get_taxa_unique: Get a unique vector of the observed taxa at a particular...

Description Usage Arguments Value See Also Examples

View source: R/almostAllAccessors.R

Description

This is a simple accessor function to make it more convenient to determine the different taxa present for a particular taxonomic rank in a given phyloseq-class object.

Usage

1
get_taxa_unique(physeq, taxonomic.rank=rank_names(physeq)[1], errorIfNULL=TRUE)

Arguments

physeq

(Required). taxonomyTable-class, or phyloseq-class.

taxonomic.rank

(Optional). Character. The taxonomic rank to use. Must select from the set indicated by get_taxa_unique. Default is to take the first column of the taxonomyTable component.

errorIfNULL

(Optional). Logical. Should the accessor stop with an error if the slot is empty (NULL)? Default TRUE.

Value

Character vector. Unique vector of the observed taxa at a particular taxonomic rank

See Also

get_taxa taxa_names sample_names

Examples

1
2
3
4

Example output

  [1] NA                              "Prosthecochloris"             
  [3] "Chloroflexus"                  "Dehalococcoides"              
  [5] "Thermus"                       "Listeria"                     
  [7] "Fusobacterium"                 "Streptobacillus"              
  [9] "Brevibacillus"                 "Acidobacteria_Gp1_Gp1"        
 [11] "Paenibacillus"                 "Bartonella"                   
 [13] "Beijerinckia"                  "Bradyrhizobium"               
 [15] "Brucella"                      "Methylobacterium"             
 [17] "Mesorhizobium"                 "Rhizobium"                    
 [19] "Parvibaculum"                  "Paracoccus"                   
 [21] "Gluconacetobacter"             "Granulibacter"                
 [23] "Gemella"                       "Azospirillum"                 
 [25] "Macrococcus"                   "Magnetospirillum"             
 [27] "Rhodospirillum"                "Staphylococcus"               
 [29] "Rickettsia"                    "Pelagibacter"                 
 [31] "Erythrobacter"                 "Sphingobium"                  
 [33] "Achromobacter"                 "Bordetella"                   
 [35] "Burkholderia"                  "Cupriavidus"                  
 [37] "Polynucleobacter"              "Ralstonia"                    
 [39] "Acidovorax"                    "Comamonas"                    
 [41] "Delftia"                       "Diaphorobacter"               
 [43] "Polaromonas"                   "Rhodoferax"                   
 [45] "Variovorax"                    "Verminephrobacter"            
 [47] "Herminiimonas"                 "Oxalobacter"                  
 [49] "Leptothrix"                    "Methylibium"                  
 [51] "Thiomonas"                     "Thiobacillus"                 
 [53] "Methylobacillus"               "Neisseriaceae"                
 [55] "Chromobacterium"               "Kingella"                     
 [57] "Laribacter"                    "Abiotrophia"                  
 [59] "Neisseria"                     "Simonsiella"                  
 [61] "Aerococcus"                    "Nitrosomonas"                 
 [63] "Nitrosospira"                  "Azoarcus"                     
 [65] "Thauera"                       "Desulfotalea"                 
 [67] "Desulfovibrio"                 "Lawsonia"                     
 [69] "Pelobacter"                    "Geobacter"                    
 [71] "Anaeromyxobacter"              "Syntrophus"                   
 [73] "Granulicatella"                "Campylobacter"                
 [75] "Helicobacter"                  "Aeromonas"                    
 [77] "Tolumonas"                     "Idiomarina"                   
 [79] "Shewanella"                    "Cardiobacterium"              
 [81] "Nitrosococcus"                 "Enterococcus"                 
 [83] "Thioalkalivibrio"              "Enterobacteriaceae"           
 [85] "Citrobacter"                   "Cronobacter"                  
 [87] "Dickeya"                       "Edwardsiella"                 
 [89] "Enterobacter"                  "Erwinia"                      
 [91] "Escherichia/Shigella"          "Klebsiella"                   
 [93] "Lactobacillus"                 "Pantoea"                      
 [95] "Pectobacterium"                "Photorhabdus"                 
 [97] "Proteus"                       "Providencia"                  
 [99] "Salmonella"                    "Serratia"                     
[101] "Sodalis"                       "Pediococcus"                  
[103] "Xenorhabdus"                   "Yersinia"                     
[105] "Leuconostoc"                   "Weissella"                    
