def eval_fun(pop, *args):
# errors = []
# for indiv in pop:
# # inverse exponential with offset, y = a * exp(b/x) + c
# predicted = (indiv[0] * np.exp(indiv[1] / args[0]) + indiv[2])
# errors.append(predicted - args[1])
# evaluate the population with some broadcasting
pred = (pop[:, 0][:, np.newaxis] *
np.exp(pop[:, 1][:, np.newaxis] / args[0][np.newaxis, :]) +
pop[:, 2][:, np.newaxis])
errors = pred - args[1][np.newaxis, :]
# sum of squared error
# errors = np.asarray(errors)
sse = np.sum(errors * errors, 1)
# sae = np.sum(np.abs(errors),1)
# calculate the weight with a normal kernel
weights = np.log(dists.normal(mean=0.0, std=pop[:, 3]).pdf(sse))
# see if return both weights and predicted vals
if save_posts:
return weights, pred
else:
return weights
def eval_prop(indiv, subj_id):
# get the true pdf for those params
mod = dists.normal(indiv[0], np.exp(indiv[1]))
pdf = mod.pdf(data[subj_id]['obs'])
if np.any(pdf == 0):
return -np.inf
weight = np.log(pdf).sum()
return weight
def eval_prop(indiv, subj_id):
# get the true pdf for those params
mod = dists.normal(indiv[0],np.exp(indiv[1]))
pdf = mod.pdf(data[subj_id]['obs'])
if np.any(pdf==0):
return -np.inf
weight = np.log(pdf).sum()
return weight
def eval_prop(indiv, do_true=False):
mod = dists.normal(indiv[0], indiv[1])
if do_true:
pdf = mod.pdf(data)
else:
mdat = mod.rvs(nsamps)
pdf, xx = kdensity(mdat, xx=data, nbins=2000, kernel="epanechnikov")
if np.any(pdf == 0):
return -np.inf
weight = np.log(pdf).sum()
return weight
def eval_prop(indiv, do_true=False):
mod = dists.normal(indiv[0], indiv[1])
if do_true:
pdf = mod.pdf(data)
else:
mdat = mod.rvs(nsamps)
pdf, xx = kdensity(mdat, xx=data, nbins=2000, kernel="epanechnikov")
if np.any(pdf == 0):
return -np.inf
weight = np.log(pdf).sum()
return weight
def mmi_model_Mood_LTA_gamma_wo_RT_p0_beta(subj_input_dir,subj_out_dir,sid):
# import some useful libraries
import numpy as np # numerical analysis linear algebra
import pandas as pd # efficient tables
#import matplotlib.pyplot as plt # plotting
from scipy import stats
from RunDEMC.density import kdensity
from RunDEMC import Model, Param, dists, calc_bpic, joint_plot
from mmi_mood_LTA_gamma_wo_RT_p0_beta import MMIModel, load_mmi_data
from joblib import Parallel, delayed
import pickle
from pathlib import Path
try:
import scoop
from scoop import futures
except ImportError:
print("Error loading scoop, reverting to joblib.")
