{ "_id": "6a1efe89b401979e7341a3ff", "Package": "FAVA", "Title": "Quantify Compositional Variability Across Relative Abundance\nVectors", "Version": "1.0.9", "Authors@R": "person(\"Maike\", \"Morrison\", , \"maike.morrison@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-0430-1401\"))", "Description": "Implements the statistic FAVA, an Fst-based Assessment of\nVariability across vectors of relative Abundances, as well as a\nsuite of helper functions which enable the visualization and\nstatistical analysis of relative abundance data. The 'FAVA' R\npackage accompanies the paper, “Quantifying compositional\nvariability in microbial communities with FAVA” by Morrison,\nXue, and Rosenberg (2025) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "URL": "https://maikemorrison.github.io/FAVA/,\nhttps://maikemorrison.github.io/FAVA/articles/microbiome_tutorial.html", "BugReports": "https://github.com/MaikeMorrison/FAVA/issues", "Config/testthat/edition": "3", "LazyData": "true", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://maikemorrison.r-universe.dev", "Date/Publication": "2025-03-27 18:50:25 UTC", "RemoteUrl": "https://github.com/maikemorrison/fava", "RemoteRef": "HEAD", "RemoteSha": "383a576d5e8bbeda44e66d6fbd37a01eec57a7fa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-18 09:26:29 UTC", "User": "root" }, "Author": "Maike Morrison [aut, cre, cph] (ORCID:\n)", "Maintainer": "Maike Morrison ", 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"Campylobacter_concisus_59747", "Enterobacter_asburiae_57214", "Enterobacter_asburiae_58142", "Enterobacter_cancerogenus_61658", "Enterobacter_cloacae_57303", "Enterobacter_cloacae_58148", "Enterobacter_cloacae_60571", "Pantoea_agglomerans_56951", "Yersinia_bercovieri_61309", "Aggregatibacter_segnis_62447", "Citrobacter_freundii_56148", "Citrobacter_freundii_56776", "Citrobacter_sp_60882", "Haemophilus_influenzae_58001", "Porphyromonas_bennonis_58999", "Porphyromonas_somerae_59001", "Atopobium_parvulum_59960", "Citrobacter_braakii_56022", "Citrobacter_freundii_57904", "Citrobacter_freundii_60527", "Enterobacter_cloacae_55011", "Enterobacter_lignolyticus_62163", "Klebsiella_oxytoca_56762", "Streptococcus_mitis_58288", "Actinobaculum_sp_59615", "Cryptobacterium_curtum_61580", "Desulfobulbus_elongatus_58796", "Fusobacterium_sp_62349", "Lautropia_mirabilis_62440", "Prevotella_oris_57058", "Slackia_exigua_56855", "Solobacterium_moorei_56880", "Streptococcus_anginosus_58032", 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"Parvimonas_sp_62612", "Streptococcus_infantis_58384", "Streptococcus_oralis_57687", "Streptococcus_peroris_62455", "Streptococcus_sanguinis_58161", "Streptococcus_sanguinis_62467", "Streptococcus_sp_59452", "Streptococcus_suis_59523", "Butyrivibrio_sp_60431", "Clostridiales_bacterium_57827", "Clostridium_sartagoforme_59444", "Eikenella_corrodens_61764", "Klebsiella_pneumoniae_54688", "Porphyromonas_uenonis_49360", "Prevotella_buccalis_58135", "Prevotella_buccalis_62098", "Prevotella_salivae_57216", "Prevotella_sp_59962", "Streptococcus_equinus_57951", "Streptococcus_sp_62585", "Clostridium_perfringens_56840", "Clostridium_sp_60465", "Lachnospiraceae_oral_61854", "Streptococcus_oralis_57895", "Actinomyces_sp_62277", "Leclercia_adecarboxylata_62497", "Mitsuaria_sp_61803", "Paenibacillus_fonticola_58976", "Porphyromonas_asaccharolytica_56465", "Streptococcus_lutetiensis_58501", "Streptococcus_sanguinis_62457", "Streptococcus_oligofermentans_60032", "Blautia_producta_61268", "Campylobacter_gracilis_61787", "Campylobacter_showae_59756", "Cardiobacterium_hominis_61979", "Clostridium_nexile_61654", "Corynebacterium_accolens_58243", "Corynebacterium_durum_58387", "Enterobacter_sp_59441", "Erysipelotrichaceae_bacterium_55770", "Eubacterium_infirmum_62424", "Klebsiella_oxytoca_54123", "Leptotrichia_hofstadii_57828", "Leptotrichia_sp_60101", "Oribacterium_sinus_61880", "Parvimonas_sp_62298", "Propionibacterium_propionicum_62297", "Pseudobutyrivibrio_ruminis_59911", "Rothia_aeria_57338", "Selenomonas_flueggei_61981", "Staphylococcus_aureus_56630", "Stomatobaculum_longum_62318", "Streptococcus_anginosus_54555", "Streptococcus_gordonii_61575", "Streptococcus_mitis_58330", "Streptococcus_mitis_60170", "Streptococcus_mitis_61874", "Streptococcus_mitis_62363", "Streptococcus_sanguinis_61395", "Streptococcus_sp_60922", "Streptococcus_sp_61583", "Veillonella_sp_62586", "Adlercreutzia_equolifaciens_60310", "Akkermansia_muciniphila_55290", "Alistipes_indistinctus_62207", "Alistipes_putredinis_61533", "Alistipes_shahii_62199", "Alistipes_sp_59510", "Bacteroides_coprocola_61586", "Bacteroides_thetaiotaomicron_56941", "Barnesiella_intestinihominis_62208", "Bifidobacterium_adolescentis_56815", "Bifidobacterium_catenulatum_58257", "Bifidobacterium_pseudocatenulatum_57754", "Bifidobacterium_ruminantium_50236", "Burkholderiales_bacterium_56577", "Campylobacter_hominis_61331", "Catenibacterium_mitsuokai_61547", "Clostridium_hathewayi_62211", "Clostridium_leptum_61499", "Clostridium_sp_60782", "Clostridium_sp_61482", "Coprobacter_sp_60889", "Coprococcus_catus_62200", "Coprococcus_sp_62244", "Desulfotomaculum_acetoxidans_61627", "Dorea_longicatena_59913", "Dorea_longicatena_61473", "Escherichia_albertii_56276", "Eubacterium_biforme_61684", "Eubacterium_cylindroides_56237", "Holdemania_sp_59514", "Kitasatospora_phosalacinea_58242", "Lachnospiraceae_bacterium_51870", "Lachnospiraceae_bacterium_56275", "Lachnospiraceae_bacterium_56833", "Lactococcus_lactis_57073", "Odoribacter_splanchnicus_62174", "Oscillibacter_sp_60799", "Paraprevotella_clara_33712", "Paraprevotella_xylaniphila_62280", "Prevotella_copri_61740", "Prevotella_corporis_50024", "Prevotella_multiformis_62454", "Prevotella_sp_59901", "Ruminococcus_obeum_62046", "Streptococcus_sp_58554", "Subdoligranulum_variabile_61478", "Sutterella_wadsworthensis_56828", "Sutterella_wadsworthensis_62218", "Alcanivorax_pacificus_61421", "Desulfovibrio_desulfuricans_58813", "Lactobacillus_sakei_57195", "Prevotella_fusca_59711", "Prevotella_stercorea_58308", "Psychromonas_sp_61206", "Ruminococcus_bromii_62047", "Ruminococcus_callidus_61479", "Streptococcus_mitis_61110", "Thermobacillus_composti_62194", "Dialister_succinatiphilus_62213", "Lactobacillus_helveticus_55908", "Lactococcus_lactis_56468", "Oxalobacter_formigenes_61802", "Bacteroidales_bacterium_58650", "Bifidobacterium_animalis_58116", "Leptotrichia_wadei_57378", "Prevotella_veroralis_57831", "Turicibacter_sanguinis_52329", "Haemophilus_haemolyticus_58562", "Coriobacteriaceae_bacterium_58649", "Escherichia_coli_53492", "Escherichia_vulneris_58627", "Serratia_liquefaciens_58210", "Streptococcus_mitis_58557", "Streptococcus_mitis_61105", "Streptococcus_oralis_58559", "Clostridium_sordellii_57678", "Haemophilus_paraphrohaemolyticus_58563", "Lachnospiraceae_bacterium_61441", "Robinsoniella_peoriensis_54117", "Streptococcus_mitis_61107", "Streptococcus_sp_58555", "Clostridium_sp_60561", "Haemophilus_sp_62278", "Kandleria_vitulina_54464", "Pseudomonas_fragi_59193", "Streptococcus_constellatus_50409", "Campylobacter_showae_58485", "Clostridiales_bacterium_58120", "Lactobacillus_acidophilus_51143", "Staphylococcus_warneri_58053", "Enterobacteriaceae_bacterium_58100", "Streptococcus_mitis_58558", "Alistipes_senegalensis_58364", "Enterobacter_aerogenes_55704", "Clostridium_hylemonae_61789", "Pseudomonas_fluorescens_57697", "Pseudomonas_fluorescens_58167", "Streptococcus_sanguinis_62463", "Actinomyces_sp_62446", "Anaerostipes_caccae_55430", "Atopobium_sp_59401", "Atopobium_sp_62583", "Bacteroides_eggerthii_54457", "Bacteroides_helcogenes_62145", "Burkholderia_glumae_61916", "Burkholderia_thailandensis_59791", "Clostridium_methylpentosum_61741", "Lachnospiraceae_bacterium_60409", "Lachnospiraceae_bacterium_62050", "Lachnospiraceae_bacterium_62587", "Phocaeicola_abscessus_52822", "Prevotella_bivia_55194", "Streptococcus_mitis_60474", "Streptococcus_sp_59302", "Varibaculum_cambriense_60384", "Peptostreptococcus_stomatis_61922", "Lactobacillus_casei_50461", "Pseudomonas_viridiflava_57558", "Streptococcus_pneumoniae_58285", "Eubacterium_limosum_60946", "Methylobacterium_extorquens_57587", "Actinomyces_dentalis_58667", "Actinomyces_massiliensis_56461", "Streptococcus_oralis_58319", "Clostridium_beijerinckii_60451", "Haliea_salexigens_58876", "Methylibium_sp_60738", "Psychrobacter_sp_60004", "Streptococcus_sp_59334", "Streptococcus_sp_61819", "Lachnoanaerobaculum_saburreum_57248", "Streptococcus_mitis_60473", "Enterorhabdus_caecimuris_59685", "Enterorhabdus_mucosicola_58833", "Ralstonia_pickettii_57911", "Clostridium_butyricum_56361", "Enterococcus_gallinarum_52312", "Ruminococcus_gauvreauii_59033", "Ralstonia_pickettii_56648", "Ralstonia_sp_59678", "Actinomyces_sp_62445", "Scardovia_wiggsiae_62335", "Actinomyces_gerencseriae_58668", "Burkholderia_dolosa_61311", "Burkholderia_sp_59408", "Burkholderia_sp_60855", "Finegoldia_magna_57293", "Gardnerella_vaginalis_58127", "Prevotella_tannerae_61946", "Streptococcus_infantarius_58294", "Streptococcus_mitis_61876", "Streptococcus_oralis_46145", "Streptococcus_oralis_58560", "Streptococcus_pneumoniae_60081", "Streptococcus_pseudopneumoniae_60472", "Veillonella_sp_62611", "Xenorhabdus_bovienii_57960" ], "rows": 77, "table": true, "tojson": true }, { "name": "xue_species_info", "title": "Table of species information", "object": "xue_species_info", "class": [ "data.table", "data.frame" ], "fields": [ "species_id", "kingdom", "phylum", "class", "order", "family", "genus", "species", "species_id_number" ], "rows": 1346, "table": true, "tojson": true }, { "name": "xue_species_similarity", "title": "Species similarity matrix for the species included in xue_microbiome_sample", "object": "xue_species_similarity", "class": [ "matrix", "array" ], "fields": [ "Actinomyces_sp_58647", "Actinomyces_sp_59161", "Actinomyces_sp_59944", "Aggregatibacter_aphrophilus_58143", "Alistipes_finegoldii_56071", "Anaerostipes_hadrus_55206", "Bacteroides_acidifaciens_59693", "Bacteroides_caccae_53434", "Bacteroides_cellulosilyticus_58046", "Bacteroides_clarus_62282", "Bacteroides_faecis_58503", "Bacteroides_finegoldii_57739", "Bacteroides_fluxus_62283", "Bacteroides_fragilis_54507", "Bacteroides_graminisolvens_48736", "Bacteroides_intestinalis_61596", "Bacteroides_massiliensis_44749", "Bacteroides_nordii_55557", "Bacteroides_ovatus_58035", "Bacteroides_rodentium_59708", "Bacteroides_sartorii_54642", "Bacteroides_uniformis_57318", "Bacteroides_vulgatus_57955", "Bacteroides_xylanisolvens_57185", "Bifidobacterium_dentium_55719", "Bifidobacterium_longum_57796", "Bilophila_wadsworthia_57364", "Blautia_wexlerae_56130", "Campylobacter_concisus_62542", "Clostridiaceae_bacterium_58376", "Clostridiales_bacterium_55367", "Clostridiales_bacterium_56470", "Clostridiales_bacterium_58600", "Clostridiales_bacterium_59661", "Clostridiales_bacterium_59663", "Clostridiales_bacterium_59664", "Clostridiales_bacterium_61057", "Clostridium_bartlettii_61535", "Clostridium_bolteae_57158", "Clostridium_clostridioforme_51842", "Clostridium_clostridioforme_59912", "Clostridium_hathewayi_55515", "Clostridium_scindens_58238", "Collinsella_sp_62205", "Coprococcus_comes_61587", "Dorea_formicigenerans_56346", "Eggerthella_lenta_56463", "Erysipelotrichaceae_bacterium_56596", "Escherichia_fergusonii_56914", "Eubacterium_brachy_60105", "Eubacterium_desmolans_60421", "Eubacterium_eligens_61678", "Eubacterium_hallii_61477", "Eubacterium_rectale_56927", "Eubacterium_siraeum_57634", "Eubacterium_ventriosum_61474", "Faecalibacterium_cf_62236", "Faecalibacterium_prausnitzii_57453", "Faecalibacterium_prausnitzii_61481", "Faecalibacterium_prausnitzii_62201", "Guyana_massiliensis_60772", "Haemophilus_haemolyticus_58348", "Haemophilus_haemolyticus_58349", "Haemophilus_haemolyticus_58351", "Haemophilus_haemolyticus_58352", "Haemophilus_influenzae_60134", "Haemophilus_parainfluenzae_57123", "Haemophilus_parainfluenzae_62356", "Haemophilus_parainfluenzae_62468", "Haemophilus_pittmaniae_58383", "Haemophilus_sputorum_53575", "Holdemania_filiformis_61753", "Oribacterium_sp_54059", "Oribacterium_sp_58077", "Oscillibacter_sp_59687", "Oscillospiraceae_bacterium_54867", "Parabacteroides_distasonis_56985", "Parabacteroides_goldsteinii_56831", "Parabacteroides_johnsonii_55217", "Parabacteroides_merdae_56972", "Phascolarctobacterium_sp_59817", "Pseudobutyrivibrio_ruminis_59908", "Roseburia_hominis_61877", "Roseburia_intestinalis_56239", "Roseburia_inulinivorans_61943", "Rothia_mucilaginosa_62109", "Ruminococcus_gnavus_57638", "Ruminococcus_lactaris_55568", "Ruminococcus_obeum_61472", "Ruminococcus_sp_55468", "Slackia_piriformis_62217", "Streptococcus_infantis_58320", "Streptococcus_intermedius_57028", "Streptococcus_mitis_59739", "Streptococcus_mitis_61341", "Streptococcus_parasanguinis_58126", "Streptococcus_parasanguinis_58381", "Streptococcus_parasanguinis_58487", "Streptococcus_parasanguinis_62442", "Streptococcus_parasanguinis_62481", "Streptococcus_salivarius