Index

_

__array_finalize__() (lmpy.matrix.Matrix method) __call__() (lmpy.statistics.pam_stats.PamStatsMetric method) __del__() (lmpy.data_wrangling.common.accepted_name_wrangler._AcceptedNameWrangler method) __enter__() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) (lmpy.point._IdigBioCsvReader 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._IdigBioCsvReader method) (lmpy.point.PointCsvReader method) (lmpy.point.PointCsvWriter method) (lmpy.point.PointDwcaReader method) (lmpy.point.PointJsonWriter method) __iter__() (lmpy.point._IdigBioCsvReader method) (lmpy.point.PointCsvReader method) (lmpy.point.PointDwcaReader method) __lt__() (lmpy.point.Point method) __next__() (lmpy.point._IdigBioCsvReader method) (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) _create_mask() (in module lmpy.sdm.model) _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_attribute_func() (lmpy.data_wrangling.occurrence.attribute_modifier_wrangler.AttributeModifierWrangler method) _get_constant_func() (lmpy.data_wrangling.occurrence.attribute_modifier_wrangler.AttributeModifierWrangler static 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) _IdigBioCsvReader (class in lmpy.point) _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) _log() (lmpy.statistics.pam_stats.PamStats 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.match_species_list_wrangler.MatchSpeciesListWrangler 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_grid() (lmpy.data_preparation.layer_encoder.LayerEncoder method) _read_layer() (lmpy.data_preparation.layer_encoder.LayerEncoder method) _read_raster_layer() (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) _resolve_gbif_synonym_match() (in module lmpy.data_wrangling.common.accepted_name_wrangler) _SpeciesListDataWrangler (class in lmpy.data_wrangling.species_list.base) _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) AcceptedNameSpeciesListWrangler (class in lmpy.data_wrangling.species_list.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) add_permutation() (lmpy.statistics.significance.PermutationTests 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

BONFERRONI (lmpy.statistics.significance.SignificanceMethod attribute) BoundingBoxFilter (class in lmpy.data_wrangling.occurrence.bounding_box_wrangler) build_grid() (in module lmpy.data_preparation.build_grid) (in module lmpy.tools.build_grid) build_parser() (in module lmpy.tools.aggregate_matrices) (in module lmpy.tools.build_grid) (in module lmpy.tools.calculate_p_values) (in module lmpy.tools.calculate_pam_stats) (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_point_heatmap) (in module lmpy.tools.create_rare_species_model) (in module lmpy.tools.create_scatter_plot) (in module lmpy.tools.create_sdm) (in module lmpy.tools.create_stat_heatmap) (in module lmpy.tools.create_tree_matrix) (in module lmpy.tools.encode_layers) (in module lmpy.tools.encode_tree_mcpa) (in module lmpy.tools.mcpa_run) (in module lmpy.tools.project_sdm) (in module lmpy.tools.randomize_pam) (in module lmpy.tools.split_occurrence_data) (in module lmpy.tools.wrangle_matrix) (in module lmpy.tools.wrangle_occurrences) (in module lmpy.tools.wrangle_species_list)

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.wrangle_occurrences) cli() (in module lmpy.tools.aggregate_matrices) (in module lmpy.tools.build_grid) (in module lmpy.tools.calculate_p_values) (in module lmpy.tools.calculate_pam_stats) (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_point_heatmap) (in module lmpy.tools.create_rare_species_model) (in module lmpy.tools.create_scatter_plot) (in module lmpy.tools.create_sdm) (in module lmpy.tools.create_stat_heatmap) (in module lmpy.tools.create_tree_matrix) (in module lmpy.tools.encode_layers) (in module lmpy.tools.encode_tree_mcpa) (in module lmpy.tools.mcpa_run) (in module lmpy.tools.project_sdm) (in module lmpy.tools.randomize_pam) (in module lmpy.tools.split_occurrence_data) (in module lmpy.tools.wrangle_matrix) (in module lmpy.tools.wrangle_occurrences) (in module lmpy.tools.wrangle_species_list) (in module lmpy.tools.wrangle_tree)

close() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) (lmpy.point._IdigBioCsvReader 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) (in module lmpy.statistics.significance) compare_signed_values() (in module lmpy.statistics.running_stats) (in module lmpy.statistics.significance) concatenate() (lmpy.matrix.Matrix class method) CONCURRENCY_FACTOR (in module lmpy.statistics.mcpa) confidence_ellipse() (in module lmpy.plots.scatter) 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) covariance_stats (lmpy.statistics.pam_stats.PamStats attribute) CovarianceMatrixMetric (class in lmpy.statistics.pam_stats) create_map_matrix() (in module lmpy.plots.map) create_maxent_layer_label() (in module lmpy.sdm.model) create_maxent_model() (in module lmpy.sdm.maxent) create_point_heatmap_matrix() (in module lmpy.plots.map) create_rare_species_model() (in module lmpy.tools.create_rare_species_model) create_scatter_plot() (in module lmpy.plots.scatter) create_sdm() (in module lmpy.sdm.model) create_stat_heatmap_matrix() (in module lmpy.plots.map)

D

Data Wrangler DATE_FORMAT (in module lmpy.log) DecimalPrecisionFilter (class in lmpy.data_wrangling.occurrence.decimal_precision_wrangler) DEFAULT_MAXENT_OPTIONS (in module lmpy.sdm.maxent) 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.point) DELIMITED_TERMS (in module lmpy.point) DESCRIPTION (in module lmpy.tools.create_sdm) (in module lmpy.tools.project_sdm) 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 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.point)

F

FDR (lmpy.statistics.significance.SignificanceMethod attribute) FIELD_TAG (in module lmpy.point) FILES_TAG (in module lmpy.point) fill_shuffle_reshape_heuristic() (in module lmpy.randomize.grady) flatten_2d() (lmpy.matrix.Matrix method) flush_writers() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method)

FORMAT (in module lmpy.log) 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) (lmpy.species_list.SpeciesList 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) (lmpy.statistics.significance.PermutationTests method)

get_report() (lmpy.data_preparation.layer_encoder.LayerEncoder method) (lmpy.data_wrangling.base._DataWrangler method) (lmpy.data_wrangling.occurrence.base._OccurrenceDataWrangler method) (lmpy.data_wrangling.tree.base._TreeDataWrangler method) get_row_col_for_x_y_func() (in module lmpy.plots.map) get_row_headers() (lmpy.matrix.Matrix method) get_significant_values() (in module lmpy.statistics.significance) get_species_seen() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter 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) Grid

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) IntersectGeometriesFilter (class in lmpy.data_wrangling.occurrence.intersect_geometries_wrangler)

IntersectionSpeciesListWrangler (class in lmpy.data_wrangling.species_list.intersect_species_list_wrangler) is_binary() (lmpy.tree.TreeWrapper method) is_ultrametric() (lmpy.tree.TreeWrapper method)

J

JAVA_CMD (in module lmpy.sdm.maxent)

JAVA_OPTS (in module lmpy.sdm.maxent)

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_species_list_wrangler 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.match_species_list_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.species_list module lmpy.data_wrangling.species_list.accepted_name_wrangler module lmpy.data_wrangling.species_list.base module lmpy.data_wrangling.species_list.intersect_species_list_wrangler module lmpy.data_wrangling.species_list.match_matrix_wrangler module lmpy.data_wrangling.species_list.match_tree_wrangler module lmpy.data_wrangling.species_list.union_species_list_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.match_species_list_wrangler module lmpy.data_wrangling.tree.subset_tree_wrangler module lmpy.log module lmpy.matrix module

lmpy.plots module lmpy.plots.map module lmpy.plots.scatter module lmpy.point module lmpy.randomize module lmpy.randomize.grady module lmpy.randomize.swap module lmpy.sdm module lmpy.sdm.maxent module lmpy.sdm.model module lmpy.spatial module lmpy.spatial.geojsonify module lmpy.spatial.spatial_index module lmpy.species_list module lmpy.statistics module lmpy.statistics.mcpa module lmpy.statistics.pam_stats module lmpy.statistics.running_stats module lmpy.statistics.significance module lmpy.tools module lmpy.tools._config_parser module lmpy.tools.aggregate_matrices module lmpy.tools.build_grid module lmpy.tools.calculate_p_values module lmpy.tools.calculate_pam_stats 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_point_heatmap module lmpy.tools.create_rare_species_model module lmpy.tools.create_scatter_plot module lmpy.tools.create_sdm module lmpy.tools.create_stat_heatmap module lmpy.tools.create_tree_matrix module lmpy.tools.encode_layers module lmpy.tools.encode_tree_mcpa module lmpy.tools.mcpa_run module lmpy.tools.project_sdm module lmpy.tools.randomize_pam module lmpy.tools.split_occurrence_data module lmpy.tools.wrangle_matrix module lmpy.tools.wrangle_occurrences module lmpy.tools.wrangle_species_list 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) lock (in module lmpy.statistics.mcpa) log() (lmpy.log.Logger method) Logger (class in lmpy.log) LONG_VERSION_PY (in module lmpy._version)

