SYMBOL INDEX (255 symbols across 11 files)

FILE: IOHMM/IOHMM.py
  class LinearModelLoader (line 47) | class LinearModelLoader(object):
  class BaseIOHMM (line 59) | class BaseIOHMM(object):
    method __init__ (line 65) | def __init__(self, num_states=2):
    method set_models (line 75) | def set_models(self, model_emissions,
    method set_inputs (line 116) | def set_inputs(self, covariates_initial, covariates_transition, covari...
    method set_outputs (line 136) | def set_outputs(self, responses_emissions):
    method set_data (line 153) | def set_data(self, dfs):
    method _initialize (line 166) | def _initialize(self, with_randomness=True):
    method E_step (line 320) | def E_step(self):
    method M_step (line 359) | def M_step(self):
    method train (line 393) | def train(self):
    method to_json (line 410) | def to_json(self, path):
    method _from_setup (line 442) | def _from_setup(
    method from_config (line 497) | def from_config(cls, json_dict):
    method from_json (line 526) | def from_json(cls, json_dict):
  class UnSupervisedIOHMM (line 557) | class UnSupervisedIOHMM(BaseIOHMM):
    method __init__ (line 563) | def __init__(self, num_states=2, EM_tol=1e-4, max_EM_iter=100):
    method set_data (line 577) | def set_data(self, dfs):
    method to_json (line 600) | def to_json(self, path):
    method _from_setup (line 620) | def _from_setup(
  class SemiSupervisedIOHMM (line 678) | class SemiSupervisedIOHMM(UnSupervisedIOHMM):
    method set_data (line 685) | def set_data(self, dfs_states):
  class SupervisedIOHMM (line 709) | class SupervisedIOHMM(BaseIOHMM):
    method __init__ (line 716) | def __init__(self, num_states=2):
    method set_data (line 728) | def set_data(self, dfs_states):

FILE: IOHMM/forward_backward.py
  function forward_backward (line 26) | def forward_backward(log_prob_initial, log_prob_transition, log_Ey, log_...
  function forward (line 64) | def forward(log_prob_initial, log_prob_transition, log_Ey, log_state={}):
  function backward (line 112) | def backward(log_prob_transition, log_Ey, log_state={}):
  function cal_log_likelihood (line 150) | def cal_log_likelihood(log_alpha):
  function cal_log_gamma (line 166) | def cal_log_gamma(log_alpha, log_beta, log_likelihood, log_state={}):
  function cal_log_epsilon (line 197) | def cal_log_epsilon(log_prob_transition, log_Ey, log_alpha, log_beta, lo...

