Index

A

AbstractModel (class in pyanno.abstract_model) all_invalid() (in module pyanno.measures.helpers) anno_container (pyanno.database.PyannoResult attribute) annotations (pyanno.annotations.AnnotationsContainer attribute) AnnotationsContainer (class in pyanno.annotations)

annotator_accuracy() (pyanno.modelB.ModelB method) annotator_accuracy_samples() (pyanno.modelB.ModelB method) are_annotations_compatible() (pyanno.abstract_model.AbstractModel method) (pyanno.modelA.ModelA method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method) assert_is_dirichlet() (in module pyanno.test.test_modelB) assert_is_distributions() (in module pyanno.test.test_modelB)

B

benchmark (class in pyanno.util) binary_distance() (in module pyanno.measures.distances)

Bunch (class in pyanno.test.test_measures)

C

chance_adjusted_agreement() (in module pyanno.measures.helpers) chance_agreement_different_frequency() (in module pyanno.measures.helpers) chance_agreement_same_frequency() (in module pyanno.measures.helpers) close() (pyanno.database.PyannoDatabase method) closed (pyanno.database.PyannoDatabase attribute) cohens_kappa() (in module pyanno.measures.agreement) cohens_weighted_kappa() (in module pyanno.measures.agreement)

coincidence_matrix() (in module pyanno.measures.helpers) compute_counts() (in module pyanno.util) compute_nclasses() (in module pyanno.measures.helpers) confusion_matrix() (in module pyanno.measures.helpers) create_band_matrix() (in module pyanno.util) create_initial_state() (pyanno.abstract_model.AbstractModel static method) (pyanno.modelA.ModelA static method) (pyanno.modelB.ModelB static method) (pyanno.modelBt.ModelBt static method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign static method) cronbachs_alpha() (in module pyanno.measures.covariation)

D

database (pyanno.database.PyannoDatabase attribute) default_alpha() (pyanno.modelB.ModelB static method) default_beta() (pyanno.modelB.ModelB static method) DEFAULT_MISSING_VALUES_ALL (pyanno.annotations.AnnotationsContainer attribute)

DEFAULT_MISSING_VALUES_NUM (pyanno.annotations.AnnotationsContainer attribute) DEFAULT_MISSING_VALUES_STR (pyanno.annotations.AnnotationsContainer attribute) diagonal_distance() (in module pyanno.measures.distances) dirichlet_llhood() (in module pyanno.util)

F

fleiss_kappa() (in module pyanno.measures.agreement) from_array() (pyanno.annotations.AnnotationsContainer static method)

from_file() (pyanno.annotations.AnnotationsContainer static method)

G

generate_annotations() (pyanno.abstract_model.AbstractModel method) (pyanno.modelA.ModelA method) (pyanno.modelB.ModelB method) (pyanno.modelBt.ModelBt method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method) generate_annotations_from_labels() (pyanno.modelB.ModelB method) (pyanno.modelBt.ModelBt method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method)

generate_labels() (pyanno.modelB.ModelB method) (pyanno.modelBt.ModelBt method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method) get_available_id() (pyanno.database.PyannoDatabase method)

I

infer_labels() (pyanno.abstract_model.AbstractModel method) (pyanno.modelA.ModelA method) (pyanno.modelB.ModelB method) (pyanno.modelBt.ModelBt method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method)

is_valid() (in module pyanno.util)

K

krippendorffs_alpha() (in module pyanno.measures.agreement)

L

labels (pyanno.annotations.AnnotationsContainer attribute) labels_count() (in module pyanno.util) labels_frequency() (in module pyanno.util)

load_annotations() (in module pyanno.annotations) log_likelihood() (pyanno.abstract_model.AbstractModel method) (pyanno.modelA.ModelA method) (pyanno.modelB.ModelB method) (pyanno.modelBt.ModelBt method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method)

