qdiv

• qdiv package
  • Overview
  • Core subpackages
    • qdiv.diversity
      • diversity
      • naive_alpha()
      • phyl_alpha()
      • func_alpha()
      • mpdq()
      • mntdq()
      • naive_beta()
      • phyl_beta()
      • func_beta()
      • bray()
      • jaccard()
      • naive_multi_beta()
      • phyl_multi_beta()
      • func_multi_beta()
      • evenness()
      • dissimilarity_by_feature()
      • beta_mpdq()
      • beta_mntdq()
    • qdiv.stats
      • stats
      • mantel()
      • permanova()
      • gower()
      • pcoa_lingoes()
      • dbrda()
      • summarize_dbrda()
      • corr()
      • bootstrap_sample_matrix()
    • qdiv.plot
      • plot
      • heatmap()
      • rarefactioncurve()
      • octave()
      • pie()
      • ordination()
      • dissimilarity_contributions()
      • phyl_tree()
      • harvey_balls()
      • alpha_diversity_profile()
      • beta_diversity_profile()
      • phylo_tree()
    • qdiv.model
      • model
      • rcq()
      • nriq()
      • ntiq()
      • beta_nriq()
      • beta_ntiq()
      • simulate_community()
      • community_sample()
      • simulate_assembly()
      • generate_interdependence_matrix()
      • make_block_tree_df()
      • make_beta_splitting_tree_df()
    • qdiv.sequences
      • sequences
      • sequence_distance_matrix()
      • tree_distance_matrix()
      • load_compressed_matrix()
      • align()
      • consensus()
      • merge_objects()
  • Main data container
    • MicrobiomeData
      • MicrobiomeData.tab
      • MicrobiomeData.tax
      • MicrobiomeData.meta
      • MicrobiomeData.seq
      • MicrobiomeData.tree
      • MicrobiomeData.load()
      • MicrobiomeData.add_tab()
      • MicrobiomeData.add_tax()
      • MicrobiomeData.add_seq_from_fasta()
      • MicrobiomeData.add_tree()
      • MicrobiomeData.add_meta()
      • MicrobiomeData.add_tax_from_sintax()
      • MicrobiomeData.add_tax_from_qiime()
      • MicrobiomeData.add_tax_from_gtdbtk()
      • MicrobiomeData.add_tab_from_coverm()
      • MicrobiomeData.add_ebd_tab_from_singlem()
      • MicrobiomeData.save()
      • MicrobiomeData.copy()
      • MicrobiomeData.info()
      • MicrobiomeData.summarize_taxa()
      • MicrobiomeData.subset_samples()
      • MicrobiomeData.subset_features()
      • MicrobiomeData.subset_abundant()
      • MicrobiomeData.merge_samples()
      • MicrobiomeData.subset_taxa()
      • MicrobiomeData.rarefy()
      • MicrobiomeData.prune_tree()
      • MicrobiomeData.rename_features()
      • MicrobiomeData.tax_prefix()
      • MicrobiomeData.clean_tax()
      • MicrobiomeData.load_example()
      • MicrobiomeData.to_dict()
      • MicrobiomeData.from_dict()