 1.0
# self.prior = expon.pdf(self.prior)
# self.prior[0:51] = 0
# self.prior *= self.prior
# self.prior /= self.prior.sum()
# # Shifted Beta
# self.prior = np.linspace(.01,1.0,101)
# self.prior = beta.pdf(self.prior,1.2,1.2)
# self.prior /= self.prior.sum()
# self.prior[0:51] = 0
# Uniform
self.prior = np.linspace(.01, 1.0, 101)
self.prior = uniform.pdf(self.prior)
self.prior /= self.prior.sum()
self.prior[0:51] = 0
self.posterior = self.likelihood * self.prior
self.posterior /= self.posterior.sum()
def run():
N = 10000 #experiments
x_Values = sorted(genRandos(0, 11, N)) #get rando nums
pdf_list = pdf(x_Values, N) #list returned
cdf_list = cdf(x_Values, N)
fig, axs = plt.subplots(2) #created 2 graphs
fig.suptitle("Part A")
plt.setp(axs, xticks=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) #x marks
axs[0].plot(list(x_Values),
pdf_list) #sorted values with appended pdf list
axs[0].set_title("Probability Distribution Function")
axs[1].plot(list(x_Values),
cdf_list) #sorted values with appended cdf list
axs[1].set_title("Cumulative Distribution Function")
#Using stats.uniform for pdf and cdf
x = np.linspace(0, 11, 10000) #spacing for graph points
fig, axs = plt.subplots(2)
fig.suptitle("Part B")
plt.setp(axs, xticks=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11])
axs[0].plot(x, uniform.pdf(x, 1, 9)) #pre built function for pdf
axs[0].set_title("Probability Distribution Function")
axs[1].plot(x, uniform.cdf(x, 1, 9)) #prebuilt function for cdf
axs[1].set_title("Cumulative Distribution Function")
plt.show()
def dunif(x, minimum=0,maximum=1):
"""
Calculates the point estimate of the uniform distribution
"""
from scipy.stats import uniform
result=uniform.pdf(x=x,loc=minimum,scale=maximum-minimum)
return result
def pdf(self, x):
pdf = 1.0
x = np.atleast_2d(x)
for ii in range(self.input_dim):
bd = self.domain[ii]
pdf *= uniform.pdf(x[:,ii], bd[0], bd[1]-bd[0])
return pdf
def prior(p_in):
"""
A function to return the prior density for a given value of p.
"""
return uniform.pdf(
p_in, 0, 1
) #giving me the pdf of any point in space, the area under the curve needs to integrate to 1
def mixture_model_pdf(x,
precision=STARTING_PRECISION,
guess_rate=STARTING_GUESS_RATE,
bias=STARTING_BIAS):
"""Returns a probability density function for a mixture model.
Parameters
----------
x : A list (or other iterable object) of values for the x axis. For example
`range(-180, 181)` would generate the PDF for every relevant value.
precision: The precision (or kappa) parameter. This is inversely related to
the standard deviation, and is a value in degrees.
guess_rate: The proportion of guess responses (0 - 1).
bias: The bias (or loc) parameter in degrees.
Returns
-------
An array with probability densities for each value of x.
