SYMBOL INDEX (305 symbols across 64 files)

FILE: pyBN/classes/_tests/test_bayesnet.py
  class BayesNetTestCase (line 44) | class BayesNetTestCase(unittest.TestCase):
    method setUp (line 46) | def setUp(self):
    method tearDown (line 52) | def tearDown(self):
    method test_isinstance (line 55) | def test_isinstance(self):
    method test_V_bif (line 58) | def test_V_bif(self):
    method test_E_bif (line 62) | def test_E_bif(self):
    method test_F_bif (line 70) | def test_F_bif(self):
    method test_V_bn (line 84) | def test_V_bn(self):
    method test_E_bn (line 88) | def test_E_bn(self):
    method test_F_bn (line 96) | def test_F_bn(self):
    method test_nodes (line 110) | def test_nodes(self):
    method test_cpt (line 115) | def test_cpt(self):
    method test_card (line 120) | def test_card(self):
    method test_scope (line 123) | def test_scope(self):
    method test_parents (line 127) | def test_parents(self):
    method test_values (line 131) | def test_values(self):
    method test_values_idx (line 134) | def test_values_idx(self):

FILE: pyBN/classes/_tests/test_factor.py
  class FactorTestCase (line 45) | class FactorTestCase(unittest.TestCase):
    method setUp (line 47) | def setUp(self):
    method tearDown (line 51) | def tearDown(self):
    method test_factor_init (line 55) | def test_factor_init(self):
    method test_factor_bn (line 58) | def test_factor_bn(self):
    method test_factor_var (line 62) | def test_factor_var(self):
    method test_factor_scope (line 65) | def test_factor_scope(self):
    method test_factor_card (line 68) | def test_factor_card(self):
    method test_factor_stride (line 72) | def test_factor_stride(self):
    method test_factor_cpt (line 76) | def test_factor_cpt(self):
    method test_multiply_factor (line 81) | def test_multiply_factor(self):
    method test_sumover_var (line 92) | def test_sumover_var(self):
    method test_sumout_var_list (line 96) | def test_sumout_var_list(self):
    method test_sumout_var (line 103) | def test_sumout_var(self):
    method test_maxout_var (line 112) | def test_maxout_var(self):
    method test_reduce_factor_by_list (line 124) | def test_reduce_factor_by_list(self):
    method test_reduce_factor (line 131) | def test_reduce_factor(self):
    method test_to_log (line 137) | def test_to_log(self):
    method test_from_log (line 142) | def test_from_log(self):
    method test_normalize (line 148) | def test_normalize(self):

FILE: pyBN/classes/bayesnet.py
  class BayesNet (line 45) | class BayesNet(object):
    method __init__ (line 51) | def __init__(self, E=None, value_dict=None, file=None):
    method __eq__ (line 88) | def __eq__(self, y):
    method __hash__ (line 97) | def __hash__(self):
    method copy (line 104) | def copy(self):
    method add_node (line 120) | def add_node(self, rv, cpt=[], parents=[], values=[]):
    method add_edge (line 124) | def add_edge(self, u, v):
    method remove_edge (line 138) | def remove_edge(self, u, v):
    method reverse_arc (line 142) | def reverse_arc(self, u, v):
    method set_data (line 147) | def set_data(self, rv, data):
    method set_cpt (line 151) | def set_cpt(self, rv, cpt):
    method set_parents (line 154) | def set_parents(self, rv, parents):
    method set_values (line 157) | def set_values(self, rv, values):
    method nodes (line 160) | def nodes(self):
    method node_idx (line 164) | def node_idx(self, rv):
    method has_node (line 170) | def has_node(self, rv):
    method has_edge (line 173) | def has_edge(self, u, v):
    method edges (line 176) | def edges(self):
    method num_edges (line 180) | def num_edges(self):
    method num_params (line 186) | def num_params(self):
    method scope_size (line 192) | def scope_size(self, rv):
    method num_nodes (line 195) | def num_nodes(self):
    method cpt (line 198) | def cpt(self, rv):
    method card (line 201) | def card(self, rv):
    method scope (line 204) | def scope(self, rv):
    method parents (line 209) | def parents(self, rv):
    method children (line 212) | def children(self, rv):
    method degree (line 215) | def degree(self, rv):
    method values (line 218) | def values(self, rv):
    method value_idx (line 221) | def value_idx(self, rv, val):
    method stride (line 228) | def stride(self, rv, n):
    method flat_cpt (line 237) | def flat_cpt(self, by_var=False, by_parents=False):
    method cpt_indices (line 250) | def cpt_indices(self, target, val_dict):
    method cpt_str_idx (line 288) | def cpt_str_idx(self, rv, idx):
    method set_structure (line 307) | def set_structure(self, edge_dict, value_dict=None):
    method adj_list (line 353) | def adj_list(self):
    method moralized_edges (line 365) | def moralized_edges(self):

