Index

_

__array_finalize__() (lmpy.matrix.Matrix method) __call__() (lmpy.statistics.pam_stats.PamStatsMetric method) __enter__() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) (lmpy.point.PointCsvReader method) (lmpy.point.PointCsvWriter method) (lmpy.point.PointDwcaReader method) (lmpy.point.PointJsonWriter method) __eq__() (lmpy.point.Point method) __exit__() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) (lmpy.point.PointCsvReader method) (lmpy.point.PointCsvWriter method) (lmpy.point.PointDwcaReader method) (lmpy.point.PointJsonWriter method) __iter__() (lmpy.point.PointCsvReader method) (lmpy.point.PointDwcaReader method) __lt__() (lmpy.point.Point method) __next__() (lmpy.point.PointCsvReader method) (lmpy.point.PointDwcaReader method) __repr__() (lmpy.point.Point method) _AcceptedNameWrangler (class in lmpy.data_wrangling.common.accepted_name_wrangler) _annotate_node() (lmpy.tree.TreeWrapper method) _annotation_method() (lmpy.tree.TreeWrapper method) _beta_helper() (in module lmpy.statistics.mcpa) _build_p_branch_length_values() (lmpy.data_preparation.tree_encoder.TreeEncoder method) _build_p_matrix_no_branch_lengths() (lmpy.data_preparation.tree_encoder.TreeEncoder method) _build_p_matrix_tip_proportion_list() (lmpy.data_preparation.tree_encoder.TreeEncoder method) _build_p_matrix_with_branch_lengths() (lmpy.data_preparation.tree_encoder.TreeEncoder method) _calculate_beta() (in module lmpy.statistics.mcpa) _calculate_r_squared() (in module lmpy.statistics.mcpa) _calculate_y_hat() (in module lmpy.statistics.mcpa) _DataWrangler (class in lmpy.data_wrangling.base) _encode_layer() (lmpy.data_preparation.layer_encoder.LayerEncoder method) _get_all_fail_condition() (lmpy.data_wrangling.occurrence.minimum_points_wrangler.MinimumPointsFilter method) _get_all_pass_condition() (lmpy.data_wrangling.occurrence.minimum_points_wrangler.MinimumPointsFilter method) _get_label_method() (lmpy.tree.TreeWrapper method) _get_pass_condition_func() (lmpy.data_wrangling.occurrence.attribute_filter_wrangler.AttributeFilterWrangler method)

_get_species_name() (lmpy.point.PointDwcaReader method) _get_window_function() (lmpy.data_preparation.layer_encoder.LayerEncoder static method) _get_x_value() (lmpy.point.PointDwcaReader method) _get_y_value() (lmpy.point.PointDwcaReader method) _label_method() (lmpy.tree.TreeWrapper static method) _label_tree_nodes() (lmpy.tree.TreeWrapper method) _load_name_map() (lmpy.data_wrangling.common.accepted_name_wrangler._AcceptedNameWrangler method) _load_wranglers() (lmpy.data_wrangling.factory.WranglerFactory method) _MatrixDataWrangler (class in lmpy.data_wrangling.matrix.base) _mcpa_for_node() (in module lmpy.statistics.mcpa) _modify_point() (lmpy.data_wrangling.occurrence.accepted_name_wrangler.AcceptedNameOccurrenceWrangler method) (lmpy.data_wrangling.occurrence.attribute_modifier_wrangler.AttributeModifierWrangler method) (lmpy.data_wrangling.occurrence.base._OccurrenceDataWrangler method) (lmpy.data_wrangling.occurrence.common_format_wrangler.CommonFormatWrangler method) (lmpy.data_wrangling.occurrence.coordinate_conversion_wrangler.CoordinateConverterWrangler method) _OccurrenceDataWrangler (class in lmpy.data_wrangling.occurrence.base) _pass_condition() (lmpy.data_wrangling.occurrence.accepted_name_wrangler.AcceptedNameOccurrenceWrangler method) (lmpy.data_wrangling.occurrence.base._OccurrenceDataWrangler method) (lmpy.data_wrangling.occurrence.bounding_box_wrangler.BoundingBoxFilter method) (lmpy.data_wrangling.occurrence.coordinate_conversion_wrangler.CoordinateConverterWrangler method) (lmpy.data_wrangling.occurrence.decimal_precision_wrangler.DecimalPrecisionFilter method) (lmpy.data_wrangling.occurrence.disjoint_geometries_wrangler.DisjointGeometriesFilter method) (lmpy.data_wrangling.occurrence.intersect_geometries_wrangler.IntersectGeometriesFilter method) (lmpy.data_wrangling.occurrence.spatial_index_wrangler.SpatialIndexFilter method) (lmpy.data_wrangling.occurrence.unique_localities_wrangler.UniqueLocalitiesFilter method) _point_intersect() (lmpy.spatial.spatial_index.SpatialIndex static method) _process_arguments() (in module lmpy.tools._config_parser) _process_metadata() (lmpy.point.PointDwcaReader method) _read_layer() (lmpy.data_preparation.layer_encoder.LayerEncoder method) _read_raster_layer() (lmpy.data_preparation.layer_encoder.LayerEncoder method) _read_shapegrid() (lmpy.data_preparation.layer_encoder.LayerEncoder method) _read_vector_layer() (lmpy.data_preparation.layer_encoder.LayerEncoder method) _report_slice() (lmpy.data_wrangling.matrix.base._MatrixDataWrangler method) _report_tip() (lmpy.data_wrangling.tree.base._TreeDataWrangler method) _standardize_matrix() (in module lmpy.statistics.mcpa) _trace_mtx_by_transverse() (in module lmpy.statistics.mcpa) _TreeDataWrangler (class in lmpy.data_wrangling.tree.base)