"""
x = np.radians(x)
pdf_vonmises = vonmises.pdf(x=x,
kappa=np.radians(precision),
loc=np.radians(bias))
pdf_uniform = uniform.pdf(x, loc=-np.pi, scale=2 * np.pi)
return pdf_vonmises * (1 - guess_rate) + pdf_uniform * guess_rate
def calculate_row(Estart):
# Set up container arrays in polar coordinates
rvals, thetavals = np.linspace(0.01, L,
N), np.linspace(-.99 * np.pi / 2,
.99 * np.pi / 2, N)
phivals = np.linspace(0, 2 * np.pi, N)
# Output array of energy deposition
a = np.zeros([N, N, N], float)
x, y, z, dEdV, total_energy = [], [], [], [], []
# parameters for rms spread (Abril Table 1 & eq 5)
a1 = -0.058
a2 = -1.868
b1 = 9.39E-3
b2 = 1.56E-3
C1 = b1 * (Estart**a1)
C2 = b2 * (Estart**a2)
# populate entries of array via a double loop
for i, r in enumerate(rvals):
if i % 10 == 0: print("starting i={0}".format(i))
# determine dEdx for this depth
dEdx_index = np.searchsorted(linear_x, r)
if dEdx_index == len(linear_dEdx):
dEdx_val = 0
dE_val = 0
else:
dEdx_val = linear_dEdx[dEdx_index]
dE_val = linear_dE[dEdx_index]
# determine spread of Gaussian at this depth (Abril eqn 4)
sigma = 0.1 + (C1 * (r * 1E4) + C2 *
(r * 1E4)**2) / (r * 1E4) # in radians
for j, theta in enumerate(thetavals):
for k, phi in enumerate(phivals):
# store energy deposited at this theta, r, phi
# We want dE/dV * (r**2 * sin(theta)), but the expression simplifies:
# dE = (dE/dr)*dr*(norm()*dtheta)*(uniform()*dphi)
# dV = r**2 *sin(theta) * dr * dtheta * dphi
# Thus we end up with just (dE/dr)*(norm())*(uniform())
a[i, j,
k] += norm.pdf(theta, 0, sigma) * dEdx_val * uniform.pdf(
phi, 0, 2 * np.pi)
# and store Cartesian data for output
x.append(r * np.sin(theta) * np.cos(phi))
y.append(r * np.sin(theta) * np.sin(phi))
z.append(r * np.cos(theta))
total_energy.append(a[i, j, k])
t = simps(simps(simps(a, phivals), thetavals), rvals)
print(t)
return x, y, z, total_energy
def simulate_and_forward_density(distrub, par=None):
if distrub == 'r':
insertion_spot = expon.rvs()
q = expon.pdf(insertion_spot)
else:
insertion_spot = uniform.rvs()
branch_length = par
q = uniform.pdf(insertion_spot * branch_length, scale=branch_length)
return insertion_spot, q
def pdf(self, x: float):
"""Find the PDF for a certain x value.
Args:
x (float): The value for which the PDF is needed.
"""
return uniform.pdf(x,
loc=self.lower_bound,
scale=self.upper_bound - self.lower_bound)
def density(self, box, samples):
samples_density = list()
for mu in samples:
p_mu = 1.0
assert len(mu) == len(box)
for (mu_j, box_j) in zip(mu, box):
p_mu *= uniform.pdf(mu_j, box_j[0], box_j[1])
samples_density.append(p_mu)
return samples_density
def expectation(n):
est = 0
for i in range(n):
qsamp = np.random.uniform(-5, 5)
fpq = qsamp**2 * (norm.pdf(qsamp, loc=0, scale=1) /
uniform.pdf(qsamp, loc=-5, scale=10))
est += fpq
return est / n
def plot_uniform(min, max):
f1 = open('uniform.csv', "r")
x_uniform = f1.read().split('\n')[:-1]
x_uniform = [float(s) for s in x_uniform]
X1 = np.arange(min - 1, max + 1, 0.1)
Y1 = uniform.pdf(X1, min, max)
plt.hist(x_uniform, bins=30, density=True)
plt.plot(X1, Y1, color='r')
plt.show()
def expectation2(n):
est = 0
samples = []
for i in range(n):
qsamp = np.random.uniform(-1, 1)
fpq = qsamp**2 * (p(qsamp) / uniform.pdf(qsamp, loc=-1, scale=2))
samples.append(fpq)
est += fpq
return est / n, samples
def uniform_distribution(select_size,
loc=-m.sqrt(3),
scale=2 * m.sqrt(3),
asked=rvs,
x=0):
if asked == rvs:
return uniform.rvs(size=select_size, loc=loc, scale=scale)
elif asked == pdf:
return uniform.pdf(x, loc=loc, scale=scale)
elif asked == cdf:
return uniform.cdf(x, loc=loc, scale=scale)
def get_pdf(dist, x, df=1, loc=0, scale=1):
if dist == 'normal':
y = norm.pdf(x, loc=loc, scale=scale)
elif dist == 'uniform':
y = uniform.pdf(x, loc=loc, scale=scale)
elif dist == 'chi2':
y = chi2.pdf(x, df)
else:
print("No distribution found with name {:s}".format(dist))
y = np.zeros_like(x)
return y
def probability(self, x, log):
if self.log:
x = np.log(x)
if log:
out = np.squeeze(uniform.logpdf(x, self._min, self.scale))
return np.sum(out) if self.multivariate else out
else:
out = np.squeeze(uniform.pdf(x, self._min, self.scale))
return np.prod(out) if self.multivariate else out
def pdf(self, x):
x = np.atleast_2d(restore_X(x))
pdf = norm.pdf(x[:,0], loc=0.1, scale=0.0161812) \
* lognorm.pdf(x[:,1], s=1.0056, scale=np.exp(7.71))
lb, ub = map(list, zip(*self.domain))
lb, ub = restore_X(np.array(lb)), restore_X(np.array(ub))
for ii in range(2, self.input_dim):
bd = self.domain[ii]
pdf *= uniform.pdf(x[:,ii], lb[ii], ub[ii]-lb[ii])
return pdf / np.prod(ub-lb)
def posterior(theta, prior, ip_data):
"""
Posterior density function.