FILE: pyBN/classes/cliquetree.py
  class CliqueTree (line 50) | class CliqueTree(object):
    method __init__ (line 75) | def __init__(self, bn):
    method __iter__ (line 105) | def __iter__(self):
    method __getitem__ (line 109) | def __getitem__(self, rv):
    method parents (line 115) | def parents(self, v):
    method children (line 122) | def children(self, n):
    method dfs_postorder (line 125) | def dfs_postorder(self, root):
    method initialize_tree (line 131) | def initialize_tree(self):
  class Clique (line 183) | class Clique(object):
    method __init__ (line 211) | def __init__(self, scope):
    method __repr__ (line 232) | def __repr__(self):
    method __rshift__ (line 235) | def __rshift__(self, other_clique):
    method __lshift__ (line 241) | def __lshift__(self, other_clique):
    method send_message (line 247) | def send_message(self, parent):
    method initialize_psi (line 290) | def initialize_psi(self):
    method send_initial_message (line 307) | def send_initial_message(self, other_clique):
    method collect_beliefs (line 332) | def collect_beliefs(self):
    method sepset (line 358) | def sepset(self, other_clique):
    method marginalize_over (line 371) | def marginalize_over(self, target):

FILE: pyBN/classes/clustergraph.py
  class ClusterGraph (line 30) | class ClusterGraph(object):
    method __init__ (line 36) | def __init__(self, bn):
    method initialize_graph (line 48) | def initialize_graph(self):
    method bethe (line 61) | def bethe(self):
    method initialize_messages (line 101) | def initialize_messages(self):
    method collect_beliefs (line 114) | def collect_beliefs(self):
    method loopy_belief_propagation (line 122) | def loopy_belief_propagation(self, target, evidence, max_iter=100):

FILE: pyBN/classes/empiricaldistribution.py
  class EmpiricalDistribution (line 32) | class EmpiricalDistribution(object):
    method __init__ (line 35) | def __init__(self, data, names=None):
    method bayes_counts (line 63) | def bayes_counts(self, bn):
    method idx_map (line 66) | def idx_map(self, rvs):
    method idx (line 71) | def idx(self, rv):
    method axis_tuple (line 74) | def axis_tuple(self, rv):
    method mpd (line 77) | def mpd(self, rv):
    method jpd (line 92) | def jpd(self, rvs):
    method cpd (line 102) | def cpd(self, lhs, rhs):
    method mi (line 121) | def mi(self, lhs, rhs, cond=None):

FILE: pyBN/classes/factor.py
  class Factor (line 33) | class Factor(object):
    method __init__ (line 109) | def __init__(self, bn, var):
    method __repr__ (line 151) | def __repr__(self):
    method __str__ (line 161) | def __str__(self):
    method __mul__ (line 170) | def __mul__(self, other_factor):
    method __sub__ (line 178) | def __sub__(self, rv_val):
    method __div__ (line 186) | def __div__(self, rv):
    method __floordiv__ (line 194) | def __floordiv__(self, rv):
    method parents (line 203) | def parents(self):
    method values (line 212) | def values(self, rv):
    method value_indices (line 215) | def value_indices(self, val_dict):
    method sepset (line 229) | def sepset(self, other_factor):
    method multiply_factor (line 245) | def multiply_factor(self, other_factor):
    method sumover_var (line 323) | def sumover_var(self, rv):
    method sumout_var_list (line 373) | def sumout_var_list(self, var_list):
    method sumout_var (line 399) | def sumout_var(self, rv):
    method maxout_var (line 453) | def maxout_var(self, rv):
    method reduce_factor_by_list (line 511) | def reduce_factor_by_list(self, evidence):
    method reduce_factor (line 545) | def reduce_factor(self, rv, val):
    method to_log (line 612) | def to_log(self):
    method from_log (line 620) | def from_log(self):
    method perturb (line 628) | def perturb(self):
    method normalize (line 636) | def normalize(self):

