def test_null_pem_model(**kwargs):
''' Test weibull survival model on simulated dataset
'''
d = load_test_dataset(n=20)
dlong = survivalstan.prep_data_long_surv(df=d, time_col='t', event_col='event')
testfit = survivalstan.fit_stan_survival_model(
model_cohort = 'test model',
model_code = model_code,
df = dlong,
sample_col = 'index',
timepoint_end_col = 'end_time',
event_col = 'end_failure',
formula = '~ 1',
iter = num_iter,
chains = 2,
seed = 9001,
make_inits = make_inits,
FIT_FUN = stancache.cached_stan_fit,
**kwargs
)
ok_('fit' in testfit)
ok_('coefs' in testfit)
ok_('loo' in testfit)
survivalstan.utils.plot_coefs([testfit])
survivalstan.utils.plot_coefs([testfit], trans=np.exp)
survivalstan.utils.plot_coefs([testfit], element='baseline')
survivalstan.utils.plot_pp_survival([testfit])
survivalstan.utils.plot_observed_survival(df=d, time_col='t', event_col='event')
fitsum = survivalstan.utils.filter_stan_summary([testfit], pars='baseline')
fitsum = survivalstan.utils.filter_stan_summary(testfit['fit'], remove_nan=True)
survivalstan.utils.print_stan_summary([testfit], pars='lp__')
survivalstan.utils.plot_stan_summary([testfit], pars='log_baseline_raw')
return(testfit)
def load_test_dataset_long(n=20):
''' Load test dataset from R survival package
'''
d = load_test_dataset(n=n)
dlong = survivalstan.prep_data_long_surv(d,
time_col='t',
event_col='event')
return dlong
def sim_test_dataset_long(n=200):
data = survivalstan.sim.sim_data_jointmodel(N=n)
ldf = survivalstan.prep_data_long_surv(data['events'],
event_col='event_value',
event_name='event_name',
time_col='time',
sample_col='subject_id')
ldf = pd.merge(ldf, data['covars'], on='subject_id', how='outer')
return (ldf)
def sim_test_dataset_long(n=200):
data = survivalstan.sim.sim_data_jointmodel(N=n)
ldf = survivalstan.prep_data_long_surv(data['events'],
event_col='event_value',
event_name='event_name',
time_col='time',
sample_col='subject_id')
ldf = pd.merge(ldf, data['covars'], on='subject_id', how='outer')
return(ldf)
def sim_test_dataset_long(n=20):
d = sim_test_dataset(n=n)
dlong = survivalstan.prep_data_long_surv(d, time_col='t', event_col='event')
return dlong
def load_test_dataset_long(n=20):
''' Load test dataset from R survival package
'''
d = load_test_dataset(n=n)
dlong = survivalstan.prep_data_long_surv(d, time_col='t', event_col='event')
return dlong
def sim_test_dataset_long(n=20):
d = sim_test_dataset(n=n)
dlong = survivalstan.prep_data_long_surv(d,
time_col='t',
event_col='event')
return dlong