Parameters:
-----------
theta : float
Unknown (logarithm of) thermal diffusivity.
prior : array_like ([dist_type, param1, param2])
Vector defining the prior distribution through the dist_type ('normal'
or 'unif'), and two parameters (floats, mean and std for Gaussian, LHS
and range for Uniform).
ip_data : dictionary
Parameters defining the inverse problem.
Returns:
--------
posterior : nparray
Value of the (un-normalised) posterior density evaluated at the input
theta.
prior : nparray
Value of the prior density evaluated at the input theta.
likelihood : nparray
Value of the likelihood function evaluated at the input theta.
"""
# Ensure input theta is nparray.
theta = np.array(theta)
# Prior density.
if prior[0] == "unif":
p0 = Unif.pdf(theta, prior[1], prior[2]-prior[1]) # Uniform pdf
elif prior[0] == "normal":
p0 = Norm.pdf(theta, prior[1], prior[2]) # Gaussian pdf
# Single theta value.
if theta.ndim == 0:
F = uxt(ip_data['x_obs'], ip_data['t_obs'], np.exp(theta)).ravel()
L = mvNorm.pdf(F, ip_data['d'], ip_data['sig_rho'])
# Multiple theta values.
elif theta.ndim == 1:
F = uxt(ip_data['x_obs'], ip_data['t_obs'], np.exp(theta))
F = F.reshape(-1, F.shape[2])
L = np.stack([mvNorm.pdf(F[:,i], ip_data['d'], ip_data['sig_rho']) for i in range(theta.shape[0])])
# Return evaluation of the posterior, prior and likelihood.
return p0*L, p0, L
def pdf(size=1e4, a=.004, b=.01):
"""Make a grid of IFR for plotting.
Args:
size (int): Number of values in grid.
a,b (float): Parameters of the distribution U(a,b).
Returns:
np.array: Grid of x-axis.
np.array: Values of U(a,b) PDF for the grid.
"""
xgrid = np.linspace(a - (b - a) / 4, b + (b - a) / 4, num=int(size))
fx = uniform.pdf(xgrid, a, b - a)
return xgrid, fx
def compute_uniform_cdf(min_val, max_val, saving_folder):
# range of values for which CDF is computed (100 is arbitrary and should be high enough)
x_range = np.linspace(0, 50, 1000)
# Cumulative distribution function
pdf = uniform.pdf(x_range, loc=min_val, scale=(max_val - min_val))
cdf = uniform.cdf(x_range, loc=min_val, scale=(max_val - min_val))
# Storing cdf, pdf and x_range vectors together
proba_mat = np.vstack([x_range, cdf, pdf]).T
return proba_mat
def _plot_prior_posterior(self, chains, show_charts):
n_bins = int(sqrt(chains.shape[0]))
n_cols = int(self.n_param**0.5)
n_rows = n_cols + 1 if self.n_param > n_cols**2 else n_cols
subplot_shape = (n_rows, n_cols)
plt.figure(figsize=(7 * 1.61, 7))
for count, param in enumerate(list(self.params)):
mu = self.prior_info.loc[str(param)]['mean']
sigma = self.prior_info.loc[str(param)]['std']
a = self.prior_info.loc[str(param)]['param a']
b = self.prior_info.loc[str(param)]['param b']
dist = self.prior_info.loc[str(param)]['distribution']
ax = plt.subplot2grid(subplot_shape,
(count // n_cols, count % n_cols))
ax.hist(chains[str(param)],
bins=n_bins,
density=True,
color='royalblue',
edgecolor='black')
ax.set_title(self.prior_dict[param]['label'])
x_min, x_max = ax.get_xlim()
x = linspace(x_min, x_max, n_bins)
if dist == 'beta':
y = beta.pdf(x, a, b)
ax.plot(x, y, color='red')
elif dist == 'gamma':
y = gamma.pdf(x, a, scale=b)
ax.plot(x, y, color='red')