FILE: pyBN/classes/factorization.py
  class Factorization (line 13) | class Factorization(object):
    method __init__ (line 15) | def __init__(self, bn, nodes=None):
    method refresh (line 37) | def refresh(self):
    method __getitem__ (line 46) | def __getitem__(self, idx):
    method __iter__ (line 49) | def __iter__(self):
    method __len__ (line 53) | def __len__(self):
    method __div__ (line 56) | def __div__(self, rv):
    method __floordiv__ (line 65) | def __floordiv__(self, rv):
    method __sub__ (line 74) | def __sub__(self, rv_val):
    method sum_product_eliminate_var (line 86) | def sum_product_eliminate_var(self, rv):
    method max_product_eliminate_var (line 101) | def max_product_eliminate_var(self, rv):
    method traceback_map (line 117) | def traceback_map(self):
    method consolidate (line 131) | def consolidate(self):
    method relevant_factors (line 138) | def relevant_factors(self, rv):
    method irrelevant_factors (line 141) | def irrelevant_factors(self, rv):

FILE: pyBN/classification/classification.py
  function mbc_predict (line 18) | def mbc_predict(data, targets, classifier=None, c_struct='DAG',f_struct=...
  function predict (line 21) | def predict(data, target, classifier=None, method='nb'):

FILE: pyBN/classification/feature_selection.py
  function fs_gambit (line 34) | def fs_gambit(data, target):
  function feature_selection (line 85) | def feature_selection(data, target, method='iamb'):

FILE: pyBN/inference/_tests/test_map_exact.py
  class MapExactTestCase (line 18) | class MapExactTestCase(unittest.TestCase):
    method setUp (line 20) | def setUp(self):
    method tearDown (line 24) | def tearDown(self):

FILE: pyBN/inference/_tests/test_marginal_approx.py
  class MarginalApproxTestCase (line 18) | class MarginalApproxTestCase(unittest.TestCase):
    method setUp (line 20) | def setUp(self):
    method tearDown (line 24) | def tearDown(self):
    method test_forward_sample (line 27) | def test_forward_sample(self):
    method test_likelihood_weighted_sample (line 37) | def test_likelihood_weighted_sample(self):
    method test_lws_allevidence (line 49) | def test_lws_allevidence(self):
    method test_gibbs (line 58) | def test_gibbs(self):

FILE: pyBN/inference/_tests/test_marginal_exact.py
  class MarginalExactTestCase (line 20) | class MarginalExactTestCase(unittest.TestCase):
    method setUp (line 22) | def setUp(self):
    method tearDown (line 26) | def tearDown(self):
    method test_marginal_ve_e_prior1 (line 29) | def test_marginal_ve_e_prior1(self):
    method test_marginal_ve_e_prior2 (line 33) | def test_marginal_ve_e_prior2(self):
    method test_marginal_ve_e_prior_middle_ev (line 53) | def test_marginal_ve_e_prior_middle_ev(self):
    method test_marginal_ve_e_prior_leaf_ev (line 57) | def test_marginal_ve_e_prior_leaf_ev(self):
    method test_marginal_ve_e_middle_prior_ev (line 61) | def test_marginal_ve_e_middle_prior_ev(self):

FILE: pyBN/inference/map_exact/ilp_map.py
  function ilp_map (line 12) | def ilp_map(bn, evidence={}):

FILE: pyBN/inference/map_exact/ve_map.py
  function ve_map (line 12) | def ve_map(bn,

FILE: pyBN/inference/marginal_approx/forward_sample.py
  function forward_sample (line 8) | def forward_sample(bn, n=1000):

FILE: pyBN/inference/marginal_approx/gibbs_sample.py
  function gibbs_sample (line 12) | def gibbs_sample(bn, n=1000, burn=200):

FILE: pyBN/inference/marginal_approx/loopy_bp.py
  function loopy_bp (line 11) | def loopy_bp(target=None, evidence=None, max_iter=100):