M

make_polygon_wkt_from_points() (in module lmpy.data_preparation.build_grid) match_headers() (in module lmpy.sdm.model) MatchMatrixSpeciesListWrangler (class in lmpy.data_wrangling.species_list.match_matrix_wrangler) MatchMatrixTreeWrangler (class in lmpy.data_wrangling.tree.match_matrix_wrangler) MatchSpeciesListMatrixWrangler (class in lmpy.data_wrangling.matrix.match_species_list_wrangler) MatchSpeciesListTreeWrangler (class in lmpy.data_wrangling.tree.match_species_list_wrangler) MatchSpeciesListWrangler (class in lmpy.data_wrangling.occurrence.match_species_list_wrangler) MatchTreeMatrixWrangler (class in lmpy.data_wrangling.matrix.match_tree_wrangler) MatchTreeSpeciesListWrangler (class in lmpy.data_wrangling.species_list.match_tree_wrangler) Matrix (class in lmpy.matrix) max_col_or_row_heuristic() (in module lmpy.randomize.grady) MAXENT_CONVERT_TOOL (in module lmpy.sdm.maxent) MAXENT_JAR (in module lmpy.sdm.maxent) MAXENT_MODEL_TOOL (in module lmpy.sdm.maxent) MAXENT_PROJECT_TOOL (in module lmpy.sdm.maxent) MAXENT_VERSION (in module lmpy.sdm.maxent) 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_species_list_wrangler 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.match_species_list_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.species_list lmpy.data_wrangling.species_list.accepted_name_wrangler lmpy.data_wrangling.species_list.base lmpy.data_wrangling.species_list.intersect_species_list_wrangler lmpy.data_wrangling.species_list.match_matrix_wrangler lmpy.data_wrangling.species_list.match_tree_wrangler lmpy.data_wrangling.species_list.union_species_list_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.match_species_list_wrangler lmpy.data_wrangling.tree.subset_tree_wrangler lmpy.log lmpy.matrix lmpy.plots lmpy.plots.map lmpy.plots.scatter lmpy.point lmpy.randomize lmpy.randomize.grady lmpy.randomize.swap lmpy.sdm lmpy.sdm.maxent lmpy.sdm.model lmpy.spatial lmpy.spatial.geojsonify lmpy.spatial.spatial_index lmpy.species_list lmpy.statistics lmpy.statistics.mcpa lmpy.statistics.pam_stats lmpy.statistics.running_stats lmpy.statistics.significance lmpy.tools lmpy.tools._config_parser lmpy.tools.aggregate_matrices lmpy.tools.build_grid lmpy.tools.calculate_p_values lmpy.tools.calculate_pam_stats lmpy.tools.convert_csv_to_lmm lmpy.tools.convert_lmm_to_csv lmpy.tools.convert_lmm_to_geojson lmpy.tools.create_point_heatmap lmpy.tools.create_rare_species_model lmpy.tools.create_scatter_plot lmpy.tools.create_sdm lmpy.tools.create_stat_heatmap lmpy.tools.create_tree_matrix lmpy.tools.encode_layers lmpy.tools.encode_tree_mcpa lmpy.tools.mcpa_run lmpy.tools.project_sdm lmpy.tools.randomize_pam lmpy.tools.split_occurrence_data lmpy.tools.wrangle_matrix lmpy.tools.wrangle_occurrences lmpy.tools.wrangle_species_list 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_species_list_wrangler.MatchSpeciesListMatrixWrangler 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.match_species_list_wrangler.MatchSpeciesListWrangler 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.species_list.accepted_name_wrangler.AcceptedNameSpeciesListWrangler attribute) (lmpy.data_wrangling.species_list.base._SpeciesListDataWrangler attribute) (lmpy.data_wrangling.species_list.intersect_species_list_wrangler.IntersectionSpeciesListWrangler attribute) (lmpy.data_wrangling.species_list.match_matrix_wrangler.MatchMatrixSpeciesListWrangler attribute) (lmpy.data_wrangling.species_list.match_tree_wrangler.MatchTreeSpeciesListWrangler attribute) (lmpy.data_wrangling.species_list.union_species_list_wrangler.UnionSpeciesListWrangler 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.match_species_list_wrangler.MatchSpeciesListTreeWrangler 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) 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._IdigBioCsvReader method) (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) PermutationTests (class in lmpy.statistics.significance) 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) plot_matrix() (in module lmpy.plots.map) 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_reader() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) project_maxent_model() (in module lmpy.sdm.maxent) project_sdm() (in module lmpy.sdm.model) 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) RAW (lmpy.statistics.significance.SignificanceMethod attribute) 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.point) 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) script_name (in module lmpy.sdm.model) 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) SignificanceMethod (class in lmpy.statistics.significance) 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 Distribution Model SPECIES_ATTRIBUTE (lmpy.point.Point attribute) species_matrix_stats (lmpy.statistics.pam_stats.PamStats attribute) SpeciesList (class in lmpy.species_list) 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) standardize_species_name() (lmpy.point.Point class method) 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) test_files() (in module lmpy.tools._config_parser) test_inputs() (in module lmpy.tools.create_sdm) test_subprocess() (in module lmpy.sdm.maxent) total_fill_percentage_heuristic() (in module lmpy.randomize.grady) transpose() (lmpy.matrix.Matrix method)