scoop = None
# ## Load and examine data
subj_input_dir=Path(subj_input_dir)
subj_out_dir=Path(subj_out_dir)
pattern=f'*{sid}*.xlsx'
input_file=list(subj_input_dir.glob(pattern))
print(input_file[0])
dat = load_mmi_data(input_file[0])
# In[4]:
#dat.at[2, 'Choice']=='Gamble'
# In[5]:
# find the minimum RT for the param range
min_RT = dat.loc[dat.RT>0, 'RT'].min()
print('Min RT:', min_RT)
# ## Use RunDEMC to fit the model to a participant's data
# define model evaluation functions for RunDEMC
def eval_mod(params, param_names, bdat=None):
# use global dat if none based in
if bdat is None:
bdat = dat
# turn param list into dict
mod_params = {x: params[n]
for n, x in enumerate(param_names)}
# try:
# print(mod_params['lambda'])
# except:
# print("Problems")
if mod_params['lambda']<0 or mod_params['lambda']>=1 :
return np.log(0), np.log(0)
if mod_params['gamma']<0 or mod_params['gamma']>=np.inf :
return np.log(0), np.log(0)
# if mod_params['beta']<0 or mod_params['beta']>1 :
# return np.log(0), np.log(0)
# if mod_params['p0']<0 or mod_params['p0']>1 :
# return np.log(0), np.log(0)
if mod_params['w_LTA']<0 or mod_params['w_LTA']>=np.inf :
return np.log(0), np.log(0)
if mod_params['w_RPE']<0 or mod_params['w_RPE']>=np.inf :
return np.log(0), np.log(0)
if mod_params['b']<=-np.inf or mod_params['b']>=np.inf :
return np.log(0), np.log(0)
if mod_params['s_v']<=0 or mod_params['s_v']>=np.inf :
return np.log(0), np.log(0)
if mod_params['c']<0 or mod_params['c']>=np.inf :
return np.log(0), np.log(0)
## calculate the log_likes and mood_log_likes
mod_res = MMIModel(params=mod_params,
ignore_non_resp=True).proc_trials(bdat.copy())
ll = mod_res.log_like.sum()
mood_ll = mod_res.mood_log_like.sum()
return ll,mood_ll
# this is the required def for RunDEMC
def eval_fun(pop, *args):
bdat = args[0]
pnames = args[1]
if scoop and scoop.IS_RUNNING:
res_tups = list(futures.map(eval_mod, [indiv for indiv in pop],
[pnames]*len(pop), [bdat]*len(pop)))
else:
res_tups= Parallel(n_jobs=-1)(delayed(eval_mod)(indiv,pnames, bdat)
for indiv in pop)
likes = np.array([rt[0] for rt in res_tups])
mood_likes = np.array([rt[1] for rt in res_tups])
return likes, mood_likes
def get_best_fit(m, burnin=250, verbose=True):
best_ind = m.weights[burnin:].argmax()
if verbose:
print("Weight:", m.weights[burnin:].ravel()[best_ind])
indiv = [m.particles[burnin:,:,i].ravel()[best_ind]
for i in range(m.particles.shape[-1])]
pp = {}
for p,v in zip(m.param_names,indiv):
pp[p] = v
if verbose:
print('"%s": %f,'%(p,v))
return pp
# ### Base model
# In[20]:
# set up model params
params = [Param(name='gamma',
display_name=r'$\gamma$',
prior=dists.gamma(1.5, 0.5),
),
Param(name='c',
display_name=r'$c$',
prior=dists.gamma(1.5, 0.5),
),
# Param(name='beta',
# display_name=r'$\beta$',
# prior=dists.normal(0, 1.4),
# transform=dists.invlogit
# ),
# Param(name='w',
# display_name=r'$w$',
# prior=dists.normal(0, 1.4),
# transform=dists.invlogit
# ),
# Param(name='a',
# display_name=r'$a$',
# prior=dists.gamma(2.0, 0.5),
# ),
# Param(name='t0',
# display_name=r'$t_0$',
# prior=dists.normal(0, 1.4),
# transform=lambda x: dists.invlogit(x)*min_RT,
# ),
# Param(name='p0',
# display_name=r'$p_0$',
# prior=dists.normal(0, 1.4),
# transform=dists.invlogit
# ),
Param(name='lambda',
display_name=r'$lambda',
prior=dists.normal(0, 1.4),
transform=dists.invlogit
),
# Param(name='lambda',
# display_name=r'$lambda',
# prior=dists.beta(0.5, 0.5)
# ),
Param(name='w_LTA',
