Index

A

add_ebd_tab_from_singlem() (qdiv.MicrobiomeData method) add_meta() (qdiv.MicrobiomeData method) add_seq_from_fasta() (qdiv.MicrobiomeData method) add_tab() (qdiv.MicrobiomeData method) add_tab_from_coverm() (qdiv.MicrobiomeData method) add_tax() (qdiv.MicrobiomeData method) add_tax_from_gtdbtk() (qdiv.MicrobiomeData method)

add_tax_from_qiime() (qdiv.MicrobiomeData method) add_tax_from_sintax() (qdiv.MicrobiomeData method) add_tree() (qdiv.MicrobiomeData method) align() (in module qdiv.sequences), [1], [2] (in module qdiv.sequences.sequence_comparisons) alpha_diversity_profile() (in module qdiv.plot), [1] (in module qdiv.plot.diversity_plots)

B

beta_diversity_profile() (in module qdiv.plot), [1] (in module qdiv.plot.diversity_plots) beta_mntdq() (in module qdiv.diversity), [1] (in module qdiv.diversity.beta_div) beta_mpdq() (in module qdiv.diversity), [1] (in module qdiv.diversity.beta_div) beta_nriq() (in module qdiv.model), [1], [2] (in module qdiv.model.null)

beta_ntiq() (in module qdiv.model), [1], [2] (in module qdiv.model.null) bootstrap_sample_matrix() (in module qdiv.stats), [1] (in module qdiv.stats.data_stats) bray() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.beta_div)

C

clean_tax() (qdiv.MicrobiomeData method) codes (qdiv.plot.ordination_plots.TextPath property) community_sample() (in module qdiv.model), [1] (in module qdiv.model.simulate) compute_Tmean() (in module qdiv.diversity.alpha_div) (in module qdiv.diversity.beta_div) consensus() (in module qdiv.sequences), [1], [2] (in module qdiv.sequences.sequence_comparisons)

contains() (qdiv.plot.ordination_plots.Patch method) contains_point() (qdiv.plot.ordination_plots.Patch method) contains_points() (qdiv.plot.ordination_plots.Patch method) copy() (qdiv.MicrobiomeData method) (qdiv.plot.ordination_plots.FontProperties method) corr() (in module qdiv.stats), [1] (in module qdiv.stats.data_stats)

D

dbrda() (in module qdiv.stats), [1], [2] (in module qdiv.stats.ordination_calculations) dissimilarity_by_feature() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.beta_div)

dissimilarity_contributions() (in module qdiv.plot), [1], [2] (in module qdiv.plot.diversity_plots) draw() (qdiv.plot.ordination_plots.Patch method)

E

evenness() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.beta_div)

F

fill (qdiv.plot.ordination_plots.Patch property) FontProperties (class in qdiv.plot.ordination_plots) from_dict() (qdiv.MicrobiomeData class method) func_alpha() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.alpha_div) (in module qdiv.plot.diversity_plots)

func_beta() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.beta_div) func_multi_beta() (in module qdiv.diversity), [1] (in module qdiv.diversity.beta_div) (in module qdiv.plot.diversity_plots)

G

generate_interdependence_matrix() (in module qdiv.model), [1] (in module qdiv.model.simulate) get_aa() (qdiv.plot.ordination_plots.Patch method) get_antialiased() (qdiv.plot.ordination_plots.Patch method) get_capstyle() (qdiv.plot.ordination_plots.Patch method) get_colors_markers() (in module qdiv.plot.diversity_plots) get_data_transform() (qdiv.plot.ordination_plots.Patch method) get_ec() (qdiv.plot.ordination_plots.Patch method) get_edgecolor() (qdiv.plot.ordination_plots.Patch method) get_extents() (qdiv.plot.ordination_plots.Patch method) get_facecolor() (qdiv.plot.ordination_plots.Patch method) get_family() (qdiv.plot.ordination_plots.FontProperties method) get_fc() (qdiv.plot.ordination_plots.Patch method) get_file() (qdiv.plot.ordination_plots.FontProperties method) get_fill() (qdiv.plot.ordination_plots.Patch method) get_fontconfig_pattern() (qdiv.plot.ordination_plots.FontProperties method) get_hatch() (qdiv.plot.ordination_plots.Patch method) get_hatch_linewidth() (qdiv.plot.ordination_plots.Patch method) get_joinstyle() (qdiv.plot.ordination_plots.Patch method) get_linestyle() (qdiv.plot.ordination_plots.Patch method)