FILE: IOHMM/linear_models.py
  class BaseModel (line 65) | class BaseModel(object):
    method __init__ (line 71) | def __init__(self,
    method fit (line 110) | def fit(self, X, Y, sample_weight=None):
    method _raise_error_if_model_not_trained (line 122) | def _raise_error_if_model_not_trained(self):
    method _raise_error_if_sample_weight_sum_zero (line 130) | def _raise_error_if_sample_weight_sum_zero(self, sample_weight):
    method _transform_X (line 139) | def _transform_X(self, X):
    method _transform_sample_weight (line 152) | def _transform_sample_weight(self, X, sample_weight=None):
    method _transform_X_sample_weight (line 169) | def _transform_X_sample_weight(self, X, sample_weight=None):
    method predict (line 184) | def predict(self, X):
    method loglike_per_sample (line 195) | def loglike_per_sample(self, X, Y):
    method loglike (line 210) | def loglike(self, X, Y, sample_weight=None):
    method to_json (line 227) | def to_json(self, path):
    method _from_json (line 267) | def _from_json(cls, json_dict, solver, fit_intercept, est_stderr,
    method from_json (line 296) | def from_json(cls, json_dict):
  class GLM (line 321) | class GLM(BaseModel):
    method __init__ (line 328) | def __init__(self,
    method fit (line 374) | def fit(self, X, Y, sample_weight=None):
    method _transform_Y (line 430) | def _transform_Y(self, Y):
    method predict (line 443) | def predict(self, X):
    method loglike_per_sample (line 456) | def loglike_per_sample(self, X, Y):
    method to_json (line 482) | def to_json(self, path):
    method _from_json (line 513) | def _from_json(cls, json_dict, solver, fit_intercept, est_stderr,
  class OLS (line 545) | class OLS(BaseModel):
    method __init__ (line 550) | def __init__(self, solver='svd', fit_intercept=True, est_stderr=False,
    method _pick_model (line 586) | def _pick_model(self):
    method fit (line 608) | def fit(self, X, Y, sample_weight=None):
    method _transform_Y (line 673) | def _transform_Y(self, Y):
    method predict (line 686) | def predict(self, X):
    method loglike_per_sample (line 699) | def loglike_per_sample(self, X, Y):
    method to_json (line 743) | def to_json(self, path):
    method _from_json (line 768) | def _from_json(cls, json_dict, solver, fit_intercept, est_stderr,
  class BaseMNL (line 800) | class BaseMNL(BaseModel):
    method __init__ (line 808) | def __init__(self, solver='lbfgs', fit_intercept=True, est_stderr=False,
    method _pick_model (line 850) | def _pick_model(self):
    method fit (line 869) | def fit(self, X, Y, sample_weight=None):
    method _label_encoder (line 928) | def _label_encoder(X, Y, sample_weight):
    method _label_decoder (line 950) | def _label_decoder(self, Y):
    method predict_log_proba (line 964) | def predict_log_proba(self, X):
    method predict (line 980) | def predict(self, X):
    method loglike_per_sample (line 995) | def loglike_per_sample(self, X, Y):
    method _from_json_MNL (line 1018) | def _from_json_MNL(cls, json_dict, solver, fit_intercept, est_stderr,
    method _from_json (line 1047) | def _from_json(cls, json_dict, solver, fit_intercept, est_stderr,
  class DiscreteMNL (line 1077) | class DiscreteMNL(BaseMNL):
    method __init__ (line 1082) | def __init__(self, solver='lbfgs', fit_intercept=True, est_stderr=False,
    method _label_encoder (line 1117) | def _label_encoder(X, Y, sample_weight):
    method _label_decoder (line 1137) | def _label_decoder(self, Y):
    method to_json (line 1162) | def to_json(self, path):
    method _from_json_MNL (line 1186) | def _from_json_MNL(cls, json_dict, solver, fit_intercept, est_stderr,
  class CrossEntropyMNL (line 1218) | class CrossEntropyMNL(BaseMNL):
    method __init__ (line 1223) | def __init__(self, solver='lbfgs', fit_intercept=True, est_stderr=False,
    method _label_encoder (line 1258) | def _label_encoder(X, Y, sample_weight):
    method _label_decoder (line 1284) | def _label_decoder(self, Y):
    method to_json (line 1300) | def to_json(self, path):
    method _from_json_MNL (line 1318) | def _from_json_MNL(cls, json_dict, solver, fit_intercept, est_stderr,

FILE: tests/test_CrossentropyMNL.py
  class CrossEntropyMNLUnaryTests (line 15) | class CrossEntropyMNLUnaryTests(unittest.TestCase):
    method setUpClass (line 18) | def setUpClass(cls):
    method test_label_encoder (line 22) | def test_label_encoder(self):
    method test_lr (line 45) | def test_lr(self):
    method test_lr_sample_weight_all_half (line 66) | def test_lr_sample_weight_all_half(self):
    method test_lr_one_data_point (line 81) | def test_lr_one_data_point(self):
  class CrossEntropyMNLBinaryTests (line 102) | class CrossEntropyMNLBinaryTests(unittest.TestCase):
    method setUpClass (line 105) | def setUpClass(cls):
    method test_lr (line 126) | def test_lr(self):
    method test_lr_disturbed (line 164) | def test_lr_disturbed(self):
    method test_lr_regularized (line 189) | def test_lr_regularized(self):
    method test_lr_sample_weight_all_half (line 214) | def test_lr_sample_weight_all_half(self):
    method test_lr_disturbed_sample_weight_all_half (line 231) | def test_lr_disturbed_sample_weight_all_half(self):
    method test_lr_sample_weight_all_zero (line 256) | def test_lr_sample_weight_all_zero(self):
    method test_lr_sample_weight_half_zero_half_one (line 264) | def test_lr_sample_weight_half_zero_half_one(self):
    method test_lr_disturbed_sample_weight_half_zero_half_one (line 284) | def test_lr_disturbed_sample_weight_half_zero_half_one(self):
    method test_lr_two_data_point (line 305) | def test_lr_two_data_point(self):
    method test_lr_disturbed_two_data_point (line 329) | def test_lr_disturbed_two_data_point(self):
    method test_lr_multicolinearty (line 353) | def test_lr_multicolinearty(self):
    method test_lr_disturbed_multicolinearty (line 379) | def test_lr_disturbed_multicolinearty(self):
  class CrossEntropyMNLMultinomialTests (line 406) | class CrossEntropyMNLMultinomialTests(unittest.TestCase):
    method setUpClass (line 409) | def setUpClass(cls):
    method test_label_encoder (line 414) | def test_label_encoder(self):
    method test_lr (line 450) | def test_lr(self):
    method test_lr_disturbed (line 480) | def test_lr_disturbed(self):
    method test_lr_regularized (line 497) | def test_lr_regularized(self):
    method test_lr_disturbed_regularized (line 513) | def test_lr_disturbed_regularized(self):
    method test_lr_sample_weight_all_half (line 529) | def test_lr_sample_weight_all_half(self):
    method test_lr_disturbed_sample_weight_all_half (line 552) | def test_lr_disturbed_sample_weight_all_half(self):
    method test_lr_sample_weight_all_zero (line 575) | def test_lr_sample_weight_all_zero(self):
    method test_lr_sample_weight_half_zero_half_one (line 583) | def test_lr_sample_weight_half_zero_half_one(self):
    method test_lr_disturbed_sample_weight_half_zero_half_one (line 603) | def test_lr_disturbed_sample_weight_half_zero_half_one(self):
    method test_lr_three_data_point (line 624) | def test_lr_three_data_point(self):
    method test_lr_disturbed_three_data_point (line 645) | def test_lr_disturbed_three_data_point(self):
    method test_lr_multicolinearty (line 666) | def test_lr_multicolinearty(self):
    method test_lr_disturbed_multicolinearty (line 689) | def test_lr_disturbed_multicolinearty(self):