_58022", "Streptococcus_salivarius_58037", "Streptococcus_sanguinis_62464", "Streptococcus_sp_57750", "Streptococcus_sp_60086", "Streptococcus_sp_62351", "Streptococcus_sp_62701", "Streptococcus_thermophilus_54772", "Streptococcus_vestibularis_56030", "Subdoligranulum_sp_62068", "Veillonella_atypica_58169", "Veillonella_dispar_61763", "Veillonella_parvula_57794", "Veillonella_sp_62404", "Actinomyces_sp_57735", "Actinomyces_sp_62581", "Anaeroglobus_geminatus_62348", "Bacteroides_oleiciplenus_62209", "Bacteroides_stercoris_56735", "Clostridiales_bacterium_52743", "Clostridiales_bacterium_55184", "Clostridiales_bacterium_55505", "Clostridium_hathewayi_61827", "Collinsella_aerofaciens_61484", "Collinsella_stercoris_61536", "Escherichia_coli_58110", "Firmicutes_bacterium_60256", "Flavobacterium_reichenbachii_61335", "Gordonibacter_pamelaeae_62044", "Intestinimonas_butyriciproducens_60001", "Mesorhizobium_sp_40295", "Porphyromonas_uenonis_61926", "Prevotella_brevis_57676", "Pseudomonas_sp_62500", "Rothia_mucilaginosa_58144", "Ruminococcus_torques_62045", "Streptococcus_sanguinis_62456", "Clostridiales_bacterium_52957", "Clostridiales_bacterium_62591", "Clostridium_glycolicum_44741", "Coprobacillus_sp_47700", "Erysipelotrichaceae_bacterium_62051", "Escherichia_coli_57907", "Megasphaera_micronuciformis_62167", "Pseudoflavonifractor_capillosus_61476", "Streptococcus_mitis_61104", "Terrisporobacter_sp_60894", "Bacteroides_fragilis_56548", "Butyrivibrio_sp_60400", "Clostridium_sp_62633", "Streptococcus_cristatus_62470", "Streptococcus_mitis_60172", "Amycolatopsis_taiwanensis_58696", "Bacteroides_salyersiae_54873", "Prevotella_timonensis_58235", "Veillonella_parvula_58184", "Actinomyces_sp_56280", "Bacteroides_faecichinchillae_59709", "Clostridiales_bacterium_43336", "Clostridium_citroniae_62210", "Fusobacterium_nucleatum_57734", "Parvimonas_micra_57958", "Ruminococcaceae_bacterium_61777", "Streptococcus_infantis_62471", "Streptococcus_infantis_62693", "Streptococcus_mitis_60171", "Streptococcus_oralis_60034", "Streptococcus_sanguinis_62460", "Acinetobacter_johnsonii_58178", "Actinomyces_sp_62582", "Bifidobacterium_reuteri_60525", "Haemophilus_haemolyticus_58350", "Lactobacillus_curvatus_54601", "Actinomyces_sp_59450", "Campylobacter_concisus_59749", "Streptococcus_infantis_62384", "Streptococcus_mitis_59293", "Actinomyces_odontolyticus_57475", "Clostridium_cf_54592", "Haemophilus_parahaemolyticus_60505", "Aggregatibacter_sp_60097", "Bifidobacterium_callitrichos_60524", "Clostridium_symbiosum_54029", "Lachnospira_multipara_55890", "Alistipes_onderdonkii_55464", "Bacteroides_stercorirosoris_59710", "Clostridiales_bacterium_59662", "Eubacterium_ramulus_59802", "Eubacterium_sulci_62452", "Klebsiella_pneumoniae_54788", "Lachnobacterium_bovis_52776", "Neisseria_flavescens_61757", "Prevotella_disiens_56471", "Prevotella_saccharolytica_57611", "Streptococcus_australis_62469", "Streptococcus_mitis_61108", "Streptococcus_mitis_61109", "Burkholderia_xenovorans_58147", "Selenomonas_sp_62361", "Actinomyces_graevenitzii_58300", "Actinomyces_naeslundii_58629", "Actinomyces_turicensis_62420", "Campylobacter_concisus_59746", "Campylobacter_concisus_59748", "Campylobacter_concisus_59753", "Campylobacter_concisus_61330