Python fit_stan_survival_model示例

示例#1

文件： test_pem_survival_model.py 项目： jonsjoberg/survivalstan

def test_pem_model(**kwargs):
    ''' Test weibull survival model on simulated dataset
    '''
    d = load_test_dataset(n=20)
    dlong = load_test_dataset_long()
    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='~ age + sex',
        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')
    return (testfit)

示例#2

文件： test_pem_survival_model.py 项目： hammerlab/survivalstan

def test_pem_model(**kwargs):
    ''' Test weibull survival model on simulated dataset
    '''
    d = load_test_dataset(n=20)
    dlong = load_test_dataset_long()
    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 = '~ age + sex',
        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')
    return(testfit)

示例#3

文件： test_pem_survival_model_varcoefs.py 项目： hammerlab/survivalstan

def test_pem_null_model(force=True, **kwargs):
    ''' Test NULL survival model on flchain dataset
    '''
    dlong = load_test_dataset_long()
    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',
        group_col = 'sex',
        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], trans=np.exp, element='grp_coefs')
    survivalstan.utils.plot_coefs([testfit], element='baseline')
    return(testfit)

示例#4

文件： test_pem_survival_model_timevarying_sim.py 项目： zeta1999/survivalstan

def test_pem_null_model(force=True, **kwargs):
    ''' Test NULL survival model on flchain dataset
    '''
    dlong = sim_test_dataset_long()
    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], trans=np.exp, element='grp_coefs')
    survivalstan.utils.plot_coefs([testfit], element='baseline')
    survivalstan.utils.plot_pp_survival([testfit])
    return (testfit)

示例#5

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)

示例#6

文件： test_pem_survival_model_timevarying.py 项目： hammerlab/survivalstan

def test_pem_model(**kwargs):
    ''' Test survival model on test dataset
    '''
    dlong = load_test_dataset_long()
    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 = '~ age + sex',
        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], trans=np.exp, element='grp_coefs')
    survivalstan.utils.plot_coefs([testfit], element='baseline')
    survivalstan.utils.plot_coefs([testfit], element='beta_time')
    survivalstan.utils.plot_coefs([testfit], element='beta_time', trans=np.exp)
    survivalstan.utils.plot_pp_survival([testfit])
    survivalstan.utils.plot_time_betas(models=[testfit], y='beta', x='end_time', coefs=[testfit['x_names'][0]])
    survivalstan.utils.plot_time_betas(models=[testfit], y='exp(beta)')
    survivalstan.utils.plot_time_betas(models=[testfit], y='exp(beta)', ylim=[0, 4])
    first_beta = survivalstan.utils.extract_time_betas([testfit], coefs=[testfit['x_names'][0]])
    survivalstan.utils.plot_time_betas(df=first_beta, by=['coef'], y='beta', x='end_time')
    return(testfit) 

示例#7

def test_pem_model(**kwargs):
    ''' Test survival model on test dataset
    '''
    dlong = load_test_dataset_long()
    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='~ age + sex',
        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], trans=np.exp, element='grp_coefs')
    survivalstan.utils.plot_coefs([testfit], element='baseline')
    survivalstan.utils.plot_coefs([testfit], element='beta_time')
    survivalstan.utils.plot_coefs([testfit], element='beta_time', trans=np.exp)
    survivalstan.utils.plot_pp_survival([testfit])
    survivalstan.utils.plot_time_betas(models=[testfit],
                                       y='beta',
                                       x='end_time',
                                       coefs=[testfit['x_names'][0]])
    survivalstan.utils.plot_time_betas(models=[testfit], y='exp(beta)')
    survivalstan.utils.plot_time_betas(models=[testfit],
                                       y='exp(beta)',
                                       ylim=[0, 4])
    first_beta = survivalstan.utils.extract_time_betas(
        [testfit], coefs=[testfit['x_names'][0]])
    survivalstan.utils.plot_time_betas(df=first_beta,
                                       by=['coef'],
                                       y='beta',
                                       x='end_time')
    return (testfit)