display_name=r'w_{LTA}',
prior=dists.normal(0, 1),
transform=np.exp,
inv_transform=np.log),
# Param(name='w_EG',
# display_name=r'w_{EG}',
# prior=dists.normal(0, 1),
# transform=np.exp,
# inv_transform=np.log),
Param(name='w_RPE',
display_name=r'w_{RPE}',
prior=dists.normal(0, 1),
transform=np.exp,
inv_transform=np.log),
Param(name='b',
display_name=r'b',
prior=dists.normal(0, 3)),
Param(name='s_v',
display_name=r's_v',
prior=dists.exp(3))
]
# grab the param names
pnames = [p.name for p in params]
m = Model('mmi', params=params,
like_fun=eval_fun,
like_args=(dat, pnames),
init_multiplier=3,
# num_chains=gsize,
verbose=True)
# do some burnin
times = m.sample(150, burnin=True)
# now map the posterior
times = m.sample(650, burnin=False)
# show the chains are mixing and converging
#plt.plot(m.weights[30:], alpha=.3);
pickle_name=subj_out_dir / f'mWgt_{sid}.pickle'
print(pickle_name)
pickle_out = open(pickle_name,"wb")
pickle.dump(m.weights, pickle_out)
pickle_out.close()
#print("Best fitting params:")
#pp = get_best_fit(m, burnin=250, verbose=True)
print("Best fitting params:")
pp = get_best_fit(m, burnin=250, verbose=True)
pickle_name=subj_out_dir / f'mBFprm_{sid}.pickle'
print(pickle_name)
pickle_out = open(pickle_name,"wb")
pickle.dump(pp, pickle_out)
pickle_out.close()
# In[42]:
#### BPIC calculations
burnin=250
log_like_prior = m.weights - m.log_likes
#print(log_like_prior)
weight_mood = m.posts + log_like_prior #m.posts is log_like_Mood
#print(weight_mood)
print("Mood_BPIC :",calc_bpic(weight_mood[burnin:])['bpic'])
Mood_BPIC=calc_bpic(weight_mood[burnin:])['bpic']
pickle_name=subj_out_dir / f'Mood_BPIC_{sid}.pickle'
print(pickle_name)
pickle_out = open(pickle_name,"wb")
pickle.dump(Mood_BPIC, pickle_out)
pickle_out.close()
log_like_RT = m.log_likes - m.posts
weight_RT = log_like_RT + log_like_prior
print("RT_BPIC :",calc_bpic(weight_RT[burnin:])['bpic'])
RT_BPIC=calc_bpic(weight_RT[burnin:])['bpic']
pickle_name=subj_out_dir / f'RT_BPIC_{sid}.pickle'
print(pickle_name)
pickle_out = open(pickle_name,"wb")
pickle.dump(RT_BPIC, pickle_out)
pickle_out.close()
print(calc_bpic(m.weights[burnin:])['bpic'])
mBPIC=calc_bpic(m.weights[burnin:])['bpic']
pickle_name=subj_out_dir / f'Total_BPIC_{sid}.pickle'
print(pickle_name)
pickle_out = open(pickle_name,"wb")
pickle.dump(mBPIC, pickle_out)
pickle_out.close()
# In[46]:
# plot the param distributions (note, we did not get full posteriors, yet)
# plt.figure(figsize=(12,10))
# burnin=30
# for i in range(len(m.param_names)):
# plt.subplot(3,4,i+1)
# plt.hist(m.particles[burnin:, :, i].flatten(), bins='auto', alpha=.5, density=True);
# plt.title(m.param_names[i])
# In[ ]:
pickle_name=subj_out_dir / f'mParticles_{sid}.pickle'
print(pickle_name)
pickle_out = open(pickle_name,"wb")
pickle.dump(m.particles, pickle_out)
pickle_out.close()
pickle_name=subj_out_dir / f'mParams_{sid}.pickle'
print(pickle_name)
pickle_out = open(pickle_name,"wb")
pickle.dump(m.param_names, pickle_out)
pickle_out.close()
if left_coherence > right_coherence:
data.at[i, 'coherence'] = str(right_coherence) + ', ' + str(
left_coherence)
elif right_coherence >= left_coherence:
data.at[i, 'coherence'] = str(left_coherence) + ', ' + str(
right_coherence)
# loop through each participant
for s in data.subj.unique():
subj_ind = data['subj'] == s
min_rt = data[subj_ind]['rt'].min()
# set up the params
params = [
Param(name='a',
prior=dists.trunc_normal(5.0, 20.0, lower=0.0, upper=50.0)),