FILE: tests/test_DiscreteMNL.py
  class DiscreteMNLUnaryTests (line 15) | class DiscreteMNLUnaryTests(unittest.TestCase):
    method setUpClass (line 18) | def setUpClass(cls):
    method test_lr (line 22) | def test_lr(self):
    method test_lr_sample_weight_all_half (line 43) | def test_lr_sample_weight_all_half(self):
    method test_lr_one_data_point (line 58) | def test_lr_one_data_point(self):
  class DiscreteMNLBinaryTests (line 80) | class DiscreteMNLBinaryTests(unittest.TestCase):
    method setUpClass (line 83) | def setUpClass(cls):
    method test_lr (line 86) | def test_lr(self):
    method test_lr_regularized (line 124) | def test_lr_regularized(self):
    method test_lr_sample_weight_all_half (line 149) | def test_lr_sample_weight_all_half(self):
    method test_lr_sample_weight_all_zero (line 166) | def test_lr_sample_weight_all_zero(self):
    method test_lr_sample_weight_half_zero_half_one (line 174) | def test_lr_sample_weight_half_zero_half_one(self):
    method test_lr_two_data_point (line 195) | def test_lr_two_data_point(self):
    method test_lr_multicolinearty (line 240) | def test_lr_multicolinearty(self):
  class DiscreteMNLMultinomialTests (line 267) | class DiscreteMNLMultinomialTests(unittest.TestCase):
    method setUpClass (line 270) | def setUpClass(cls):
    method test_lr (line 273) | def test_lr(self):
    method test_lr_regularized (line 303) | def test_lr_regularized(self):
    method test_lr_sample_weight_all_half (line 319) | def test_lr_sample_weight_all_half(self):
    method test_lr_sample_weight_all_zero (line 342) | def test_lr_sample_weight_all_zero(self):
    method test_lr_sample_weight_half_zero_half_one (line 350) | def test_lr_sample_weight_half_zero_half_one(self):
    method test_lr_three_data_point (line 371) | def test_lr_three_data_point(self):
    method test_lr_multicolinearty (line 392) | def test_lr_multicolinearty(self):