elif dist == 'invgamma':
y = (b**a) * invgamma.pdf(x, a) * exp((1 - b) / x)
ax.plot(x, y, color='red')
elif dist == 'uniform':
y = uniform.pdf(x, loc=a, scale=b - a)
ax.plot(x, y, color='red')
else: # Normal
y = norm.pdf(x, loc=mu, scale=sigma)
ax.plot(x, y, color='red')
plt.tight_layout()
if show_charts:
plt.show()
def inferPosterior(self, state, action, prior='uniform'): """ Uses inference engine to compute posterior probability from the likelihood and prior (beta distribution). """ if prior == 'beta': # Beta Distribution self.prior = np.linspace(.01,1.0,101) self.prior = beta.pdf(self.prior,1.4,1.4) self.prior /= self.prior.sum() elif prior == 'shiftExponential': # Shifted Exponential self.prior = np.zeros(101) for i in range(50): self.prior[i + 50] = i * .02 self.prior[100] = 1.0 self.prior = expon.pdf(self.prior) self.prior[0:51] = 0 self.prior *= self.prior self.prior /= self.prior.sum() elif prior == 'shiftBeta': # Shifted Beta self.prior = np.linspace(.01,1.0,101) self.prior = beta.pdf(self.prior,1.2,1.2) self.prior /= self.prior.sum() self.prior[0:51] = 0 elif prior == 'uniform': # Uniform self.prior = np.zeros(len(self.sims)) self.prior = uniform.pdf(self.prior) self.prior /= self.prior.sum() self.posterior = self.likelihood * self.prior self.posterior /= self.posterior.sum()
def inferPosterior(self, state, action): """ Uses inference engine to compute posterior probability from the likelihood and prior (beta distribution). """ # Beta Distribution # self.prior = np.linspace(.01,1.0,101) # self.prior = beta.pdf(self.prior,1.4,1.4) # self.prior /= self.prior.sum() # Shifted Exponential # self.prior = np.zeros(101) # for i in range(50): # self.prior[i + 50] = i * .02 # self.prior[100] = 1.0 # self.prior = expon.pdf(self.prior) # self.prior[0:51] = 0 # self.prior *= self.prior # self.prior /= self.prior.sum() # # Shifted Beta # self.prior = np.linspace(.01,1.0,101) # self.prior = beta.pdf(self.prior,1.2,1.2) # self.prior /= self.prior.sum() # self.prior[0:51] = 0 # Uniform self.prior = np.linspace(.01,1.0,101) self.prior = uniform.pdf(self.prior) self.prior /= self.prior.sum() self.prior[0:51] = 0 self.posterior = self.likelihood * self.prior self.posterior /= self.posterior.sum()
def build_para(self, charts=False):
home = '/home/nealbob'
folder = '/Dropbox/Thesis/STATS/chapter3/'
folder2 = '/Dropbox/Thesis/STATS/chapter2/'
folder7 = '/Dropbox/Thesis/STATS/chapter7/'
out = '/Dropbox/Thesis/IMG/chapter3/'
out7 = '/Dropbox/Thesis/IMG/chapter7/'
img_ext = '.pdf'
MDB_dams = pandas.read_csv(home + folder + 'MDB_dams.csv')
AUS_RIVERS = pandas.read_csv(home + folder + 'AUS_RIVERS.csv')
OMEGA = pandas.read_csv(home + folder7 + 'omega.csv')
#MDB_table = pandas.read_csv(home + folder + 'MDB_table.csv')
#open(home + folder + "MDB_table.tex", "w").write(MDB_table.to_latex(index=False, float_format=lambda x: '%10.1f' % x ))
################# WATER SUPPLY ################
#---------------# K - capacity
K = MDB_dams['K']
sample = (K > 50000)
K = K[sample] / 1000
bins = np.linspace(min(K), max(K), 18)
data = [K]
chart = {'OUTFILE' : (home + out + 'K' + img_ext),
'XLABEL' : 'Storage capacity (GL)',
'XMIN' : min(K),