A

AcceptedNameMatrixWrangler (class in lmpy.data_wrangling.matrix.accepted_name_wrangler) AcceptedNameOccurrenceWrangler (class in lmpy.data_wrangling.occurrence.accepted_name_wrangler) AcceptedNameTreeWrangler (class in lmpy.data_wrangling.tree.accepted_name_wrangler) add_feature() (lmpy.spatial.spatial_index.SpatialIndex method) add_node_labels() (lmpy.tree.TreeWrapper method) all_ones_heuristic() (in module lmpy.randomize.grady)

all_zeros_heuristic() (in module lmpy.randomize.grady) alpha() (in module lmpy.statistics.pam_stats) alpha_proportional() (in module lmpy.statistics.pam_stats) annotate_tree() (lmpy.tree.TreeWrapper method) annotate_tree_tips() (lmpy.tree.TreeWrapper method) AttributeFilterWrangler (class in lmpy.data_wrangling.occurrence.attribute_filter_wrangler) AttributeModifierWrangler (class in lmpy.data_wrangling.occurrence.attribute_modifier_wrangler)

B

BoundingBoxFilter (class in lmpy.data_wrangling.occurrence.bounding_box_wrangler)

build_shapegrid() (in module lmpy.data_preparation.build_grid) (in module lmpy.tools.build_shapegrid)

C

c_score() (in module lmpy.statistics.pam_stats) calculate_covariance_statistics() (lmpy.statistics.pam_stats.PamStats method) calculate_diversity_statistics() (lmpy.statistics.pam_stats.PamStats method) calculate_site_statistics() (lmpy.statistics.pam_stats.PamStats method) calculate_species_statistics() (lmpy.statistics.pam_stats.PamStats method) clean_data() (in module lmpy.tools.clean_occurrences) cli() (in module lmpy.tools.build_shapegrid) (in module lmpy.tools.calculate_pam_stats) (in module lmpy.tools.clean_occurrences) (in module lmpy.tools.convert_csv_to_lmm) (in module lmpy.tools.convert_lmm_to_csv) (in module lmpy.tools.convert_lmm_to_geojson) (in module lmpy.tools.create_rare_species_model) (in module lmpy.tools.create_tree_matrix) (in module lmpy.tools.encode_layers) (in module lmpy.tools.mcpa_run) (in module lmpy.tools.randomize_pam) (in module lmpy.tools.split_occurrence_data) (in module lmpy.tools.wrangle_matrix) (in module lmpy.tools.wrangle_tree)

close() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) (lmpy.point.PointCsvReader method) (lmpy.point.PointCsvWriter method) (lmpy.point.PointDwcaReader method) (lmpy.point.PointJsonWriter method) (lmpy.spatial.spatial_index.SpatialIndex method) CommonFormatWrangler (class in lmpy.data_wrangling.occurrence.common_format_wrangler) compare_absolute_values() (in module lmpy.statistics.running_stats) compare_signed_values() (in module lmpy.statistics.running_stats) concatenate() (lmpy.matrix.Matrix class method) CONCURRENCY_FACTOR (in module lmpy.statistics.mcpa) convert_csv_to_lmm() (in module lmpy.tools.convert_csv_to_lmm) convert_lmm_to_csv() (in module lmpy.tools.convert_lmm_to_csv) CoordinateConverterWrangler (class in lmpy.data_wrangling.occurrence.coordinate_conversion_wrangler) CORE_TAG (in module lmpy.point) (in module lmpy.tools.process_idigbio) covariance_stats (lmpy.statistics.pam_stats.PamStats attribute) CovarianceMatrixMetric (class in lmpy.statistics.pam_stats) create_rare_species_model() (in module lmpy.tools.create_rare_species_model)

D

DecimalPrecisionFilter (class in lmpy.data_wrangling.occurrence.decimal_precision_wrangler) DEFAULT_META_FILENAME (in module lmpy.point) DEFAULT_SPECIES_TERM (in module lmpy.point) DEFAULT_X_TERM (in module lmpy.point) DEFAULT_Y_TERM (in module lmpy.point)

DELIMITED_BY_ATT (in module lmpy.tools.process_idigbio) DELIMITED_TERMS (in module lmpy.tools.process_idigbio) DisjointGeometriesFilter (class in lmpy.data_wrangling.occurrence.disjoint_geometries_wrangler) diversity_stats (lmpy.statistics.pam_stats.PamStats attribute) DiversityMetric (class in lmpy.statistics.pam_stats) DWCA_OCCURRENCE_PARAMS (in module lmpy.point)

E

encode_biogeographic_hypothesis() (lmpy.data_preparation.layer_encoder.LayerEncoder method) encode_largest_class() (lmpy.data_preparation.layer_encoder.LayerEncoder method) encode_mean_value() (lmpy.data_preparation.layer_encoder.LayerEncoder method)

encode_phylogeny() (lmpy.data_preparation.tree_encoder.TreeEncoder method) encode_presence_absence() (lmpy.data_preparation.layer_encoder.LayerEncoder method) EncodingException EXTENSION_TAG (in module lmpy.tools.process_idigbio)

F

FIELD_TAG (in module lmpy.point) (in module lmpy.tools.process_idigbio) FILES_TAG (in module lmpy.point) (in module lmpy.tools.process_idigbio) fill_shuffle_reshape_heuristic() (in module lmpy.randomize.grady)

flatten_2d() (lmpy.matrix.Matrix method) flush_writers() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) from_base_tree() (lmpy.tree.TreeWrapper class method) from_config() (lmpy.data_wrangling.base._DataWrangler class method) from_file() (lmpy.data_preparation.tree_encoder.TreeEncoder class method) from_filename() (lmpy.tree.TreeWrapper class method)

G

geojsonify_matrix() (in module lmpy.spatial.geojsonify) geojsonify_matrix_with_shapefile() (in module lmpy.spatial.geojsonify) get_annotations() (lmpy.tree.TreeWrapper method) get_attribute() (lmpy.point.Point method) get_attribute_names() (lmpy.point.Point method) get_column_headers() (lmpy.matrix.Matrix method) get_config() (in module lmpy._version) get_distance_matrix() (lmpy.tree.TreeWrapper method) get_distance_matrix_dendropy() (lmpy.tree.TreeWrapper method) get_encoded_matrix() (lmpy.data_preparation.layer_encoder.LayerEncoder method) get_field_process_func() (in module lmpy.point) get_geojson() (lmpy.data_preparation.layer_encoder.LayerEncoder method) get_headers() (lmpy.matrix.Matrix method) get_keywords() (in module lmpy._version) get_labels() (lmpy.tree.TreeWrapper method)

get_metadata() (lmpy.matrix.Matrix method) get_p_values() (in module lmpy.statistics.mcpa) get_report() (lmpy.data_wrangling.base._DataWrangler method) (lmpy.data_wrangling.occurrence.base._OccurrenceDataWrangler method) (lmpy.data_wrangling.tree.base._TreeDataWrangler method) get_row_headers() (lmpy.matrix.Matrix method) get_srs_for_epsg() (in module lmpy.data_wrangling.occurrence.coordinate_conversion_wrangler) get_variance_covariance_matrix() (lmpy.tree.TreeWrapper method) get_versions() (in module lmpy._version) get_wranglers() (lmpy.data_wrangling.factory.WranglerFactory method) get_writer_filename_func() (in module lmpy.data_preparation.occurrence_splitter) get_writer_key_from_fields_func() (in module lmpy.data_preparation.occurrence_splitter) git_get_keywords() (in module lmpy._version) git_pieces_from_vcs() (in module lmpy._version) git_versions_from_keywords() (in module lmpy._version) grady_randomize() (in module lmpy.randomize.grady)

