}
"""
from bumps.names import *
from bugs.parse import load, define_pars
from bugs.model import logit, probit, cloglog, inverse, dnorm_llf, dbin_llf
# data: N=8, x[N],n[N],r[N]
vars = "x n r N".split()
_, data = load('../examples/Beetlesdata.txt')
x, n, r, N = (data[p] for p in vars)
xbar = np.mean(x)
# init: alpha.star, beta
pars = 'alpha.star,beta'.split(',')
_, init = load('../examples/Beetlesinits.txt')
p0, labels = define_pars(init, pars)
model_name = sys.argv[1] if len(sys.argv) > 1 else 'logit'
available_models = {
'logit': logit,
'probit': probit,
'cloglog': cloglog,
}
inv_p_model = inverse[available_models[model_name]]
def nllf(pars):
cost = 0
alpha_star, beta = pars
p = np.array([inv_p_model(alpha_star + beta * (xi - xbar)) for xi in x])
cost += np.sum(dbin_llf(r, p, n))
}
theta[1] ~ dnorm(0.0, 0.001)
theta[2] ~ dnorm(0.0, 0.001)
}
"""
from bumps.names import *
from bugs.parse import load, define_pars
from bugs.model import dbin_llf, dnorm_llf, logit, inverse
# J=3, y[J], n[J], Z[J], tau, alpha, beta
_, data = load('../examples/Airdata.txt')
# J = data["J"]
# theta[2], X[J]
_, init = load('../examples/Airinits.txt')
p0, labels = define_pars(init, ("theta", "X"))
def nllf(pars):
theta, X = pars[0:2], pars[2:]
p = np.array([inverse[logit](theta[0] + theta[1] * Xj) for Xj in X])
mu = data["alpha"] + data["beta"] * data["Z"]
cost = 0
cost += np.sum(dbin_llf(data["y"], p, data["n"]))
cost += np.sum(dnorm_llf(X, mu, data["tau"]))
cost += dnorm_llf(theta[0], 0.0, 0.001)
cost += dnorm_llf(theta[1], 0.0, 0.001)
return -cost
problem = DirectProblem(nllf, p0, labels=labels, dof=1)