'XMAX' : max(K),
'BINS' : bins}
if charts:
self.build_chart(chart, data, chart_type='hist')
#---------------# I_over_K - mean inflow over storage capacity
K = MDB_dams['K']
E_I = MDB_dams['mean_I']
sample = (K > 50000)
I_over_K = E_I[sample] / K[sample]
I_K_param = np.zeros(2)
I_K_param[0] = np.percentile(I_over_K, 10)
I_K_param[1] = np.percentile(I_over_K, 83)
x = np.linspace(0.2, 5, 500)
y = uniform.pdf(x, loc=I_K_param[0], scale=(I_K_param[1]-I_K_param[0]))
bins = np.linspace(min(I_over_K), 4, 18)
bins[17] = 15
data = [I_over_K, x, y]
data2 = [I_over_K]
chart = {'OUTFILE' : (home + out + 'I_over_K' + img_ext),
'XLABEL' : 'Mean annual inflow over storage capacity',
'XMIN' : 0,
'XMAX' : 4,
'BINS' : bins}
chart2 = {'OUTFILE' : (home + out + 'I_over_K_2' + img_ext),
'XLABEL' : 'Mean annual inflow over storage capacity',
'XMIN' : 0,
'XMAX' : 4,
'BINS' : bins}
if charts:
self.build_chart(chart, data, chart_type='hist')
self.build_chart(chart2, data2, chart_type='hist')
#---------------# SD_over_I - SD of inflow over mean inflow
sample = AUS_RIVERS['MAR'] < 700
SD_over_I = AUS_RIVERS['Cv'][sample]
bins = np.linspace(min(SD_over_I), max(SD_over_I), 13)
x = np.linspace(min(SD_over_I), max(SD_over_I), 500)
y = uniform.pdf(x, loc=0.43, scale=(1-0.4))
data = [SD_over_I, x, y]
data2 = [SD_over_I]
chart = {'OUTFILE' : (home + out + 'SD_over_I' + img_ext),
'XLABEL' : 'Standard deviation of annual inflow over mean',
'XMIN' : 0,
'XMAX' : max(SD_over_I),
'BINS' : bins}
chart2 = {'OUTFILE' : (home + out + 'SD_over_I_2' + img_ext),
'XLABEL' : 'Standard deviation of annual inflow over mean',
'XMIN' : 0,
'XMAX' : max(SD_over_I),
'BINS' : bins}
if charts:
self.build_chart(chart, data, chart_type='hist')
self.build_chart(chart2, data2, chart_type='hist')
#---------------# SA_over_K - surface area over capacity
SA = MDB_dams['sa']
sample = (K > 50000)
SA_over_K = SA[sample] / K[sample]
bins = np.linspace(min(SA_over_K), max(SA_over_K), 28)
SA_K_param = np.zeros(2)
SA_K_param[0] = np.percentile(SA_over_K, 10)
SA_K_param[1] = np.percentile(SA_over_K, 81.5)
x = np.linspace(min(SA_over_K), max(SA_over_K), 500)
y = uniform.pdf(x, loc=SA_K_param[0], scale=(SA_K_param[1] - SA_K_param[0]))
data = [SA_over_K, x, y]
data2 = [SA_over_K]
chart = {'OUTFILE' : (home + out + 'SA_over_K' + img_ext),
'XLABEL' : 'Storage surface area over storage capacity',
'XMIN' : min(SA_over_K),
'XMAX' : max(SA_over_K),
'BINS' : bins}
chart2 = {'OUTFILE' : (home + out + 'SA_over_K_2' + img_ext),
'XLABEL' : 'Storage surface area over storage capacity',
'XMIN' : min(SA_over_K),
'XMAX' : max(SA_over_K),
'BINS' : bins}
if charts:
self.build_chart(chart, data, chart_type='hist')
self.build_chart(chart2, data2, chart_type='hist')
#---------------# evap - net evaporation rate
evap = 0.75 * (MDB_dams['net_evap'] / 1000)
folder = '/Dropbox/Thesis/STATS/chapter3/'
evap = evap[sample]
folder = '/Dropbox/Thesis/STATS/chapter3/'
sample2 = evap > 0
evap = evap[sample2]
bins = np.linspace(min(evap), max(evap), 18)
evap_param = np.zeros(2)
evap_param[0] = np.percentile(evap, 15)
evap_param[1] = np.percentile(evap, 85)
x = np.linspace(min(evap), max(evap), 500)