M

majority_vote() (in module pyanno.util) map() (pyanno.abstract_model.AbstractModel method) (pyanno.modelA.ModelA method) (pyanno.modelB.ModelB method) (pyanno.modelBt.ModelBt method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method) MISSING_VALUE (in module pyanno.util) missing_values (pyanno.annotations.AnnotationsContainer attribute) mle() (pyanno.abstract_model.AbstractModel method) (pyanno.modelA.ModelA method) (pyanno.modelB.ModelB method) (pyanno.modelBt.ModelBt method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method)

model (pyanno.database.PyannoResult attribute) ModelA (class in pyanno.modelA) ModelB (class in pyanno.modelB) ModelBt (class in pyanno.modelBt) ModelBtLoopDesign (class in pyanno.modelBt_loopdesign)

N

name (pyanno.annotations.AnnotationsContainer attribute) nannotators (pyanno.annotations.AnnotationsContainer attribute) nclasses (pyanno.annotations.AnnotationsContainer attribute)

ninf_to_num() (in module pyanno.util) nitems (pyanno.annotations.AnnotationsContainer attribute) normalize() (in module pyanno.util)

O

observed_agreement_frequency() (in module pyanno.measures.helpers)

optimize_step_size() (in module pyanno.sampling)

P

pairwise_matrix() (in module pyanno.measures.helpers) pearsons_rho() (in module pyanno.measures.covariation) plot_hinton_diagram() (in module pyanno.plots.hinton_plot) plot_pairwise_statistics() (in module pyanno.plots.pyanno_plots) plot_posterior() (in module pyanno.plots.annotations_plot) plot_square_matrix() (in module pyanno.plots.matrix_plot) plot_theta_parameters() (in module pyanno.plots.theta_plot) plot_theta_tensor() (in module pyanno.plots.theta_tensor_plot) pyanno (module) pyanno.abstract_model (module) pyanno.annotations (module) pyanno.database (module) pyanno.measures (module) pyanno.measures.agreement (module) pyanno.measures.covariation (module) pyanno.measures.distances (module) pyanno.measures.helpers (module)

pyanno.modelA (module) pyanno.modelB (module) pyanno.modelBt (module) pyanno.modelBt_loopdesign (module) pyanno.sampling (module) pyanno.test.test_annotations (module) pyanno.test.test_measures (module) pyanno.test.test_modelA (module) pyanno.test.test_modelB (module) pyanno.test.test_modelBt (module) pyanno.test.test_sampling (module) pyanno.test.test_util (module) pyanno.util (module) PyannoDatabase (class in pyanno.database) PyannoResult (class in pyanno.database) PyannoValueError

R

random_categorical() (in module pyanno.util) raw_annotations (pyanno.annotations.AnnotationsContainer attribute)

remove() (pyanno.database.PyannoDatabase method) retrieve_id() (pyanno.database.PyannoDatabase method)

S

sample_distribution() (in module pyanno.sampling) sample_from_proposal_distribution() (in module pyanno.sampling) sample_posterior_over_accuracy() (pyanno.abstract_model.AbstractModel method) (pyanno.modelA.ModelA method) (pyanno.modelB.ModelB method) (pyanno.modelBt.ModelBt method) (pyanno.modelBt_loopdesign.ModelBtLoopDesign method) save_to() (pyanno.annotations.AnnotationsContainer method) scotts_pi() (in module pyanno.measures.agreement)

setUp() (pyanno.test.test_measures.TestMeasures method) SMALLEST_FLOAT (in module pyanno.util) spearmans_rho() (in module pyanno.measures.covariation) store_result() (pyanno.database.PyannoDatabase method) string_wrap() (in module pyanno.util)

T

test_all_invalid() (pyanno.test.test_measures.TestMeasures method) test_annotations_compatibility() (pyanno.test.test_modelA.TestModelA method) (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_chance_agreement_different_frequency() (pyanno.test.test_measures.TestMeasures method) test_chance_agreement_same_frequency() (pyanno.test.test_measures.TestMeasures method) test_cohens_kappa() (pyanno.test.test_measures.TestMeasures method) test_cohens_kappa2() (pyanno.test.test_measures.TestMeasures method) test_cohens_weighted_kappa() (pyanno.test.test_measures.TestMeasures method) test_cohens_weighted_kappa2() (pyanno.test.test_measures.TestMeasures method) test_coincidence_matrix() (pyanno.test.test_measures.TestMeasures method) test_confusion_matrix() (pyanno.test.test_measures.TestMeasures method) test_confusion_matrix_missing() (pyanno.test.test_measures.TestMeasures method) test_create_model() (pyanno.test.test_modelBt.TestModelBt method) test_cronbachs_alpha() (pyanno.test.test_measures.TestMeasures method) test_cronbachs_alpha2() (pyanno.test.test_measures.TestMeasures method) test_fix_map_nans() (pyanno.test.test_modelA.TestModelA method) (pyanno.test.test_modelB.TestModelB method) test_fleiss_kappa() (pyanno.test.test_measures.TestMeasures method) test_fleiss_kappa_nannotations() (pyanno.test.test_measures.TestMeasures method) test_from_array() (pyanno.test.test_annotations.TestAnnotations method) test_from_file_inconsistent_nannotators() (pyanno.test.test_annotations.TestAnnotations method) test_from_file_numerical_labels() (pyanno.test.test_annotations.TestAnnotations method) test_from_file_string_labels() (pyanno.test.test_annotations.TestAnnotations method) test_from_file_with_commas() (pyanno.test.test_annotations.TestAnnotations method) test_generate_agreement() (pyanno.test.test_modelA.TestModelA method) test_generate_annotations() (pyanno.test.test_modelA.TestModelA method) (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_generate_incorrectness() (pyanno.test.test_modelA.TestModelA method) test_generate_samples() (pyanno.test.test_modelB.TestModelB method) test_generate_triplet_annotation() (pyanno.test.test_modelA.TestModelA method) test_inference() (pyanno.test.test_modelA.TestModelA method) (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_krippendorffs_alpha() (pyanno.test.test_measures.TestMeasures method)

test_krippendorffs_alpha2() (pyanno.test.test_measures.TestMeasures method) test_labels_count() (pyanno.test.test_util.TestUtil method) test_labels_frequency() (pyanno.test.test_util.TestUtil method) test_log_likelihood() (pyanno.test.test_modelA.TestModelA method) (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_log_likelihood_loop_design() (pyanno.test.test_modelBt.TestModelBt method) test_majority_vote() (pyanno.test.test_util.TestUtil method) test_map_estimation() (pyanno.test.test_modelA.TestModelA method) (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_map_stability() (pyanno.test.test_modelB.TestModelB method) test_matrix() (pyanno.test.test_measures.TestMeasures method) test_missing_annotations() (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_ml_estimation() (pyanno.test.test_modelA.TestModelA method) test_mle_estimation() (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_observed_agreement() (pyanno.test.test_measures.TestMeasures method) test_pearsons_rho() (pyanno.test.test_measures.TestMeasures method) test_raise_error_on_incompatible_annotation() (pyanno.test.test_modelA.TestModelA method) (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_random_categorical() (pyanno.test.test_util.TestUtil method) test_random_model() (pyanno.test.test_modelB.TestModelB method) test_sample_distribution() (pyanno.test.test_sampling.TestSampling method) test_sampling_theta() (pyanno.test.test_modelA.TestModelA method) (pyanno.test.test_modelB.TestModelB method) (pyanno.test.test_modelBt.TestModelBt method) test_scotts_pi() (pyanno.test.test_measures.TestMeasures method) test_spearmans_rho() (pyanno.test.test_measures.TestMeasures method) TestAnnotations (class in pyanno.test.test_annotations) TestMeasures (class in pyanno.test.test_measures) TestModelA (class in pyanno.test.test_modelA) TestModelB (class in pyanno.test.test_modelB) TestModelBt (class in pyanno.test.test_modelBt) TestSampling (class in pyanno.test.test_sampling) TestUtil (class in pyanno.test.test_util)

V

value (pyanno.database.PyannoResult attribute)