H

HANDLERS (in module lmpy._version) has_branch_lengths() (lmpy.tree.TreeWrapper method)

has_polytomies() (lmpy.tree.TreeWrapper method) hexagon_wkt_generator() (in module lmpy.data_preparation.build_grid)

I

ID_TAG (in module lmpy.point) (in module lmpy.tools.process_idigbio)

IntersectGeometriesFilter (class in lmpy.data_wrangling.occurrence.intersect_geometries_wrangler) is_binary() (lmpy.tree.TreeWrapper method) is_ultrametric() (lmpy.tree.TreeWrapper method)

L

lande() (in module lmpy.statistics.pam_stats) LayerEncoder (class in lmpy.data_preparation.layer_encoder) legendre() (in module lmpy.statistics.pam_stats) lmpy module lmpy._version module lmpy.data_preparation module lmpy.data_preparation.build_grid module lmpy.data_preparation.layer_encoder module lmpy.data_preparation.occurrence_splitter module lmpy.data_preparation.tree_encoder module lmpy.data_wrangling module lmpy.data_wrangling.base module lmpy.data_wrangling.common module lmpy.data_wrangling.common.accepted_name_wrangler module lmpy.data_wrangling.factory module lmpy.data_wrangling.matrix module lmpy.data_wrangling.matrix.accepted_name_wrangler module lmpy.data_wrangling.matrix.base module lmpy.data_wrangling.matrix.match_tree_wrangler module lmpy.data_wrangling.matrix.purge_empty_slices_wrangler module lmpy.data_wrangling.matrix.subset_reorder_slices_wrangler module lmpy.data_wrangling.occurrence module lmpy.data_wrangling.occurrence.accepted_name_wrangler module lmpy.data_wrangling.occurrence.attribute_filter_wrangler module lmpy.data_wrangling.occurrence.attribute_modifier_wrangler module lmpy.data_wrangling.occurrence.base module lmpy.data_wrangling.occurrence.bounding_box_wrangler module lmpy.data_wrangling.occurrence.common_format_wrangler module lmpy.data_wrangling.occurrence.coordinate_conversion_wrangler module lmpy.data_wrangling.occurrence.decimal_precision_wrangler module lmpy.data_wrangling.occurrence.disjoint_geometries_wrangler module lmpy.data_wrangling.occurrence.intersect_geometries_wrangler module lmpy.data_wrangling.occurrence.minimum_points_wrangler module lmpy.data_wrangling.occurrence.spatial_index_wrangler module lmpy.data_wrangling.occurrence.unique_localities_wrangler module lmpy.data_wrangling.tree module lmpy.data_wrangling.tree.accepted_name_wrangler module lmpy.data_wrangling.tree.base module

lmpy.data_wrangling.tree.match_matrix_wrangler module lmpy.data_wrangling.tree.subset_tree_wrangler module lmpy.matrix module lmpy.point module lmpy.randomize module lmpy.randomize.grady module lmpy.randomize.swap module lmpy.spatial module lmpy.spatial.geojsonify module lmpy.spatial.spatial_index module lmpy.statistics module lmpy.statistics.mcpa module lmpy.statistics.pam_stats module lmpy.statistics.running_stats module lmpy.tools module lmpy.tools._config_parser module lmpy.tools.build_shapegrid module lmpy.tools.calculate_pam_stats module lmpy.tools.clean_occurrences module lmpy.tools.convert_csv_to_lmm module lmpy.tools.convert_lmm_to_csv module lmpy.tools.convert_lmm_to_geojson module lmpy.tools.create_rare_species_model module lmpy.tools.create_tree_matrix module lmpy.tools.encode_layers module lmpy.tools.mcpa_run module lmpy.tools.process_idigbio module lmpy.tools.randomize_pam module lmpy.tools.split_occurrence_data module lmpy.tools.wrangle_matrix module lmpy.tools.wrangle_tree module lmpy.tree module LmTreeException load() (lmpy.matrix.Matrix class method) load_csv() (lmpy.matrix.Matrix class method) load_flo() (lmpy.matrix.Matrix class method) LOCATION_TAG (in module lmpy.point) (in module lmpy.tools.process_idigbio) lock (in module lmpy.statistics.mcpa) LONG_VERSION_PY (in module lmpy._version)