y = uniform.pdf(x, loc=evap_param[0], scale=(evap_param[1]-evap_param[0]))
data = [evap, x, y]
data2 = [evap]
chart = {'OUTFILE' : (home + out + 'evap' + img_ext),
'XLABEL' : 'Average annual evaporation rate (meters)',
'XMIN' : min(evap),
'XMAX' : max(evap),
'BINS' : bins}
chart2 = {'OUTFILE' : (home + out + 'evap_2' + img_ext),
'XLABEL' : 'Average annual evaporation rate (meters)',
'XMIN' : min(evap),
'XMAX' : max(evap),
'BINS' : bins}
if charts:
self.build_chart(chart, data, chart_type='hist')
self.build_chart(chart2, data2, chart_type='hist')
#---------------# d_loss - delivery losses in irrigation areas
d_loss = np.zeros([5, 2])
Murray = pandas.read_csv(home + folder2 + 'Murray_loss.csv')
y = Murray['Loss']
N = len(y)
X = np.vstack([Murray['Pumped'], np.ones(N)]).T
d_loss[0,:] = np.linalg.lstsq(X, y)[0]
d_loss[0,1] = d_loss[0,1] / np.mean(Murray['Pumped'])
Shep = pandas.read_csv(home + folder2 + 'Shep_loss.csv')
y = Shep['Loss']
N = len(y)
X = np.vstack([Shep['Pumped'], np.ones(N)]).T
d_loss[1,:] = np.linalg.lstsq(X, y)[0]
d_loss[1,1] = d_loss[1,1] / (np.mean(Shep['Pumped']))
Jemm = pandas.read_csv(home + folder2 + 'Jemm_loss.csv')
y = Jemm['Loss']
N = len(y)
X = np.vstack([Jemm['Pumped'], np.ones(N)]).T
d_loss[2,:] = np.linalg.lstsq(X, y)[0]
d_loss[2,1] = d_loss[2,1] / (np.mean(Jemm['Pumped']))
Coll = pandas.read_csv(home + folder2 + 'Coll_loss.csv')
y = Coll['Loss']
N = len(y)
X = np.vstack([Coll['Pumped'], np.ones(N)]).T
d_loss[3,:] = np.linalg.lstsq(X, y)[0]
d_loss[3,1] = d_loss[3,1] / (np.mean(Coll['Pumped']))
MIA = pandas.read_csv(home + folder2 + 'MIA_loss.csv')
y = MIA['Loss']
N = len(y)
X = np.vstack([MIA['Pumped'], np.ones(N)]).T
d_loss[4,:] = np.linalg.lstsq(X, y)[0]
d_loss[4,1] = d_loss[4,1] / (np.mean(MIA['Pumped']))
#---------------# Inflow autocorrelation
rho_param = [0.2, 0.3]
################# WATER DEMAND ################
#---------------# Theta parameters (yield functions)
theta_mu = np.zeros([6, 2])
theta_mu[:,0] = np.array([154.7, 236.7, -35.8, 20.7, 14.9, -48.5])
#theta_mu[:,1] = np.array([-1785.4, 2545.3, -157.2, 1924.3, -537.5, -118.9])
theta_mu[:,1] = np.array([-1773.8, 2135.0, -133.3, 1597.1, -520.9, -100.8])
#clow = (41.5+14.9+231.7)*0.1
#chigh = (-76.5+2153.9-537.5)*0.1
theta_sig = np.zeros([6, 2])
#theta_sig[:,0] = np.array([0, 51.1, 16.8, 96.8, 38.8, 17.3])
#theta_sig[:,1] = np.array([0, 306.2, 22.3, 2370.1, 952.2, 151.4])
theta_sig[:,0] = np.array([0, 51.1, 16.8, 0, 0, 17.3])
theta_sig[:,1] = np.array([0, 306.2, 22.3, 0, 0, 151.4])
q_bar_limits = np.zeros([2,2])
q_bar_limits[:, 0] = np.array([0.5, 6.5])
q_bar_limits[:, 1] = np.array([5, 14])
w_ha = np.linspace(0,3,100)
profit_ha = theta_mu[0,0] + theta_mu[1,0]*w_ha + theta_mu[2,0] * w_ha**2 + theta_mu[3,0]*1 + theta_mu[4,0]*1**2 + theta_mu[5,0]*1*w_ha
data = [[w_ha, profit_ha]]
chart = {'OUTFILE' : (home + out + 'low_yield' + img_ext),
'XLABEL' : 'Water use per unit land (ML / HA)',
'XMIN' : min(w_ha),
'XMAX' : max(w_ha),
'YMIN' : 0,
'YMAX' : max(profit_ha)*1.05,
'YLABEL' : 'Profit per unit land (\$ / HA)'}
if charts:
self.build_chart(chart, data, chart_type='plot')
w_ha = np.linspace(0,9,100)