示例#8

文件： test_pem_survival_model_sim.py 项目： hammerlab/survivalstan

def test_pem_model_sim_covar_with_form():
    dlong = sim_test_dataset_long()
    testfit = survivalstan.fit_stan_survival_model(
        model_cohort = 'test model',
        model_code = model_code,
        df = dlong,
        formula = 'surv(event_status=end_failure, time=end_time, subject=index) ~ age + sex',
        iter = num_iter,
        chains = 2,
        seed = 9001,
        make_inits = make_inits,
        FIT_FUN = stancache.cached_stan_fit,
        )
    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')
    return(testfit)

示例#9

文件： test_exp_survival_model.py 项目： zeta1999/survivalstan

def test_model_with_formula():
    ''' Test survival model using `surv` syntax
    '''
    d = load_test_dataset()
    testfit = survivalstan.fit_stan_survival_model(
        model_cohort = 'test model',
        model_code = model_code,
        df = d,
        formula = 'surv(event_status=event, time=t) ~ age + sex',
        iter = num_iter,
        chains = 2,
        seed = 9001,
        make_inits = make_inits,
        FIT_FUN = stancache.cached_stan_fit,
        )
    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)
    return(testfit)

示例#10

def test_pem_model_sim_covar_with_form():
    dlong = sim_test_dataset_long()
    testfit = survivalstan.fit_stan_survival_model(
        model_cohort='test model',
        model_code=model_code,
        df=dlong,
        formula=
        'surv(event_status=end_failure, time=end_time, subject=index) ~ age + sex',
        iter=num_iter,
        chains=2,
        seed=9001,
        make_inits=make_inits,
        FIT_FUN=stancache.cached_stan_fit,
    )
    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')
    return (testfit)

示例#11

def test_model(**kwargs):
    ''' Test weibull survival model on simulated dataset
    '''
    d = sim_test_dataset()
    testfit = survivalstan.fit_stan_survival_model(
        model_cohort='test model',
        model_code=model_code,
        df=d,
        time_col='t',
        event_col='event',
        formula='~ age + sex',
        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)
    return (testfit)

示例#12

def test_null_model(**kwargs):
    ''' Test NULL survival model on flchain dataset
    '''
    d = load_test_dataset()
    testfit = survivalstan.fit_stan_survival_model(
        model_cohort='test model',
        model_code=model_code,
        df=d,
        time_col='t',
        event_col='event',
        formula='~ 1',
        iter=num_iter,
        chains=2,
        seed=9001,
        make_inits=make_inits,
        FIT_FUN=stancache.cached_stan_fit,
        drop_intercept=False,
        **kwargs)
    ok_('fit' in testfit)
    ok_('coefs' in testfit)
    survivalstan.utils.plot_coefs([testfit])
    survivalstan.utils.plot_coefs([testfit], trans=np.exp)
    return (testfit)

示例#13

文件： test_exp_survival_model.py 项目： hammerlab/survivalstan

def test_null_model(**kwargs):
    ''' Test NULL survival model on flchain dataset
    '''
    d = load_test_dataset()
    testfit = survivalstan.fit_stan_survival_model(
        model_cohort = 'test model',
        model_code = model_code,
        df = d,
        time_col = 't',
        event_col = 'event',
        formula = '~ 1',
        iter = num_iter,
        chains = 2,
        seed = 9001,
        make_inits = make_inits,
        FIT_FUN = stancache.cached_stan_fit,
        )
    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)
    return(testfit)

示例#14

文件： test_byo-gamma_survival_model_sim.py 项目： hammerlab/survivalstan

def test_model(**kwargs):
    ''' Test weibull survival model on simulated dataset
    '''
    d = sim_test_dataset()
    testfit = survivalstan.fit_stan_survival_model(
        model_cohort = 'test model',
        model_code = model_code,
        df = d,
        time_col = 't',
        event_col = 'event',
        formula = '~ age + sex',
        iter = num_iter,
        chains = 2,
        seed = 9001,
        make_inits = make_inits,
        FIT_FUN = stancache.cached_stan_fit,
        drop_intercept = False,
        **kwargs
        )
    ok_('fit' in testfit)
    ok_('coefs' in testfit)
    survivalstan.utils.plot_coefs([testfit])
    survivalstan.utils.plot_coefs([testfit], trans=np.exp)
    return(testfit)