Tree 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

UnionSpeciesListWrangler (class in lmpy.data_wrangling.species_list.union_species_list_wrangler)

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_species_list_wrangler.MatchSpeciesListMatrixWrangler 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.match_species_list_wrangler.MatchSpeciesListWrangler 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.species_list.accepted_name_wrangler.AcceptedNameSpeciesListWrangler attribute) (lmpy.data_wrangling.species_list.intersect_species_list_wrangler.IntersectionSpeciesListWrangler attribute) (lmpy.data_wrangling.species_list.match_matrix_wrangler.MatchMatrixSpeciesListWrangler attribute) (lmpy.data_wrangling.species_list.match_tree_wrangler.MatchTreeSpeciesListWrangler attribute) (lmpy.data_wrangling.species_list.union_species_list_wrangler.UnionSpeciesListWrangler attribute) (lmpy.data_wrangling.tree.accepted_name_wrangler.AcceptedNameTreeWrangler attribute) (lmpy.data_wrangling.tree.match_matrix_wrangler.MatchMatrixTreeWrangler attribute) (lmpy.data_wrangling.tree.match_species_list_wrangler.MatchSpeciesListTreeWrangler 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) workdir (in module lmpy.tools.create_sdm) (in module lmpy.tools.project_sdm) 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_species_list_wrangler.MatchSpeciesListMatrixWrangler 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_species_list() (in module lmpy.tools.wrangle_species_list) (lmpy.data_wrangling.species_list.accepted_name_wrangler.AcceptedNameSpeciesListWrangler method) (lmpy.data_wrangling.species_list.base._SpeciesListDataWrangler method) (lmpy.data_wrangling.species_list.intersect_species_list_wrangler.IntersectionSpeciesListWrangler method) (lmpy.data_wrangling.species_list.match_matrix_wrangler.MatchMatrixSpeciesListWrangler method) (lmpy.data_wrangling.species_list.match_tree_wrangler.MatchTreeSpeciesListWrangler method) (lmpy.data_wrangling.species_list.union_species_list_wrangler.UnionSpeciesListWrangler 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.match_species_list_wrangler.MatchSpeciesListTreeWrangler method) (lmpy.data_wrangling.tree.subset_tree_wrangler.SubsetTreeWrangler method) WranglerFactory (class in lmpy.data_wrangling.factory) write() (lmpy.matrix.Matrix method) (lmpy.species_list.SpeciesList 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_species_list() (lmpy.data_preparation.occurrence_splitter.OccurrenceSplitter method) write_tiff() (in module lmpy.tools.create_rare_species_model)

X

X_ATTRIBUTE (lmpy.point.Point attribute)

Y

Y_ATTRIBUTE (lmpy.point.Point attribute)