FILE: pyBN/inference/marginal_approx/lw_sample.py
  function lw_sample (line 10) | def lw_sample(bn, evidence={}, target=None, n=1000):

FILE: pyBN/inference/marginal_exact/exact_bp.py
  function exact_bp (line 13) | def exact_bp(bn, target=None, evidence=None, downward_pass=False):

FILE: pyBN/inference/marginal_exact/ve_marginal.py
  function marginal_ve_e (line 12) | def marginal_ve_e(bn, target, evidence={}):

FILE: pyBN/io/_tests/test_reading.py
  class ReadingTestCase (line 16) | class ReadingTestCase(unittest.TestCase):
    method setUp (line 18) | def setUp(self):
    method tearDown (line 23) | def tearDown(self):
    method test_read_bn_vertices (line 26) | def test_read_bn_vertices(self):
    method test_read_bif_vertices (line 29) | def test_read_bif_vertices(self):

FILE: pyBN/io/_tests/test_writing.py
  function suite (line 13) | def suite():
  class WritingTestCase (line 18) | class WritingTestCase(unittest.TestCase):
    method setUp (line 20) | def setUp(self):
    method tearDown (line 22) | def tearDown(self):

FILE: pyBN/io/read.py
  function read_bn (line 24) | def read_bn(path):
  function read_bif (line 57) | def read_bif(path):
  function read_json (line 145) | def read_json(path):
  function read_mat (line 218) | def read_mat(path, delim=' '):

FILE: pyBN/io/write.py
  function write_bn (line 20) | def write_bn(bn, path):
  function write_json (line 51) | def write_json(bn, path):

FILE: pyBN/learning/parameter/bayes.py
  function bayes_estimator (line 15) | def bayes_estimator(bn, data, equiv_sample=None, prior_dict=None, nodes=...

FILE: pyBN/learning/parameter/mle.py
  function mle_fast (line 14) | def mle_fast(bn, data, nodes=None, counts=False, np=False):
  function mle_estimator (line 71) | def mle_estimator(bn, data, nodes=None, counts=False):

FILE: pyBN/learning/structure/_tests/test_chow_liu.py
  class ChowLiuTestCase (line 18) | class ChowLiuTestCase(unittest.TestCase):
    method setUp (line 20) | def setUp(self):
    method tearDown (line 25) | def tearDown(self):
    method test_chow_liu1_V (line 28) | def test_chow_liu1_V(self):
    method test_chow_liu1_E (line 33) | def test_chow_liu1_E(self):
    method test_chow_liu1_F (line 38) | def test_chow_liu1_F(self):

FILE: pyBN/learning/structure/_tests/test_grow_shrink.py
  class GrowShrinkTestCase (line 19) | class GrowShrinkTestCase(unittest.TestCase):
    method setUp (line 21) | def setUp(self):
    method tearDown (line 26) | def tearDown(self):
    method test_gs1_V (line 29) | def test_gs1_V(self):
    method test_gs1_E (line 34) | def test_gs1_E(self):
    method test_gs1_F (line 39) | def test_gs1_F(self):
    method test_gs_data (line 46) | def test_gs_data(self):

FILE: pyBN/learning/structure/_tests/test_orient_edges.py
  class OrientEdgesTestCase (line 18) | class OrientEdgesTestCase(unittest.TestCase):
    method setUp (line 20) | def setUp(self):
    method tearDown (line 22) | def tearDown(self):
    method test_orient_edges_pc (line 25) | def test_orient_edges_pc(self):
    method test_orient_edges_gs (line 31) | def test_orient_edges_gs(self):

FILE: pyBN/learning/structure/_tests/test_pc.py
  class PCTestCase (line 18) | class PCTestCase(unittest.TestCase):
    method setUp (line 20) | def setUp(self):
    method tearDown (line 25) | def tearDown(self):
    method test_pc1_V (line 28) | def test_pc1_V(self):
    method test_pc1_E (line 33) | def test_pc1_E(self):
    method test_pc1_F (line 38) | def test_pc1_F(self):

FILE: pyBN/learning/structure/constraint/fast_iamb.py
  function fast_iamb (line 42) | def fast_iamb(data, k=5, alpha=0.05, feature_selection=None, debug=False):