get_linewidth() (qdiv.plot.ordination_plots.Patch method) get_ls() (qdiv.plot.ordination_plots.Patch method) get_lw() (qdiv.plot.ordination_plots.Patch method) get_math_fontfamily() (qdiv.plot.ordination_plots.FontProperties method) get_name() (qdiv.plot.ordination_plots.FontProperties method) get_patch_transform() (qdiv.plot.ordination_plots.Patch method) get_path() (qdiv.plot.ordination_plots.Patch method) get_size() (qdiv.plot.ordination_plots.FontProperties method) (qdiv.plot.ordination_plots.TextPath method) get_size_in_points() (qdiv.plot.ordination_plots.FontProperties method) get_slant() (qdiv.plot.ordination_plots.FontProperties method) get_stretch() (qdiv.plot.ordination_plots.FontProperties method) get_style() (qdiv.plot.ordination_plots.FontProperties method) get_transform() (qdiv.plot.ordination_plots.Patch method) get_variant() (qdiv.plot.ordination_plots.FontProperties method) get_verts() (qdiv.plot.ordination_plots.Patch method) get_weight() (qdiv.plot.ordination_plots.FontProperties method) get_window_extent() (qdiv.plot.ordination_plots.Patch method) gower() (in module qdiv.stats), [1] (in module qdiv.stats.distance_tests)

H

harvey_balls() (in module qdiv.plot), [1], [2] (in module qdiv.plot.diversity_plots)

heatmap() (in module qdiv.plot), [1], [2] (in module qdiv.plot.relative_abundance_plots)

I

info() (qdiv.MicrobiomeData method)

J

jaccard() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.beta_div)

L

load() (qdiv.MicrobiomeData class method) load_compressed_matrix() (in module qdiv.sequences), [1] (in module qdiv.sequences.sequence_comparisons)

load_example() (qdiv.MicrobiomeData class method)

M

make_beta_splitting_tree_df() (in module qdiv.model), [1] (in module qdiv.model.simulate) make_block_tree_df() (in module qdiv.model), [1] (in module qdiv.model.simulate) mantel() (in module qdiv.stats), [1], [2] (in module qdiv.stats.distance_tests) marginal_factor_tests_dbrda() (in module qdiv.stats.ordination_calculations) merge_objects() (in module qdiv.sequences), [1], [2] (in module qdiv.sequences.sequence_comparisons) merge_samples() (in module qdiv.io) (qdiv.MicrobiomeData method) meta (qdiv.MicrobiomeData attribute) MicrobiomeData (class in qdiv) mntdq() (in module qdiv.diversity), [1] (in module qdiv.diversity.alpha_div) module qdiv.data_object qdiv.diversity, [1] qdiv.diversity.alpha_div qdiv.diversity.beta_div qdiv.io qdiv.model, [1] qdiv.model.null qdiv.model.simulate qdiv.plot, [1] qdiv.plot.diversity_plots qdiv.plot.ordination_plots qdiv.plot.relative_abundance_plots qdiv.sequences, [1] qdiv.sequences.sequence_comparisons qdiv.stats, [1] qdiv.stats.data_stats qdiv.stats.distance_tests qdiv.stats.ordination_calculations

mpdq() (in module qdiv.diversity), [1] (in module qdiv.diversity.alpha_div)

N

naive_alpha() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.alpha_div) (in module qdiv.plot.diversity_plots) naive_beta() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.beta_div) naive_multi_beta() (in module qdiv.diversity), [1] (in module qdiv.diversity.beta_div) (in module qdiv.plot.diversity_plots)

nriq() (in module qdiv.model), [1], [2] (in module qdiv.model.null) ntiq() (in module qdiv.model), [1], [2] (in module qdiv.model.null)

O

octave() (in module qdiv.plot), [1], [2] (in module qdiv.plot.relative_abundance_plots)

ordination() (in module qdiv.plot), [1], [2] (in module qdiv.plot.ordination_plots)

P

Patch (class in qdiv.plot.ordination_plots) pcoa_lingoes() (in module qdiv.stats), [1], [2] (in module qdiv.stats.ordination_calculations) permanova() (in module qdiv.stats), [1], [2] (in module qdiv.stats.distance_tests) phyl_alpha() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.alpha_div) (in module qdiv.plot.diversity_plots) phyl_beta() (in module qdiv.diversity), [1], [2] (in module qdiv.diversity.beta_div)

phyl_multi_beta() (in module qdiv.diversity), [1] (in module qdiv.diversity.beta_div) (in module qdiv.plot.diversity_plots) phyl_tree() (in module qdiv.plot), [1], [2] (in module qdiv.plot.diversity_plots) phylo_tree() (in module qdiv.plot), [1] pie() (in module qdiv.plot), [1], [2] (in module qdiv.plot.relative_abundance_plots) prune_tree() (qdiv.MicrobiomeData method)