Param(name='b', prior=dists.normal(0.0, 5.0)),
Param(name='c',
prior=dists.trunc_normal(5.0, 10.0, lower=0.0, upper=30.0)),
Param(name='kappa',
prior=dists.normal(0.0, 1.4),
transform=dists.invlogit),
Param(name='beta',
prior=dists.normal(0.0, 1.4),
transform=dists.invlogit),
Param(name='alpha',
prior=dists.trunc_normal(2.5, 10.0, lower=0.0, upper=30.0)),
Param(name='t0', prior=dists.uniform(0., min_rt))
]
pnames = [p.name for p in params]
# instantiate model object
m = Model('urdm_lca',
for c in ['+', '=', '~']:
ind = (dat.condition == c) & (dat.rt < max_rt)
d = {
'rt': np.log(np.array(dat[ind].rt) + log_shift),
'resp': np.array(~dat[ind]['correct'], dtype=np.int)
}
ddat[c] = d
# store minimum RT
min_rt = dat[(dat['rt'] >= 0.)]['rt'].min()
# define priors
params = [
Param(name='r',
display_name=r'$r$',
prior=dists.normal(-2.0, 1.0),
transform=lambda x: dists.invlogit(x) * (20. - 0.) + (0.)),
Param(name='p',
display_name=r'$p$',
prior=dists.normal(-0.8, 1.2),
transform=lambda x: dists.invlogit(x) * (20. - 0.) + (0.)),
Param(name='sd0',
display_name=r'$\sigma_0$',
prior=dists.normal(-1.0, 1.2),
transform=lambda x: dists.invlogit(x) * (30. - 0.1) + (0.1)),
Param(name='K',
display_name=r'$K$',
prior=dists.normal(0.0, 1.4),
transform=dists.invlogit),
Param(name='L',
display_name=r'$L$',
import numpy as np
from RunDEMC import RunDEMC, Param, dists
from RunDEMC import DE
from RunDEMC import joint_plot, violin_plot
from RunDEMC.density import kdensity
from joblib import Parallel, delayed
import pylab as pl
n_jobs = 2
nsamps = 20000
ndat = 1000
xx = np.linspace(-10, 10, nsamps)
mu = 1.0
sd = 2.0
dmod = dists.normal(mu, sd)
data = dmod.rvs(ndat)
def eval_prop(indiv, do_true=False):
mod = dists.normal(indiv[0], indiv[1])
if do_true:
pdf = mod.pdf(data)
else:
mdat = mod.rvs(nsamps)
pdf, xx = kdensity(mdat, xx=data, nbins=2000, kernel="epanechnikov")
if np.any(pdf == 0):
return -np.inf
weight = np.log(pdf).sum()
return weight
import numpy as np
from RunDEMC import RunDEMC, Param, dists
from RunDEMC import DE
from RunDEMC import joint_plot, violin_plot
from RunDEMC.density import kdensity
from joblib import Parallel, delayed
import pylab as pl
n_jobs = 2
nsamps = 20000
ndat = 1000
xx = np.linspace(-10, 10, nsamps)
mu = 1.0
sd = 2.0
dmod = dists.normal(mu, sd)
data = dmod.rvs(ndat)
def eval_prop(indiv, do_true=False):
mod = dists.normal(indiv[0], indiv[1])
if do_true:
pdf = mod.pdf(data)
else:
mdat = mod.rvs(nsamps)
pdf, xx = kdensity(mdat, xx=data, nbins=2000, kernel="epanechnikov")
if np.any(pdf == 0):
return -np.inf
weight = np.log(pdf).sum()
return weight
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
from RunDEMC import RunDEMC, Param, dists
from RunDEMC import DE
from RunDEMC.hierarchy import Hierarchy, HyperParam
import numpy as np
from joblib import Parallel, delayed
# generate the data
n_jobs = 1
nsubj = 4
nobs = 1000
mu = 1.0
sigma = .5
dmod_mean = dists.normal(mu, sigma)
alpha = 4
beta = 10
dmod_std = dists.invgamma(alpha, beta)
data = {}
for s in range(nsubj):
# draw a mean and std from hypers
smean = dmod_mean.rvs()
sstd = np.sqrt(dmod_std.rvs())
dmod = dists.normal(smean, sstd)
data[s] = {'mean': smean,
'std': sstd,
'obs': dmod.rvs(nobs)}
# set up model evaluation
pdf will randomly pick from hyperparam chains and provide the pdf from
the supplied distribution.
log_prior: convenience method for looping over params for a proposal
and calling each param's pdf to get the log_like for that param.