FILE: pyBN/learning/structure/constraint/grow_shrink.py
  function gs (line 48) | def gs(data, alpha=0.05, feature_selection=None, debug=False):

FILE: pyBN/learning/structure/constraint/iamb.py
  function iamb (line 55) | def iamb(data, alpha=0.05, feature_selection=None, debug=False):

FILE: pyBN/learning/structure/constraint/lambda_iamb.py
  function lambda_iamb (line 13) | def lambda_iamb(data, L=1.5, alpha=0.05, feature_selection=None):

FILE: pyBN/learning/structure/constraint/path_condition.py
  function pc (line 55) | def pc(data, alpha=0.05):

FILE: pyBN/learning/structure/exact/gobnilp.py
  function ilp (line 28) | def ilp(data, settings=None, edge_reqs=None, nonedge_reqs=None, ind_reqs...

FILE: pyBN/learning/structure/hybrid/mmhc.py
  function mmhc (line 12) | def mmhc(data, alpha=0.05, metric='AIC', max_iter=100, method='hc'):

FILE: pyBN/learning/structure/hybrid/mmpc.py
  function mmpc (line 23) | def mmpc(data, alpha=0.05):

FILE: pyBN/learning/structure/mdbn.py
  function bridge (line 56) | def bridge(c_bn, f_bn, data):
  function mdbn (line 93) | def mdbn(data, f_cols, c_cols, f_struct='DAG', c_struct='DAG', wrapper=F...

FILE: pyBN/learning/structure/naive/TAN.py
  function TAN (line 13) | def TAN(data, target):

FILE: pyBN/learning/structure/naive/naive_bayes.py
  function naive_bayes (line 18) | def naive_bayes(data, target, estimator='mle'):

FILE: pyBN/learning/structure/score/bayes_scores.py
  function BDe (line 26) | def BDe(bn, data, ess=1, ed=None):
  function BDeu (line 74) | def BDeu(bn, data, ess=1, ed=None):
  function K2 (line 123) | def K2(bn, data, ed=None):

FILE: pyBN/learning/structure/score/hill_climbing.py
  function hc (line 42) | def hc(data, metric='AIC', max_iter=100, debug=False, restriction=None):

FILE: pyBN/learning/structure/score/info_scores.py
  function info_score (line 38) | def info_score(bn, nrow, metric='BIC'):
  function log_likelihood (line 53) | def log_likelihood(bn, nrow):
  function MDL (line 118) | def MDL(bn, nrow):
  function BIC (line 125) | def BIC(bn, nrow):
  function AIC (line 136) | def AIC(bn, nrow):

FILE: pyBN/learning/structure/score/random_restarts.py
  function hc_rr (line 38) | def hc_rr(data, M=5, R=3, metric='AIC', max_iter=100, debug=False, restr...

FILE: pyBN/learning/structure/score/tabu.py
  function tabu (line 29) | def tabu(data, k=5, metric='AIC', max_iter=100, debug=False, restriction...

FILE: pyBN/learning/structure/tree/chow_liu.py
  function chow_liu (line 21) | def chow_liu(data,edges_only=False):

FILE: pyBN/plotting/plot.py
  function plot (line 21) | def plot(bn, save=False):
  function plot_nx (line 24) | def plot_nx(bn,**kwargs):
  function iplot (line 35) | def iplot(bn, h=350, w=450):
  function plot_gv (line 73) | def plot_gv(bn, save=False):

FILE: pyBN/utils/_tests/test_independence_tests.py
  class ConstraintTestsTestCase (line 17) | class ConstraintTestsTestCase(unittest.TestCase):
    method setUp (line 19) | def setUp(self):
    method tearDown (line 26) | def tearDown(self):
    method test_mi_two_vars_value_a (line 29) | def test_mi_two_vars_value_a(self):
    method test_mi_two_vars_value_b (line 32) | def test_mi_two_vars_value_b(self):
    method test_mi_two_vars_symmetry (line 35) | def test_mi_two_vars_symmetry(self):
    method test_mi_three_vars_value_a (line 38) | def test_mi_three_vars_value_a(self):
    method test_mi_three_vars_symmetry (line 41) | def test_mi_three_vars_symmetry(self):
    method test_mi_random_three (line 44) | def test_mi_random_three(self):
    method test_mi_random_four (line 49) | def test_mi_random_four(self):