Q

qdiv.data_object module qdiv.diversity module, [1] qdiv.diversity.alpha_div module qdiv.diversity.beta_div module qdiv.io module qdiv.model module, [1] qdiv.model.null module qdiv.model.simulate module qdiv.plot module, [1]

qdiv.plot.diversity_plots module qdiv.plot.ordination_plots module qdiv.plot.relative_abundance_plots module qdiv.sequences module, [1] qdiv.sequences.sequence_comparisons module qdiv.stats module, [1] qdiv.stats.data_stats module qdiv.stats.distance_tests module qdiv.stats.ordination_calculations module

R

ra_to_branches() (in module qdiv.diversity.alpha_div) (in module qdiv.diversity.beta_div) rarefactioncurve() (in module qdiv.plot), [1], [2] (in module qdiv.plot.relative_abundance_plots)

rarefy() (in module qdiv.io) (qdiv.MicrobiomeData method) rcq() (in module qdiv.model), [1], [2] (in module qdiv.model.null) rename_features() (qdiv.MicrobiomeData method)

S

save() (qdiv.MicrobiomeData method) seq (qdiv.MicrobiomeData attribute) sequence_distance_matrix() (in module qdiv.sequences), [1], [2] (in module qdiv.sequences.sequence_comparisons) set() (qdiv.plot.ordination_plots.Patch method) set_aa() (qdiv.plot.ordination_plots.Patch method) set_alpha() (qdiv.plot.ordination_plots.Patch method) set_antialiased() (qdiv.plot.ordination_plots.Patch method) set_capstyle() (qdiv.plot.ordination_plots.Patch method) set_color() (qdiv.plot.ordination_plots.Patch method) set_ec() (qdiv.plot.ordination_plots.Patch method) set_edgecolor() (qdiv.plot.ordination_plots.Patch method) set_facecolor() (qdiv.plot.ordination_plots.Patch method) set_family() (qdiv.plot.ordination_plots.FontProperties method) set_fc() (qdiv.plot.ordination_plots.Patch method) set_file() (qdiv.plot.ordination_plots.FontProperties method) set_fill() (qdiv.plot.ordination_plots.Patch method) set_fontconfig_pattern() (qdiv.plot.ordination_plots.FontProperties method) set_hatch() (qdiv.plot.ordination_plots.Patch method) set_hatch_linewidth() (qdiv.plot.ordination_plots.Patch method) set_joinstyle() (qdiv.plot.ordination_plots.Patch method) set_linestyle() (qdiv.plot.ordination_plots.Patch method) set_linewidth() (qdiv.plot.ordination_plots.Patch method) set_ls() (qdiv.plot.ordination_plots.Patch method)

set_lw() (qdiv.plot.ordination_plots.Patch method) set_math_fontfamily() (qdiv.plot.ordination_plots.FontProperties method) set_name() (qdiv.plot.ordination_plots.FontProperties method) set_size() (qdiv.plot.ordination_plots.FontProperties method) (qdiv.plot.ordination_plots.TextPath method) set_slant() (qdiv.plot.ordination_plots.FontProperties method) set_stretch() (qdiv.plot.ordination_plots.FontProperties method) set_style() (qdiv.plot.ordination_plots.FontProperties method) set_variant() (qdiv.plot.ordination_plots.FontProperties method) set_weight() (qdiv.plot.ordination_plots.FontProperties method) simulate_assembly() (in module qdiv.model), [1] (in module qdiv.model.simulate) simulate_community() (in module qdiv.model), [1] (in module qdiv.model.simulate) subset_abundant() (in module qdiv.io) (qdiv.MicrobiomeData method) subset_features() (in module qdiv.io) (qdiv.MicrobiomeData method) subset_samples() (in module qdiv.io) (qdiv.MicrobiomeData method) subset_taxa() (in module qdiv.io) (qdiv.MicrobiomeData method) summarize_dbrda() (in module qdiv.stats), [1], [2] (in module qdiv.stats.ordination_calculations) summarize_taxa() (qdiv.MicrobiomeData method)

T

tab (qdiv.MicrobiomeData attribute) tax (qdiv.MicrobiomeData attribute) tax_prefix() (qdiv.MicrobiomeData method) TextPath (class in qdiv.plot.ordination_plots)

to_dict() (qdiv.MicrobiomeData method) tree (qdiv.MicrobiomeData attribute) tree_distance_matrix() (in module qdiv.sequences), [1], [2] (in module qdiv.sequences.sequence_comparisons)

U

update_from() (qdiv.plot.ordination_plots.Patch method)

V

vertices (qdiv.plot.ordination_plots.TextPath property)