[107] "Lactococcus"                   "Pasteurellaceae"              
[109] "Actinobacillus"                "Aggregatibacter"              
[111] "Haemophilus"                   "Histophilus"                  
[113] "Streptococcus"                 "Pasteurella"                  
[115] "Acinetobacter"                 "Enhydrobacter"                
[117] "Azotobacter"                   "Cellvibrio"                   
[119] "Pseudomonas"                   "Clostridiales"                
[121] "Aliivibrio"                    "Photobacterium"               
[123] "Vibrio"                        "Stenotrophomonas"             
[125] "Xanthomonas"                   "Brachyspira"                  
[127] "Treponema"                     "Aminobacterium"               
[129] "Aminomonas"                    "Pyramidobacter"               
[131] "Acholeplasma"                  "Entomoplasmataceae"           
[133] "Mesoplasma"                    "Mycoplasma"                   
[135] "Verrucomicrobia"               "Akkermansia"                  
[137] "Opitutus"                      "Coraliomargarita"             
[139] "Methanobrevibacter"            "Methanosphaera"               
[141] "Methanocella"                  "Cyanobacteria"                
[143] "Family_XII_GpXII"              "Cyanobacteria_Family_XI_GpXI" 
[145] "Family_IX_GpIX"                "Megasphaera"                  
[147] "Acidaminococcus"               "Mitsuokella"                  
[149] "Selenomonas"                   "Veillonella"                  
[151] "Dialister"                     "Ruminococcaceae"              
[153] "Subdoligranulum"               "Faecalibacterium"             
[155] "Acetivibrio"                   "Anaerotruncus"                
[157] "Ruminococcus"                  "Alkaliphilus"                 
[159] "Clostridium"                   "Symbiobacterium"              
[161] "Thermincola"                   "Desulfitobacterium"           
[163] "Desulfotomaculum"              "Pelotomaculum"                
[165] "Finegoldia"                    "Peptoniphilus"                
[167] "Parvimonas"                    "Anaerococcus"                 
[169] "Syntrophomonas"                "Syntrophothermus"             
[171] "Peptostreptococcaceae"         "Filifactor"                   
[173] "Sporacetigenium"               "Peptostreptococcus"           
[175] "Heliobacterium"                "Lachnospiraceae"              
[177] "Oribacterium"                  "Coprococcus"                  
[179] "Roseburia"                     "Catonella"                    
[181] "Dorea"                         "Shuttleworthia"               
[183] "Anaerostipes"                  "Anaerofustis"                 
[185] "Eubacterium"                   "Blautia"                      
[187] "Anaerosporobacter"             "Marvinbryantia"               
[189] "Carboxydothermus"              "Caldicellulosiruptor"         
[191] "Halothermothrix"               "Ammonifex"                    
[193] "Caldanaerobacter"              "Moorella"                     
[195] "Thermoanaerobacter"            "Bulleidia"                    
[197] "Catenibacterium"               "Coprobacillus"                
[199] "Erysipelothrix"                "Holdemania"                   
[201] "Turicibacter"                  "Bacteroides"                  
[203] "Porphyromonadaceae"            "Parabacteroides"              
[205] "Porphyromonas"                 "Prevotella"                   
[207] "Alistipes"                     "Capnocytophaga"               
[209] "Chryseobacterium"              "Croceibacter"                 
[211] "Zunongwangia"                  "Cytophaga"                    
[213] "Dyadobacter"                   "Bacillales"                   
[215] "Pedobacter"                    "Sphingobacterium"             
[217] "Alicyclobacillus"              "Actinomycetales"              
[219] "Actinomyces"                   "Mobiluncus"                   
[221] "Corynebacterium"               "Gordonia"                     
[223] "Nocardia"                      "Anoxybacillus"                
[225] "Rhodococcus"                   "Bacillus"                     
[227] "Stackebrandtia"                "Brevibacterium"               
[229] "Exiguobacterium"               "Kytococcus"                   
[231] "Geobacillus"                   "Micrococcus"                  
[233] "Rothia"                        "Xylanimonas"                  
[235] "Oceanobacillus"                "Propionibacterium"            
[237] "Saccharopolyspora"             "Streptomyces"                 