FILE: pyBN/utils/_tests/test_markov_blanket.py
  class ConstraintTestsTestCase (line 19) | class ConstraintTestsTestCase(unittest.TestCase):
    method setUp (line 21) | def setUp(self):
    method tearDown (line 25) | def tearDown(self):
    method test_markov_blanket (line 28) | def test_markov_blanket(self):

FILE: pyBN/utils/_tests/test_orient_edges.py
  class OrientEdgesTestCase (line 18) | class OrientEdgesTestCase(unittest.TestCase):
    method setUp (line 20) | def setUp(self):
    method tearDown (line 22) | def tearDown(self):
    method test_orient_edges_pc (line 25) | def test_orient_edges_pc(self):
    method test_orient_edges_gs (line 31) | def test_orient_edges_gs(self):

FILE: pyBN/utils/_tests/test_random_sample.py
  class RandomSampleTestCase (line 19) | class RandomSampleTestCase(unittest.TestCase):
    method setUp (line 21) | def setUp(self):
    method tearDown (line 25) | def tearDown(self):
    method test_random_sample (line 28) | def test_random_sample(self):

FILE: pyBN/utils/class_equivalence.py
  function are_class_equivalent (line 16) | def are_class_equivalent(x,y):

FILE: pyBN/utils/data.py
  function replace_strings (line 15) | def replace_strings(data, return_values=False):
  function unique_bins (line 38) | def unique_bins(data):

FILE: pyBN/utils/discretize.py
  function discretize (line 19) | def discretize(data, cols=None, bins=None):

FILE: pyBN/utils/graph.py
  function would_cause_cycle (line 14) | def would_cause_cycle(e, u, v, reverse=False):
  function topsort (line 31) | def topsort(edge_dict, root=None):
  function dfs_postorder (line 58) | def dfs_postorder(edge_dict, root=None):
  function mst (line 61) | def mst(edge_dict):
  function make_chordal (line 132) | def make_chordal(bn, v=None,e=None):
  function is_chordal (line 210) | def is_chordal(edge_list):

FILE: pyBN/utils/hybrid_distance.py
  function hybrid_distance (line 22) | def hybrid_distance(x,y, alpha, s='hamming', p='euclidean'):

FILE: pyBN/utils/independence_tests.py
  function are_independent (line 24) | def are_independent(data, alpha=0.05, method='mi_test'):
  function mutual_information (line 31) | def mutual_information(data, conditional=False):
  function mi_test (line 105) | def mi_test(data, test=True):
  function entropy (line 228) | def entropy(data):
  function mi_from_en (line 307) | def mi_from_en(data):
  function chi2_test (line 349) | def chi2_test(data):

FILE: pyBN/utils/markov_blanket.py
  function markov_blanket (line 23) | def markov_blanket(bn):
  function resolve_markov_blanket (line 51) | def resolve_markov_blanket(Mb, data,alpha=0.05):
  function mb_fitness (line 116) | def mb_fitness(data, Mb, target=None):

FILE: pyBN/utils/orient_edges.py
  function orient_edges_MB (line 21) | def orient_edges_MB(edge_dict, Mb, data, alpha):
  function orient_edges_gs2 (line 98) | def orient_edges_gs2(edge_dict, Mb, data, alpha):
  function orient_edges_CS (line 121) | def orient_edges_CS(edge_dict, block_dict):

FILE: pyBN/utils/parameter_distance.py
  function euclidean (line 35) | def euclidean(x,y):
  function manhattan (line 48) | def manhattan(x,y):
  function minkowski (line 61) | def minkowski(x,y,p=1.5):
  function kl_divergence (line 80) | def kl_divergence(x,y):
  function js_divergence (line 95) | def js_divergence(x,y):
  function hellinger (line 112) | def hellinger(x,y):

FILE: pyBN/utils/random_sample.py
  function random_sample (line 17) | def random_sample(bn, n=1000):

FILE: pyBN/utils/structure_distance.py
  function missing_edges (line 52) | def missing_edges(x,y):
  function extra_edges (line 67) | def extra_edges(x,y):
  function incorrect_direction_edges (line 82) | def incorrect_direction_edges(x,y):
  function hamming (line 95) | def hamming(x,y):