", "Campylobacter_sp_62066", "Fusobacterium_nucleatum_56829", "Fusobacterium_nucleatum_57345", "Fusobacterium_nucleatum_57855", "Fusobacterium_periodonticum_58002", "Fusobacterium_periodonticum_61765", "Gemella_sanguinis_57791", "Lactobacillus_reuteri_57957", "Oribacterium_sp_57590", "Streptococcus_gallolyticus_57748", "Streptococcus_mitis_61111", "Streptococcus_pneumoniae_60082", "Streptococcus_sanguinis_62461", "Actinomyces_sp_58589", "Actinomyces_viscosus_57672", "Bifidobacterium_moukalabense_60512", "Fusobacterium_nucleatum_57450", "Neisseria_elongata_61756", "Streptococcus_sanguinis_62459", "Campylobacter_concisus_59750", "Campylobacter_curvus_57251", "Clostridium_paraputrificum_59909", "Clostridium_sp_61556", "Enterococcus_faecalis_56297", "Lactobacillus_rhamnosus_57549", "Streptococcus_sanguinis_62462", "Burkholderia_pseudomallei_60511", "Clostridium_spiroforme_61500", "Dialister_invisus_61905", "Granulicatella_adiacens_61980", "Lactobacillus_paracasei_55666", "Selenomonas_noxia_56778", "Bacteroides_pectinophilus_61619", "Campylobacter_concisus_59747", "Enterobacter_asburiae_57214", "Enterobacter_asburiae_58142", "Enterobacter_cancerogenus_61658", "Enterobacter_cloacae_57303", "Enterobacter_cloacae_58148", "Enterobacter_cloacae_60571", "Pantoea_agglomerans_56951", "Yersinia_bercovieri_61309", "Aggregatibacter_segnis_62447", "Citrobacter_freundii_56148", "Citrobacter_freundii_56776", "Citrobacter_sp_60882", "Haemophilus_influenzae_58001", "Porphyromonas_bennonis_58999", "Porphyromonas_somerae_59001", "Atopobium_parvulum_59960", "Citrobacter_braakii_56022", "Citrobacter_freundii_57904", "Citrobacter_freundii_60527", "Enterobacter_cloacae_55011", "Enterobacter_lignolyticus_62163", "Klebsiella_oxytoca_56762", "Streptococcus_mitis_58288", "Actinobaculum_sp_59615", "Cryptobacterium_curtum_61580", "Desulfobulbus_elongatus_58796", "Fusobacterium_sp_62349", "Lautropia_mirabilis_62440", "Prevotella_oris_57058", "Slackia_exigua_56855", "Solobacterium_moorei_56880", "Streptococcus_anginosus_58032", "Streptococcus_anginosus_58303", "Streptococcus_caballi_59077", "Streptococcus_constellatus_57767", "Streptococcus_mitis_58382", "Streptococcus_mitis_59740", "Streptococcus_mitis_61875", "Streptococcus_sanguinis_62466", "Streptococcus_sp_61820", "Weissella_confusa_59158", "Atopobium_rimae_61781", "Bacteroides_gallinarum_48315", "Citrobacter_youngae_61659", "Clostridium_aerotolerans_60450", "Clostridium_intestinale_59988", "Clostridium_sp_59312", "Lachnospiraceae_bacterium_62206", "Neisseria_flavescens_61924", "Neisseria_subflava_61760", "Ruminococcus_sp_58571", "Shuttleworthia_satelles_57139", "Streptococcus_anginosus_58223", "Streptococcus_sanguinis_62458", "Streptococcus_sanguinis_62465", "Clostridium_lentocellum_62000", "Kingella_oralis_61952", "Klebsiella_oxytoca_57801", "Lysinibacillus_fusiformis_58088", "Rothia_dentocariosa_57938", "Aggregatibacter_actinomycetemcomitans_57720", "Eikenella_corrodens_58486", "Lachnospiraceae_bacterium_62350", "Neisseria_mucosa_61632", "Parvimonas_sp_62612", "Streptococcus_infantis_58384", "Streptococcus_oralis_57687", "Streptococcus_peroris_62455", "Streptococcus_sanguinis_58161", "Streptococcus_sanguinis_62467", "Streptococcus_sp_59452", "Streptococcus_suis_59523