profit_ha = theta_mu[0,1] + theta_mu[1,1]*w_ha + theta_mu[2,1] * w_ha**2 + theta_mu[3,1]*1 + theta_mu[4,1]*1**2 + theta_mu[5,1]*1*w_ha
data = [[w_ha, profit_ha]]
chart = {'OUTFILE' : (home + out + 'high_yield' + img_ext),
'XLABEL' : 'Water use per unit land (ML / HA)',
'XMIN' : min(w_ha),
'XMAX' : max(w_ha),
'YMIN' : min(profit_ha)*1.5,
'YMAX' : max(profit_ha)*1.05,
'YLABEL' : 'Profit per unit land (\$ / HA)'}
if charts:
self.build_chart(chart, data, chart_type='plot')
#---------------# Epsilon parameters (yield functions)
rho_eps_param = np.array([0.3, 0.5])
sig_eta_param = np.array([0.1, 0.2])
################# Final Parameters ################
self.I_K_param = I_K_param
self.SD_I_param = np.array([0.4, 1])
self.rho_param = [0.2, 0.3]
self.SA_K_param = SA_K_param
self.evap_param = evap_param
self.d_loss_param_a = np.array([0, 0.15])
self.d_loss_param_b = np.array([0.15, 0.30])
self.theta_mu = theta_mu
self.theta_sig = theta_sig / 3
self.q_bar_limits = q_bar_limits
self.rho_eps_param = np.array([0.3, 0.5])
self.sig_eta_param = np.array([0.1, 0.2])
self.prop_high = np.array([0.05, 0.35])
self.target_price = 10 #np.array([50,200])
self.t_cost_param = np.array([10, 100])
self.Lambda_high_param = np.array([1, 2])
self.relative_risk_aversion = np.array([0, 3])
#### Summer-Winter model - chapter 7
self.ch7_param = {}
self.ch7_param['omega_mu'] = [0.55, 0.75]
self.ch7_param['omega_sig'] = [0.09, 0.12]
self.ch7_param['omega_ab'] = [0.3, 0.90]
self.ch7_param['delta_a'] = [0.02, 0.06]
self.ch7_param['omegadelta'] = [0.22, 0.36]
self.ch7_param['F_bar'] = [1, 1]
self.ch7_param['delta_b'] = [0.3, 0.6]
self.ch7_param['delta_Ea'] = [0, 0.1]
self.ch7_param['delta_Eb'] = [0.1, 0.3]
self.ch7_param['delta_R'] = [0, 0.2]
self.ch7_param['b_1'] = [0, 0.6]
self.ch7_param['b_value'] = [30, 130]
self.ch7_param['Bhat_alpha'] = [0.1, 0.5]
self.ch7_param['inflow_share'] = [0, 0.5]
self.ch7_param['capacity_share'] = [0, 0.5]
self.ch7_param['High'] = [1, 1]
self.ch7_param['e_sig'] = [0, 1]
para_dist = [self.I_K_param, self.SD_I_param, self.rho_param, self.SA_K_param, self.evap_param, self.d_loss_param_a, self.d_loss_param_b, self.t_cost_param, self.Lambda_high_param, [100, 100], [30, 70], [30, 70], self.theta_mu, self.theta_sig, self.q_bar_limits, self.rho_eps_param, self.sig_eta_param, self.prop_high, self.target_price, self.relative_risk_aversion, self.ch7_param]
with open('para_dist.pkl', 'wb') as f:
pickle.dump(para_dist, f)
f.close()
rows = ['$E[I_t]/K$', '$c_v$', '$\rho_I$' ,'$\alpha K^{2/3} / K $' , '$\delta_0$', '$\delta_{1a}$', '$\delta_{1b}$', '$\tau$', '$\Lambda_{high}$', '$n$', '$n_low$', '$n_high$', ]
cols = ['Min', 'Central case', 'Max']
n_rows = 12
data = []
for i in range(n_rows):
record = {}
record['Min'] = para_dist[i][0]
record['Central case'] = np.mean(para_dist[i])
record['Max'] = para_dist[i][1]
data.append(record)
tab = pandas.DataFrame(data)
tab.index = rows
tab_text = tab.to_latex(float_format = '{:,.2f}'.format, columns=['Min', 'Central case', 'Max' ], index=True)
with open(home + folder + "para_table.txt", "w") as f:
f.write(tab_text)
f.close()
def prior(p_in):
"""
A function to return the prior density for a given value of p.
