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()
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
# set up the data
xData = np.array([5.357, 9.861, 5.457, 5.936, 6.161, 6.731])
yData = np.array([0.376, 7.104, 0.489, 1.049, 1.327, 2.077])
# set up the parameters
params = [
Param(name='a', prior=dists.uniform(-100, 100)),
Param(name='b', prior=dists.uniform(-100, 100)),
Param(name='c', prior=dists.uniform(-100, 100)),
Param(
name='delta',
display_name=r'$\mathbf{\delta}$',
prior=dists.exp(20),
init_prior=dists.uniform(0, 10),
),
]
# set up mod
mod = Model(name='fun',
params=params,
like_fun=eval_fun,
like_args=(xData, yData),
ddat = {}
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'$L$',
left_coherence = data.at[i, 'left_coherence']
right_coherence = data.at[i, 'right_coherence']
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
nchains = 25
hyper_mu = HyperParam(name='mu',
mu=0.0,
sigma=10.0,
alpha=4,
beta=10,
nchains=nchains)
hyper_sd = HyperParam(name='sd',
mu=np.log(1.0),
sigma=1.0,
alpha=4,
beta=10,
nchains=nchains)
hparams = [hyper_mu, hyper_sd]
params = [Param(name='mu', prior=hyper_mu,), # init_prior=dists.uniform(-20,20)),
# init_prior=dists.uniform(0,20)),
Param(name='sd', prior=hyper_sd,),
]
# set up abc
models = [DEMC(params, eval_fun, eval_args=(subj_num,),
num_groups=1, group_size=nchains,
proposal_gen=DE(gamma_best=None, rand_base=True),
migration_prob=0.0, initial_zeros_ok=False,
use_priors=True, save_posts=False, verbose=False)
for subj_num in range(nsubj)]
hier = Hierarchy(hparams, models)
def eval_fun(abc, pop, *args):
res = Parallel(n_jobs=n_jobs)(delayed(eval_prop)(indiv, args[0])
for indiv in pop)
weights = np.asarray(res)
if abc._save_posts:
return weights, None
else:
return weights
# set up the parameters
params = [
Param(name='mu', prior=dists.uniform(-20, 20)),
Param(name='sd', prior=dists.uniform(0, 20)),
]
burnin = 50
iterations = 500
# set up abc
do_true = True
abc_true = DEMC(params,
eval_fun,
eval_args=(do_true, ),
num_groups=1,
group_size=25,
proposal_gen=DE(gamma_best=None, rand_base=True),
migration_prob=0.0,
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]))
for d in dat[sub]
])
for s in dat.keys():
# Append a new model, note the use of the hyperpriors
params = [
# sig_b is the sigmoid transition point
#Param(name='sig_b',
# prior=dists.uniform(0., 15.0), # change to number of tau stars
# ),
# new item strength
Param(
name='alpha',
display_name=r'$\alpha$',
prior=dists.uniform(0, 10.0),
#init_prior=dists.trunc_normal(mean=.25,std=.5,lower=0,upper=5)
),
Param(
name='nu',
display_name=r'$\nu$',
prior=dists.uniform(0, 10.0),
#init_prior=dists.trunc_normal(mean=.25,std=.5,lower=0,upper=5)
),
# threshold
Param(
name='a',
display_name=r'$a$',
prior=dists.uniform(0, 10.0),
#init_prior=dists.trunc_normal(mean=.25,std=.5,lower=0,upper=5)
),
]
r_r = list(set(list(balloon_frame['range'])))
ranges = []
for r in gg:
if r == r_r[0]:
ranges.append(0)
elif r == r_r[1]:
ranges.append(1)
else:
ranges.append(2)
ranges = np.asarray(ranges, dtype=np.int16)
# priors
params = [
Param(name='alpha',
display_name=r'$\alpha$',
prior=dists.trunc_normal(mean=0.5,
std=5.0,
lower=0,
upper=1.)),
Param(name='beta',
display_name=r'$\beta$',
prior=dists.trunc_normal(mean=5.,
std=5.,
lower=-10.,
upper=10.)),
Param(name='gamma',
display_name=r'$\gamma$',
prior=dists.trunc_normal(mean=1.0,
std=5.,
lower=0.,
upper=2.)),
Param(name='gamma_n',
# get the subject's RTs
RTs = data_sub['resp_rt']
# select RTs greater than 350 ms
RTs_x = RTs[RTs > .35]
# get minimum RT (that is greater than 350 ms) -- this is needed for t0 prior
min_RT = np.min(RTs_x)
print('*** subject ', s)
# 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',
# all proposals
log_like = -0.5 * np.sum(np.log(2 * np.pi * sigma[:, np.newaxis]**2) +
(ydata - y_model)**2 / sigma[:, np.newaxis]**2,
axis=1)
return log_like
# set up the parameters
gsize = None # None will let model figure out a good number
# Fixed slope across participants
# Using a custom uniform prior
beta = Param(name='beta',
display_name=r'$\beta$',
prior=dists.CustomDist(
pdf=lambda x: np.exp(-1.5 * np.log(1 + x**2)),
rvs=dists.laplace(0, 5).rvs))
# Fixed noise across subjects
# Using a custom Jeffreys' prior
sigma = Param(name='sigma',
display_name=r'$\sigma$',
prior=dists.CustomDist(pdf=lambda x: np.exp(-np.log(x)),
rvs=dists.dists.invgamma(1, 1).rvs))
# Hyperprior over intercept using a normal distribution
halpha = HyperPrior('alpha',
dists.normal,
params=[
Param(name='mu', prior=dists.uniform(-50, 50)),
Param(name='sig', prior=dists.invgamma(1, 1))