M

main() (in module lmpy.tools.process_idigbio) make_polygon_wkt_from_points() (in module lmpy.data_preparation.build_grid) MatchMatrixTreeWrangler (class in lmpy.data_wrangling.tree.match_matrix_wrangler) MatchTreeMatrixWrangler (class in lmpy.data_wrangling.matrix.match_tree_wrangler) Matrix (class in lmpy.matrix) max_col_or_row_heuristic() (in module lmpy.randomize.grady) mcpa() (in module lmpy.statistics.mcpa) mcpa_parallel() (in module lmpy.statistics.mcpa) mean_nearest_taxon_distance() (in module lmpy.statistics.pam_stats) mean_pairwise_distance() (in module lmpy.statistics.pam_stats) min_col_or_row_heuristic() (in module lmpy.randomize.grady) MinimumPointsFilter (class in lmpy.data_wrangling.occurrence.minimum_points_wrangler) module lmpy lmpy._version lmpy.data_preparation lmpy.data_preparation.build_grid lmpy.data_preparation.layer_encoder lmpy.data_preparation.occurrence_splitter lmpy.data_preparation.tree_encoder lmpy.data_wrangling lmpy.data_wrangling.base lmpy.data_wrangling.common lmpy.data_wrangling.common.accepted_name_wrangler lmpy.data_wrangling.factory lmpy.data_wrangling.matrix lmpy.data_wrangling.matrix.accepted_name_wrangler lmpy.data_wrangling.matrix.base lmpy.data_wrangling.matrix.match_tree_wrangler lmpy.data_wrangling.matrix.purge_empty_slices_wrangler lmpy.data_wrangling.matrix.subset_reorder_slices_wrangler lmpy.data_wrangling.occurrence lmpy.data_wrangling.occurrence.accepted_name_wrangler lmpy.data_wrangling.occurrence.attribute_filter_wrangler lmpy.data_wrangling.occurrence.attribute_modifier_wrangler lmpy.data_wrangling.occurrence.base lmpy.data_wrangling.occurrence.bounding_box_wrangler lmpy.data_wrangling.occurrence.common_format_wrangler lmpy.data_wrangling.occurrence.coordinate_conversion_wrangler lmpy.data_wrangling.occurrence.decimal_precision_wrangler lmpy.data_wrangling.occurrence.disjoint_geometries_wrangler lmpy.data_wrangling.occurrence.intersect_geometries_wrangler lmpy.data_wrangling.occurrence.minimum_points_wrangler lmpy.data_wrangling.occurrence.spatial_index_wrangler lmpy.data_wrangling.occurrence.unique_localities_wrangler lmpy.data_wrangling.tree lmpy.data_wrangling.tree.accepted_name_wrangler lmpy.data_wrangling.tree.base lmpy.data_wrangling.tree.match_matrix_wrangler lmpy.data_wrangling.tree.subset_tree_wrangler lmpy.matrix lmpy.point lmpy.randomize lmpy.randomize.grady lmpy.randomize.swap lmpy.spatial lmpy.spatial.geojsonify lmpy.spatial.spatial_index lmpy.statistics lmpy.statistics.mcpa lmpy.statistics.pam_stats lmpy.statistics.running_stats lmpy.tools lmpy.tools._config_parser lmpy.tools.build_shapegrid lmpy.tools.calculate_pam_stats lmpy.tools.clean_occurrences lmpy.tools.convert_csv_to_lmm lmpy.tools.convert_lmm_to_csv lmpy.tools.convert_lmm_to_geojson lmpy.tools.create_rare_species_model lmpy.tools.create_tree_matrix lmpy.tools.encode_layers lmpy.tools.mcpa_run lmpy.tools.process_idigbio lmpy.tools.randomize_pam lmpy.tools.split_occurrence_data lmpy.tools.wrangle_matrix lmpy.tools.wrangle_tree lmpy.tree

MTX_IDX (lmpy.tree.PhyloTreeKeys attribute), [1]