", "Butyrivibrio_sp_60431", "Clostridiales_bacterium_57827", "Clostridium_sartagoforme_59444", "Eikenella_corrodens_61764", "Klebsiella_pneumoniae_54688", "Porphyromonas_uenonis_49360", "Prevotella_buccalis_58135", "Prevotella_buccalis_62098", "Prevotella_salivae_57216", "Prevotella_sp_59962", "Streptococcus_equinus_57951", "Streptococcus_sp_62585", "Clostridium_perfringens_56840", "Clostridium_sp_60465", "Lachnospiraceae_oral_61854", "Streptococcus_oralis_57895", "Actinomyces_sp_62277", "Leclercia_adecarboxylata_62497", "Mitsuaria_sp_61803", "Paenibacillus_fonticola_58976", "Porphyromonas_asaccharolytica_56465", "Streptococcus_lutetiensis_58501", "Streptococcus_sanguinis_62457", "Streptococcus_oligofermentans_60032", "Blautia_producta_61268", "Campylobacter_gracilis_61787", "Campylobacter_showae_59756", "Cardiobacterium_hominis_61979", "Clostridium_nexile_61654", "Corynebacterium_accolens_58243", "Corynebacterium_durum_58387", "Enterobacter_sp_59441", "Erysipelotrichaceae_bacterium_55770", "Eubacterium_infirmum_62424", "Klebsiella_oxytoca_54123", "Leptotrichia_hofstadii_57828", "Leptotrichia_sp_60101", "Oribacterium_sinus_61880", "Parvimonas_sp_62298", "Propionibacterium_propionicum_62297", "Pseudobutyrivibrio_ruminis_59911", "Rothia_aeria_57338", "Selenomonas_flueggei_61981", "Staphylococcus_aureus_56630", "Stomatobaculum_longum_62318", "Streptococcus_anginosus_54555", "Streptococcus_gordonii_61575", "Streptococcus_mitis_58330", "Streptococcus_mitis_60170", "Streptococcus_mitis_61874", "Streptococcus_mitis_62363", "Streptococcus_sanguinis_61395", "Streptococcus_sp_60922", "Streptococcus_sp_61583", "Veillonella_sp_62586", "Adlercreutzia_equolifaciens_60310", "Akkermansia_muciniphila_55290", "Alistipes_indistinctus_62207", "Alistipes_putredinis_61533", "Alistipes_shahii_62199", "Alistipes_sp_59510", "Bacteroides_coprocola_61586", "Bacteroides_thetaiotaomicron_56941", "Barnesiella_intestinihominis_62208", "Bifidobacterium_adolescentis_56815", "Bifidobacterium_catenulatum_58257", "Bifidobacterium_pseudocatenulatum_57754", "Bifidobacterium_ruminantium_50236", "Burkholderiales_bacterium_56577", "Campylobacter_hominis_61331", "Catenibacterium_mitsuokai_61547", "Clostridium_hathewayi_62211", "Clostridium_leptum_61499", "Clostridium_sp_60782", "Clostridium_sp_61482", "Coprobacter_sp_60889", "Coprococcus_catus_62200", "Coprococcus_sp_62244", "Desulfotomaculum_acetoxidans_61627", "Dorea_longicatena_59913", "Dorea_longicatena_61473", "Escherichia_albertii_56276", "Eubacterium_biforme_61684", "Eubacterium_cylindroides_56237", "Holdemania_sp_59514", "Kitasatospora_phosalacinea_58242", "Lachnospiraceae_bacterium_51870", "Lachnospiraceae_bacterium_56275", "Lachnospiraceae_bacterium_56833", "Lactococcus_lactis_57073", "Odoribacter_splanchnicus_62174", "Oscillibacter_sp_60799", "Paraprevotella_clara_33712", "Paraprevotella_xylaniphila_62280", "Prevotella_copri_61740", "Prevotella_corporis_50024", "Prevotella_multiformis_62454", "Prevotella_sp_59901", "Ruminococcus_obeum_62046", "Streptococcus_sp_58554", "Subdoligranulum_variabile_61478", "Sutterella_wadsworthensis_56828", "Sutterella_wadsworthensis_62218", "Alcanivorax_pacificus_61421", "Desulfovibrio_desulfuricans_58813", "Lactobacillus_sakei_57195", "Prevotella_fusca_59711", "Prevotella_stercorea_58308", "Psychromonas_sp_61206", "Ruminococcus_bromii_62047", "Ruminococcus_callidus_61479", "Streptococcus_mitis_61110", "Thermobacillus_composti_62194", "Dialister_succinatiphilus_62213", "Lactobacillus_helveticus_55908", "Lactococcus_lactis_56468", "Oxalobacter_formigenes_61802", "Bacteroidales_bacterium_58650", "Bifidobacterium_animalis_58116", "Leptotrichia_wadei_57378", "Prevotella_veroralis_57831", "Turicibacter_sanguinis_52329", "Haemophilus_haemolyticus_58562", "Coriobacteriaceae_bacterium_58649", "Escherichia_coli_53492", "Escherichia_vulneris_58627", "Serratia_liquefaciens_58210", "Streptococcus_mitis_58557", "Streptococcus_mitis_61105", "Streptococcus_oralis_58559", "Clostridium_sordellii_57678", "Haemophilus_paraphrohaemolyticus_58563", "Lachnospiraceae_bacterium_61441", "Robinsoniella_peoriensis_54117", "Streptococcus_mitis_61107", "Streptococcus_sp_58555", "Clostridium_sp_60561", "Haemophilus_sp_62278", "Kandleria_vitulina_54464", "Pseudomonas_fragi_59193", "Streptococcus_constellatus_50409", "Campylobacter_showae_58485", "Clostridiales_bacterium_58120", "Lactobacillus_acidophilus_51143", "Staphylococcus_warneri_58053", "Enterobacteriaceae_bacterium_58100", "Streptococcus_mitis_58558", "Alistipes_senegalensis_58364", "Enterobacter_aerogenes_55704", "Clostridium_hylemonae_61789", "Pseudomonas_fluorescens_57697", "Pseudomonas_fluorescens_58167", "Streptococcus_sanguinis_62463", "Actinomyces_sp_62446", "Anaerostipes_caccae_55430", "Atopobium_sp_59401", "Atopobium_sp_62583", "Bacteroides_eggerthii_54457", "Bacteroides_helcogenes_62145", "Burkholderia_glumae_61916", "Burkholderia_thailandensis_59791", "Clostridium_methylpentosum_61741", "Lachnospiraceae_bacterium_60409", "Lachnospiraceae_bacterium_62050", "Lachnospiraceae_bacterium_62587", "Phocaeicola_abscessus_52822", "Prevotella_bivia_55194", "Streptococcus_mitis_60474", "Streptococcus_sp_59302", "Varibaculum_cambriense_60384", "Peptostreptococcus_stomatis_61922", "Lactobacillus_casei_50461", "Pseudomonas_viridiflava_57558", "Streptococcus_pneumoniae_58285", "Eubacterium_limosum_60946", "Methylobacterium_extorquens_57587", "Actinomyces_dentalis_58667", "Actinomyces_massiliensis_56461", "Streptococcus_oralis_58319", "Clostridium_beijerinckii_60451", "Haliea_salexigens_58876", "Methylibium_sp_60738", "Psychrobacter_sp_60004", "Streptococcus_sp_59334", "Streptococcus_sp_61819", "Lachnoanaerobaculum_saburreum_57248", 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similarity matrix for the species included in xue_microbiome_sample", "topics": [ "xue_species_similarity" ] }, { "page": "xue_species_tree", "title": "Phylogenetic tree for the species included in xue_microbiome_sample", "topics": [ "xue_species_tree" ] } ], "_readme": "https://github.com/maikemorrison/fava/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "microbiome_tutorial.Rmd", "filename": "microbiome_tutorial.html", "title": "Analysis of microbiome data with FAVA", "author": "Maike Morrison", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Overview", "Data specifications", "Optional: species similarity matrix", "Example analysis", "0 - Example data", "1 - 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