FILE: tests/test_GLM.py
  class PoissonTests (line 15) | class PoissonTests(unittest.TestCase):
    method setUpClass (line 18) | def setUpClass(cls):
    method test_glm_IRLS (line 24) | def test_glm_IRLS(self):
    method test_glm_regularized (line 94) | def test_glm_regularized(self):
    method test_glm_sample_weight_all_half (line 133) | def test_glm_sample_weight_all_half(self):
    method test_glm_sample_weight_all_zero (line 178) | def test_glm_sample_weight_all_zero(self):
    method test_GLM_sample_weight_half_zero_half_one (line 186) | def test_GLM_sample_weight_half_zero_half_one(self):
    method test_glm_one_data_point (line 220) | def test_glm_one_data_point(self):
    method test_ols_multicolinearty (line 240) | def test_ols_multicolinearty(self):
  class GammaTests (line 275) | class GammaTests(unittest.TestCase):
    method setUpClass (line 278) | def setUpClass(cls):
    method test_glm_IRLS (line 283) | def test_glm_IRLS(self):
    method test_glm_regularized (line 361) | def test_glm_regularized(self):
    method test_glm_sample_weight_all_half (line 364) | def test_glm_sample_weight_all_half(self):
    method test_glm_sample_weight_all_zero (line 413) | def test_glm_sample_weight_all_zero(self):
    method test_GLM_sample_weight_half_zero_half_one (line 421) | def test_GLM_sample_weight_half_zero_half_one(self):
    method test_glm_one_data_point (line 455) | def test_glm_one_data_point(self):
    method test_ols_multicolinearty (line 458) | def test_ols_multicolinearty(self):
  class GaussianTests (line 489) | class GaussianTests(unittest.TestCase):
    method setUpClass (line 492) | def setUpClass(cls):
    method test_glm_IRLS (line 497) | def test_glm_IRLS(self):
    method test_glm_regularized (line 574) | def test_glm_regularized(self):
    method test_glm_sample_weight_all_half (line 577) | def test_glm_sample_weight_all_half(self):
    method test_glm_sample_weight_all_zero (line 626) | def test_glm_sample_weight_all_zero(self):
    method test_GLM_sample_weight_half_zero_half_one (line 634) | def test_GLM_sample_weight_half_zero_half_one(self):
    method test_glm_one_data_point (line 668) | def test_glm_one_data_point(self):
    method test_ols_multicolinearty (line 671) | def test_ols_multicolinearty(self):
  class BinomialTests (line 702) | class BinomialTests(unittest.TestCase):
    method setUpClass (line 705) | def setUpClass(cls):
    method test_glm_IRLS (line 710) | def test_glm_IRLS(self):
    method test_glm_regularized (line 841) | def test_glm_regularized(self):
    method test_glm_sample_weight_all_half (line 845) | def test_glm_sample_weight_all_half(self):
    method test_glm_sample_weight_all_zero (line 956) | def test_glm_sample_weight_all_zero(self):
    method test_GLM_sample_weight_half_zero_half_one (line 964) | def test_GLM_sample_weight_half_zero_half_one(self):
    method test_glm_one_data_point (line 999) | def test_glm_one_data_point(self):
    method test_ols_multicolinearty (line 1020) | def test_ols_multicolinearty(self):
  class InverseGaussianTests (line 1053) | class InverseGaussianTests(unittest.TestCase):
    method setUpClass (line 1056) | def setUpClass(cls):
    method test_glm_IRLS (line 1063) | def test_glm_IRLS(self):
    method test_glm_regularized (line 1125) | def test_glm_regularized(self):
    method test_glm_sample_weight_all_half (line 1128) | def test_glm_sample_weight_all_half(self):
    method test_glm_sample_weight_all_zero (line 1168) | def test_glm_sample_weight_all_zero(self):
    method test_GLM_sample_weight_half_zero_half_one (line 1176) | def test_GLM_sample_weight_half_zero_half_one(self):
    method test_glm_one_data_point (line 1211) | def test_glm_one_data_point(self):
    method test_ols_multicolinearty (line 1214) | def test_ols_multicolinearty(self):
  class NegativeBinomialTests (line 1245) | class NegativeBinomialTests(unittest.TestCase):
    method setUpClass (line 1248) | def setUpClass(cls):
    method test_glm_IRLS (line 1257) | def test_glm_IRLS(self):
    method test_glm_regularized (line 1329) | def test_glm_regularized(self):
    method test_glm_sample_weight_all_half (line 1332) | def test_glm_sample_weight_all_half(self):
    method test_glm_sample_weight_all_zero (line 1378) | def test_glm_sample_weight_all_zero(self):
    method test_GLM_sample_weight_half_zero_half_one (line 1386) | def test_GLM_sample_weight_half_zero_half_one(self):
    method test_glm_one_data_point (line 1420) | def test_glm_one_data_point(self):
    method test_ols_multicolinearty (line 1423) | def test_ols_multicolinearty(self):

FILE: tests/test_HMM_utils.py
  class HMMUtilsTests (line 8) | class HMMUtilsTests(unittest.TestCase):
    method setUpClass (line 11) | def setUpClass(cls):
    method test_cal_alpha_beta (line 32) | def test_cal_alpha_beta(self):
    method test_forward_backward (line 68) | def test_forward_backward(self):