N

name (lmpy.data_wrangling.base._DataWrangler attribute) (lmpy.data_wrangling.matrix.accepted_name_wrangler.AcceptedNameMatrixWrangler attribute) (lmpy.data_wrangling.matrix.base._MatrixDataWrangler attribute) (lmpy.data_wrangling.matrix.match_tree_wrangler.MatchTreeMatrixWrangler attribute) (lmpy.data_wrangling.matrix.purge_empty_slices_wrangler.PurgeEmptySlicesWrangler attribute) (lmpy.data_wrangling.matrix.subset_reorder_slices_wrangler.SubsetReorderSlicesWrangler attribute) (lmpy.data_wrangling.occurrence.accepted_name_wrangler.AcceptedNameOccurrenceWrangler attribute) (lmpy.data_wrangling.occurrence.attribute_filter_wrangler.AttributeFilterWrangler attribute) (lmpy.data_wrangling.occurrence.attribute_modifier_wrangler.AttributeModifierWrangler attribute) (lmpy.data_wrangling.occurrence.base._OccurrenceDataWrangler attribute) (lmpy.data_wrangling.occurrence.bounding_box_wrangler.BoundingBoxFilter attribute) (lmpy.data_wrangling.occurrence.common_format_wrangler.CommonFormatWrangler attribute) (lmpy.data_wrangling.occurrence.coordinate_conversion_wrangler.CoordinateConverterWrangler attribute) (lmpy.data_wrangling.occurrence.decimal_precision_wrangler.DecimalPrecisionFilter attribute) (lmpy.data_wrangling.occurrence.disjoint_geometries_wrangler.DisjointGeometriesFilter attribute) (lmpy.data_wrangling.occurrence.intersect_geometries_wrangler.IntersectGeometriesFilter attribute) (lmpy.data_wrangling.occurrence.minimum_points_wrangler.MinimumPointsFilter attribute) (lmpy.data_wrangling.occurrence.spatial_index_wrangler.SpatialIndexFilter attribute) (lmpy.data_wrangling.occurrence.unique_localities_wrangler.UniqueLocalitiesFilter attribute) (lmpy.data_wrangling.tree.accepted_name_wrangler.AcceptedNameTreeWrangler attribute) (lmpy.data_wrangling.tree.base._TreeDataWrangler attribute) (lmpy.data_wrangling.tree.match_matrix_wrangler.MatchMatrixTreeWrangler attribute) (lmpy.data_wrangling.tree.subset_tree_wrangler.SubsetTreeWrangler attribute)

none_getter() (in module lmpy.point) NotThisMethod num_sites() (in module lmpy.statistics.pam_stats) num_species() (in module lmpy.statistics.pam_stats)

O

OCCURRENCE_ROW_TYPE (in module lmpy.point) (in module lmpy.tools.process_idigbio) OccurrenceSplitter (class in lmpy.data_preparation.occurrence_splitter) omega() (in module lmpy.statistics.pam_stats) omega_proportional() (in module lmpy.statistics.pam_stats)

open() (lmpy.point.PointCsvReader method) (lmpy.point.PointCsvWriter method) (lmpy.point.PointDwcaReader method) (lmpy.point.PointJsonWriter method) open_writer() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method)

P

p_values (lmpy.statistics.running_stats.RunningStats property) PamDistMatrixMetric (class in lmpy.statistics.pam_stats) PamStats (class in lmpy.statistics.pam_stats) PamStatsMetric (class in lmpy.statistics.pam_stats) pearson_correlation() (in module lmpy.statistics.pam_stats) pep440_split_post() (in module lmpy._version) phi() (in module lmpy.statistics.pam_stats) phi_average_proportional() (in module lmpy.statistics.pam_stats) phylogenetic_diversity() (in module lmpy.statistics.pam_stats) PhyloTreeKeys (class in lmpy.tree) plus_or_dot() (in module lmpy._version) Point (class in lmpy.point)

PointCsvReader (class in lmpy.point) PointCsvWriter (class in lmpy.point) PointDwcaReader (class in lmpy.point) PointJsonWriter (class in lmpy.point) process_idb_dwca() (in module lmpy.tools.process_idigbio) process_meta_xml() (in module lmpy.tools.process_idigbio) process_reader() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) prune_tips_without_attribute() (lmpy.tree.TreeWrapper method) psi() (in module lmpy.statistics.pam_stats) psi_average_proportional() (in module lmpy.statistics.pam_stats) PurgeEmptySlicesWrangler (class in lmpy.data_wrangling.matrix.purge_empty_slices_wrangler) push() (lmpy.statistics.running_stats.RunningStats method)