"""
return uniform.pdf(p_in,0,1)
integrand[i] = prior_pdf[i] * likelihood(y, n_values[i])
return np.sum(integrand)
ev = evidence(Y_SEEN, n_values, prior_pdf)
# get the posterior
post_pdf = np.empty(len(n_values), dtype=float)
for i in xrange(len(n_values)):
post_pdf[i] = likelihood(Y_SEEN, n_values[i]) * prior_pdf[i] / ev
post_mean = np.int(np.round(trapz(n_values * post_pdf, n_values)))
post_stdev = np.int(np.round(np.sqrt(trapz((n_values-post_mean)**2 * post_pdf, n_values))))
print post_mean, post_stdev
# redo for non-informative prior
prior_pdf_uniform = uniform.pdf(n_values, loc=1, scale=FACT*N_MEAN)
ev = evidence(Y_SEEN, n_values, prior_pdf_uniform)
# get the posterior
post_pdf_uniform = np.empty(len(n_values), dtype=float)
for i in xrange(len(n_values)):
post_pdf_uniform[i] = likelihood(Y_SEEN, n_values[i]) * prior_pdf_uniform[i] / ev
post_mean = np.int(np.round(trapz(n_values * post_pdf_uniform, n_values)))
post_stdev = np.int(np.round(np.sqrt(trapz((n_values-post_mean)**2 * post_pdf_uniform, n_values))))
print post_mean, post_stdev
fig, axes = plt.subplots(1, 2)
plt.sca(axes[0])
plt.plot(n_values, prior_pdf, label='geometric')
def generateDistributionPlotValues(self, specification) :
sample_number = 1000
x_values = []
y_values = []
# Generate plot values from selected distribution via PDF
distribution = specification['distribution']
if distribution == 'uniform' :
lower = specification['settings']['lower']
upper = specification['settings']['upper']
base = upper - lower
incr = base/sample_number
for i in range(sample_number) :
x_values.append(lower+i*incr)
y_values = uniform.pdf(x_values, loc=lower, scale=base).tolist()
elif distribution == 'normal' :
mean = specification['settings']['mean']
std_dev = specification['settings']['std_dev']
x_min = mean - 3*std_dev
x_max = mean + 3*std_dev
incr = (x_max - x_min)/sample_number
for i in range(sample_number) :
x_values.append(x_min+i*incr)
y_values = norm.pdf(x_values, loc=mean, scale=std_dev).tolist()
elif distribution == 'triangular' :
a = specification['settings']['a']
base = specification['settings']['b'] - a
c_std = (specification['settings']['c'] - a)/base
incr = base/sample_number
for i in range(sample_number) :
x_values.append(a+i*incr)
y_values = triang.pdf(x_values, c_std, loc=a, scale=base).tolist()
elif distribution == 'lognormal' :
lower = specification['settings']['lower']
scale = specification['settings']['scale']
sigma = specification['settings']['sigma']
x_max = lognorm.isf(0.01, sigma, loc=lower, scale=scale)
incr = (x_max - lower)/sample_number
for i in range(sample_number) :
x_values.append(lower+i*incr)
y_values = lognorm.pdf(x_values, sigma, loc=lower, scale=scale).tolist()
elif distribution == 'beta' :
lower = specification['settings']['lower']
base = specification['settings']['upper'] - lower
incr = base/sample_number
for i in range(sample_number) :
x_values.append(lower+i*incr)
a = specification['settings']['alpha']
b = specification['settings']['beta']
y_values = beta.pdf(x_values, a, b, loc=lower, scale=base).tolist()
# Remove any nan/inf values
remove_indexes = []
for i in range(sample_number) :
if not np.isfinite(y_values[i]) :
remove_indexes.append(i)
for i in range(len(remove_indexes)) :
x_values = np.delete(x_values, i)
y_values = np.delete(y_values, i)
return { 'x_values' : x_values, 'y_values' : y_values }