FILE: tests/test_OLS.py
  class UnivariateOLSTests (line 34) | class UnivariateOLSTests(unittest.TestCase):
    method setUpClass (line 37) | def setUpClass(cls):
    method test_ols (line 40) | def test_ols(self):
    method test_ols_l1_regularized (line 100) | def test_ols_l1_regularized(self):
    method test_ols_l2_regularized (line 104) | def test_ols_l2_regularized(self):
    method test_ols_elastic_net_regularized (line 156) | def test_ols_elastic_net_regularized(self):
    method test_ols_sample_weight_all_half (line 160) | def test_ols_sample_weight_all_half(self):
    method test_ols_sample_weight_all_zero (line 202) | def test_ols_sample_weight_all_zero(self):
    method test_ols_sample_weight_half_zero_half_one (line 210) | def test_ols_sample_weight_half_zero_half_one(self):
    method test_ols_one_data_point (line 242) | def test_ols_one_data_point(self):
    method test_ols_multicolinearty (line 261) | def test_ols_multicolinearty(self):
  class IndependentMultivariateOLSTests (line 293) | class IndependentMultivariateOLSTests(unittest.TestCase):
    method setUpClass (line 296) | def setUpClass(cls):
    method test_ols (line 301) | def test_ols(self):
    method test_ols_l2_regularized (line 353) | def test_ols_l2_regularized(self):
    method test_ols_l1_regularized (line 381) | def test_ols_l1_regularized(self):
    method test_ols_sample_weight_all_half (line 385) | def test_ols_sample_weight_all_half(self):
    method test_ols_sample_weight_all_zero (line 422) | def test_ols_sample_weight_all_zero(self):
    method test_ols_sample_weight_half_zero_half_one (line 429) | def test_ols_sample_weight_half_zero_half_one(self):
    method test_ols_one_data_point (line 461) | def test_ols_one_data_point(self):
    method test_ols_multicolinearty (line 483) | def test_ols_multicolinearty(self):
  class PerfectCorrelationMultivariateOLSTests (line 512) | class PerfectCorrelationMultivariateOLSTests(unittest.TestCase):
    method setUpClass (line 515) | def setUpClass(cls):
    method test_ols (line 522) | def test_ols(self):
    method test_ols_l1_regularized (line 573) | def test_ols_l1_regularized(self):
    method test_ols_l2_regularized (line 577) | def test_ols_l2_regularized(self):
    method test_ols_elastic_net_regularized (line 628) | def test_ols_elastic_net_regularized(self):
    method test_ols_sample_weight_all_half (line 632) | def test_ols_sample_weight_all_half(self):
    method test_ols_sample_weight_all_zero (line 677) | def test_ols_sample_weight_all_zero(self):
    method test_ols_sample_weight_half_zero_half_one (line 684) | def test_ols_sample_weight_half_zero_half_one(self):
    method test_ols_one_data_point (line 716) | def test_ols_one_data_point(self):
    method test_ols_multicolinearty (line 737) | def test_ols_multicolinearty(self):

FILE: tests/test_SemiSupervisedIOHMM.py
  class SemiSupervisedIOHMMTests (line 16) | class SemiSupervisedIOHMMTests(unittest.TestCase):
    method setUpClass (line 19) | def setUpClass(cls):
    method _mock_states (line 24) | def _mock_states(cls):
    method setUp (line 36) | def setUp(self):
    method test_train_no_covariates (line 39) | def test_train_no_covariates(self):
    method test_from_json (line 101) | def test_from_json(self):
    method test_from_config (line 144) | def test_from_config(self):

FILE: tests/test_SupervisedIOHMM.py
  class SupervisedIOHMMTests (line 13) | class SupervisedIOHMMTests(unittest.TestCase):
    method setUpClass (line 16) | def setUpClass(cls):
    method _mock_states (line 21) | def _mock_states(cls):
    method test_train_no_covariates (line 31) | def test_train_no_covariates(self):
    method test_from_json (line 77) | def test_from_json(self):
    method test_from_config (line 104) | def test_from_config(self):

FILE: tests/test_UnSupervisedIOHMM.py
  class UnSupervisedIOHMMTests (line 12) | class UnSupervisedIOHMMTests(unittest.TestCase):
    method setUpClass (line 15) | def setUpClass(cls):
    method setUp (line 18) | def setUp(self):
    method test_train_no_covariates (line 21) | def test_train_no_covariates(self):
    method test_train_covariates_for_transition (line 63) | def test_train_covariates_for_transition(self):
    method test_train_multivariate (line 100) | def test_train_multivariate(self):
    method test_from_json (line 150) | def test_from_json(self):
    method test_from_config (line 180) | def test_from_config(self):