R

randomize_pam() (in module lmpy.tools.randomize_pam) register_metric() (lmpy.statistics.pam_stats.PamStats method) register_vcs_handler() (in module lmpy._version) render() (in module lmpy._version) render_git_describe() (in module lmpy._version) render_git_describe_long() (in module lmpy._version) render_pep440() (in module lmpy._version) render_pep440_branch() (in module lmpy._version) render_pep440_old() (in module lmpy._version)

render_pep440_post() (in module lmpy._version) render_pep440_post_branch() (in module lmpy._version) render_pep440_pre() (in module lmpy._version) reorder() (lmpy.data_wrangling.matrix.base._MatrixDataWrangler method) report_point() (lmpy.data_wrangling.occurrence.base._OccurrenceDataWrangler method) resolve_names() (lmpy.data_wrangling.common.accepted_name_wrangler._AcceptedNameWrangler method) resolve_names_gbif() (in module lmpy.data_wrangling.common.accepted_name_wrangler) ROW_TYPE_ATT (in module lmpy.tools.process_idigbio) run_command() (in module lmpy._version) RunningStats (class in lmpy.statistics.running_stats)

S

save() (lmpy.matrix.Matrix method) (lmpy.spatial.spatial_index.SpatialIndex method) schluter_site_variance_ratio() (in module lmpy.statistics.pam_stats) schluter_species_variance_ratio() (in module lmpy.statistics.pam_stats) search() (lmpy.spatial.spatial_index.SpatialIndex method) set_attribute() (lmpy.point.Point method) set_column_headers() (lmpy.matrix.Matrix method) set_headers() (lmpy.matrix.Matrix method) set_row_headers() (lmpy.matrix.Matrix method) sigma_sites() (in module lmpy.statistics.pam_stats) sigma_species() (in module lmpy.statistics.pam_stats) site_matrix_stats (lmpy.statistics.pam_stats.PamStats attribute) site_pam_dist_mtx_stats (lmpy.statistics.pam_stats.PamStats attribute) site_tree_distance_matrix_stats (lmpy.statistics.pam_stats.PamStats attribute)

site_tree_stats (lmpy.statistics.pam_stats.PamStats attribute) SiteMatrixMetric (class in lmpy.statistics.pam_stats) slice() (lmpy.matrix.Matrix method) slice_by_header() (lmpy.matrix.Matrix method) SpatialIndex (class in lmpy.spatial.spatial_index) SpatialIndexFilter (class in lmpy.data_wrangling.occurrence.spatial_index_wrangler) species_matrix_stats (lmpy.statistics.pam_stats.PamStats attribute) SpeciesMatrixMetric (class in lmpy.statistics.pam_stats) square_wkt_generator() (in module lmpy.data_preparation.build_grid) SQUID (lmpy.tree.PhyloTreeKeys attribute), [1] standard_deviation (lmpy.statistics.running_stats.RunningStats property) SubsetReorderSlicesWrangler (class in lmpy.data_wrangling.matrix.subset_reorder_slices_wrangler) SubsetTreeWrangler (class in lmpy.data_wrangling.tree.subset_tree_wrangler) sum_pairwise_distance() (in module lmpy.statistics.pam_stats) swap_randomize() (in module lmpy.randomize.swap)

T

T (lmpy.matrix.Matrix property) TERM_TYPE_ATT (in module lmpy.tools.process_idigbio) test_dwca() (in module lmpy.tools.process_idigbio) total_fill_percentage_heuristic() (in module lmpy.randomize.grady) transpose() (lmpy.matrix.Matrix method)

TreeDistanceMatrixMetric (class in lmpy.statistics.pam_stats) TreeEncoder (class in lmpy.data_preparation.tree_encoder) TreeMetric (class in lmpy.statistics.pam_stats) TreeWrapper (class in lmpy.tree) trial_swap() (in module lmpy.randomize.swap)

U

UniqueLocalitiesFilter (class in lmpy.data_wrangling.occurrence.unique_localities_wrangler)