"""
from RunDEMC import Model, HyperPrior, Hierarchy, Param, dists
# set up the hyper priors
h_alpha = HyperPrior(name='h_alpha',
dist=dists.normal,
params=[
Param(name='mu', prior=dists.normal(1, .5)),
Param(name='sigma', prior=dists.invgamma(4, 10))
])
h_beta = HyperPrior(name='h_beta',
dist=dists.normal,
params=[
Param(name='mu', prior=dists.normal(1, .5)),
Param(name='sigma', prior=dists.invgamma(4, 10))
])
# set up lower level (i.e., subject)
def subj_like(pop, *args):
return np.log(dists.beta(pop[:, 0], pop[:, 1]).pdf(args[0]))
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
from RunDEMC import RunDEMC, Param, dists
from RunDEMC import DE
from RunDEMC.hierarchy import Hierarchy,HyperParam
import numpy as np
from joblib import Parallel, delayed
# generate the data
n_jobs = 1
nsubj = 4
nobs = 1000
mu=1.0
sigma=.5
dmod_mean = dists.normal(mu,sigma)
alpha=4
beta=10
dmod_std = dists.invgamma(alpha,beta)
data = {}
for s in range(nsubj):
# draw a mean and std from hypers
smean = dmod_mean.rvs()
sstd = np.sqrt(dmod_std.rvs())
dmod = dists.normal(smean,sstd)
data[s] = {'mean': smean,
'std': sstd,
'obs': dmod.rvs(nobs)}
# set up model evaluation
def eval_prop(indiv, subj_id):
pdf will randomly pick from hyperparam chains and provide the pdf from
the supplied distribution.
log_prior: convenience method for looping over params for a proposal
and calling each param's pdf to get the log_like for that param.
"""
from RunDEMC import Model, HyperPrior, Hierarchy, Param, dists
# set up the hyper priors
h_alpha = HyperPrior(name='h_alpha',
dist=dists.normal,
params=[Param(name='mu', prior=dists.normal(1,.5)),
Param(name='sigma', prior=dists.invgamma(4,10))])
h_beta = HyperPrior(name='h_beta',
dist=dists.normal,
params=[Param(name='mu', prior=dists.normal(1,.5)),
Param(name='sigma', prior=dists.invgamma(4,10))])
# set up lower level (i.e., subject)
def subj_like(pop, *args):
return np.log(dists.beta(pop[:,0],pop[:,1]).pdf(args[0]))
submods = [Model(name='subj_%s'%s,
params=[Param(name='alpha', prior=h_alpha),
Param(name='beta', prior=h_beta)],
like_fun=subj_like,
# get name of output file
out_file = 'cab_' + s[:-4] + '.tgz'
# define model parameters and priors
params = [
Param(name='lambda',
display_name=r'$\lambda$',
prior=dists.trunc_normal(.5, 2, 0, 5)),
#
Param(name='alpha',
display_name=r'$\alpha$',
prior=dists.trunc_normal(1., 4, 0, 10)),
Param(name='omega',
display_name=r'$\omega$',
prior=dists.normal(mean=0, std=1.4),
transform=dists.invlogit),
Param(
name='delta',
display_name=r'$\delta$',
prior=dists.trunc_normal(1., 10, 0, 20.0),
),
Param(name='sigma',
display_name=r'$\sigma$',
prior=dists.normal(mean=0, std=1.4),
transform=dists.invlogit),
Param(
name='nu',
display_name=r'$\nu$',
prior=dists.trunc_normal(mean=2., std=10., lower=0., upper=10.),
),
'xdata': xdata,
'ydata': ydata,
'alpha': alpha,
'beta': beta,
'sigma': sigma
}
# generate data
nsubj = 5
alpha_sd = 10
# only across-subject variability is intercept
data = []
for i in range(nsubj):
alpha = dists.normal(theta_true[0], alpha_sd).rvs()
data.append(gen_subj_data(alpha))
##################
# Set up the Model
##################
# define the evaluation function
def subj_like(pop, *args):
alpha, beta, sigma = (pop[:, 0], pop[:, 1], pop[:, 2])
xdata = args[0]['xdata']
ydata = args[0]['ydata']
y_model = (alpha + beta * xdata[:, np.newaxis]).T