V

validate() (lmpy.data_preparation.tree_encoder.TreeEncoder method) variance (lmpy.statistics.running_stats.RunningStats property) version (lmpy.data_wrangling.base._DataWrangler attribute) (lmpy.data_wrangling.matrix.accepted_name_wrangler.AcceptedNameMatrixWrangler attribute) (lmpy.data_wrangling.matrix.match_tree_wrangler.MatchTreeMatrixWrangler attribute) (lmpy.data_wrangling.matrix.purge_empty_slices_wrangler.PurgeEmptySlicesWrangler attribute) (lmpy.data_wrangling.matrix.subset_reorder_slices_wrangler.SubsetReorderSlicesWrangler attribute) (lmpy.data_wrangling.occurrence.accepted_name_wrangler.AcceptedNameOccurrenceWrangler attribute) (lmpy.data_wrangling.occurrence.attribute_filter_wrangler.AttributeFilterWrangler attribute) (lmpy.data_wrangling.occurrence.attribute_modifier_wrangler.AttributeModifierWrangler attribute) (lmpy.data_wrangling.occurrence.bounding_box_wrangler.BoundingBoxFilter attribute) (lmpy.data_wrangling.occurrence.common_format_wrangler.CommonFormatWrangler attribute) (lmpy.data_wrangling.occurrence.coordinate_conversion_wrangler.CoordinateConverterWrangler attribute) (lmpy.data_wrangling.occurrence.decimal_precision_wrangler.DecimalPrecisionFilter attribute) (lmpy.data_wrangling.occurrence.disjoint_geometries_wrangler.DisjointGeometriesFilter attribute) (lmpy.data_wrangling.occurrence.intersect_geometries_wrangler.IntersectGeometriesFilter attribute) (lmpy.data_wrangling.occurrence.minimum_points_wrangler.MinimumPointsFilter attribute) (lmpy.data_wrangling.occurrence.spatial_index_wrangler.SpatialIndexFilter attribute) (lmpy.data_wrangling.occurrence.unique_localities_wrangler.UniqueLocalitiesFilter attribute) (lmpy.data_wrangling.tree.accepted_name_wrangler.AcceptedNameTreeWrangler attribute) (lmpy.data_wrangling.tree.match_matrix_wrangler.MatchMatrixTreeWrangler attribute) (lmpy.data_wrangling.tree.subset_tree_wrangler.SubsetTreeWrangler attribute)

VersioneerConfig (class in lmpy._version) versions_from_parentdir() (in module lmpy._version)

W

whittaker() (in module lmpy.statistics.pam_stats) wrangle_matrix() (in module lmpy.tools.wrangle_matrix) (lmpy.data_wrangling.matrix.accepted_name_wrangler.AcceptedNameMatrixWrangler method) (lmpy.data_wrangling.matrix.base._MatrixDataWrangler method) (lmpy.data_wrangling.matrix.match_tree_wrangler.MatchTreeMatrixWrangler method) (lmpy.data_wrangling.matrix.purge_empty_slices_wrangler.PurgeEmptySlicesWrangler method) (lmpy.data_wrangling.matrix.subset_reorder_slices_wrangler.SubsetReorderSlicesWrangler method) wrangle_points() (lmpy.data_wrangling.occurrence.base._OccurrenceDataWrangler method) (lmpy.data_wrangling.occurrence.minimum_points_wrangler.MinimumPointsFilter method) (lmpy.data_wrangling.occurrence.unique_localities_wrangler.UniqueLocalitiesFilter method) wrangle_single_point() (lmpy.data_wrangling.occurrence.base._OccurrenceDataWrangler method) wrangle_tree() (in module lmpy.tools.wrangle_tree) (lmpy.data_wrangling.tree.accepted_name_wrangler.AcceptedNameTreeWrangler method) (lmpy.data_wrangling.tree.base._TreeDataWrangler method) (lmpy.data_wrangling.tree.match_matrix_wrangler.MatchMatrixTreeWrangler method) (lmpy.data_wrangling.tree.subset_tree_wrangler.SubsetTreeWrangler method)

WranglerFactory (class in lmpy.data_wrangling.factory) write() (lmpy.matrix.Matrix method) write_csv() (lmpy.matrix.Matrix method) write_map_to_file() (lmpy.data_wrangling.common.accepted_name_wrangler._AcceptedNameWrangler method) write_points() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) (lmpy.point.PointCsvWriter method) (lmpy.point.PointJsonWriter method) write_tiff() (in module lmpy.tools.create_rare_species_model)