[239] "Bifidobacterium"               "Gardnerella"                  
[241] "Parascardovia"                 "Scardovia"                    
[243] "Atopobium"                     "Collinsella"                  
[245] "Cryptobacterium"               "Eggerthella"                  
[247] "Gordonibacter"                 "Slackia"                      
[249] "Acetobacter"                   "Acidimicrobium"               
[251] "Acidiphilium"                  "Acidithiobacillus"            
[253] "Acidobacteria_Gp3_Gp3"         "Acidothermus"                 
[255] "Actinosynnema"                 "Aeromicrobium"                
[257] "Aeropyrum"                     "Afipia"                       
[259] "Alcanivorax"                   "Alkalilimnicola"              
[261] "Allochromatium"                "Alphaproteobacteria"          
[263] "Alteromonas"                   "Anaerobaculum"                
[265] "Anaplasma"                     "Aquifex"                      
[267] "Arcanobacterium"               "Archaeoglobus"                
[269] "Arcobacter"                    "Arsenophonus"                 
[271] "Arthrobacter"                  "Azorhizobium"                 
[273] "Bdellovibrio"                  "Beutenbergia"                 
[275] "Borrelia"                      "Brachybacterium"              
[277] "Bradyrhizobiaceae"             "Caldivirga"                   
[279] "Candidatus_Korarchaeum"        "Catenulispora"                
[281] "Caulobacter"                   "Cellulomonas"                 
[283] "Chitinophaga"                  "Chlamydia"                    
[285] "Chlamydophila"                 "Chlorobaculum"                
[287] "Chlorobiaceae"                 "Chlorobium"                   
[289] "Chloroherpeton"                "Chromohalobacter"             
[291] "Clavibacter"                   "Colwellia"                    
[293] "Conexibacter"                  "Coprothermobacter"            
[295] "Cyanobacteria_Family_II_GpIIa" "Cyanobacteria_Family_II_GpIIb"
[297] "Cyanobacteria_Family_I_GpI"    "Deferribacter"                
[299] "Dehalogenimonas"               "Deinococcus"                  
[301] "Denitrovibrio"                 "Desulfatibacillum"            
[303] "Desulfobacteraceae"            "Desulfobacterium"             
[305] "Desulfohalobium"               "Desulfomicrobium"             
[307] "Desulfurivibrio"               "Desulfurococcus"              
[309] "Dichelobacter"                 "Dictyoglomus"                 
[311] "Dinoroseobacter"               "Ehrlichia"                    
[313] "Ensifer"                       "Family_X_GpX"                 
[315] "Ferribacterium"                "Ferroglobus"                  
[317] "Fervidobacterium"              "Fibrobacter"                  
[319] "Flavobacteriales"              "Flavobacterium"               
[321] "Francisella"                   "Frankineae"                   
[323] "Gammaproteobacteria"           "Gemmatimonas"                 
[325] "Geodermatophilus"              "Glaciecola"                   
[327] "Gluconobacter"                 "Gramella"                     
[329] "Hahella"                       "Haliangium"                   
[331] "Haloarcula"                    "Halobacterium"                
[333] "Haloferax"                     "Halomicrobium"                
[335] "Haloquadratum"                 "Halorhabdus"                  
[337] "Halorhodospira"                "Halorubrum"                   
[339] "Haloterrigena"                 "Halothiobacillus"             
[341] "Herpetosiphon"                 "Hirschia"                     
[343] "Hydrogenobacter"               "Hydrogenobaculum"             
[345] "Hyperthermus"                  "Hyphomicrobium"               
[347] "Hyphomonas"                    "Ignicoccus"                   
[349] "Jonesia"                       "Jonquetella"                  
[351] "Kangiella"                     "Kineococcus"                  
[353] "Kocuria"                       "Kosmotoga"                    
[355] "Kribbella"                     "Legionella"                   
[357] "Leifsonia"                     "Leptospira"                   
[359] "Leptotrichia"                  "Lysinibacillus"               
[361] "Maricaulis"                    "Marinobacter"                 
[363] "Marinomonas"                   "Meiothermus"                  
[365] "Metallosphaera"                "Methanocaldococcus"           
[367] "Methanococcoides"              "Methanococcus"                
[369] "Methanocorpusculum"            "Methanoculleus"               
[371] "Methanohalophilus"             "Methanomicrobiales"           
[373] "Methanopyrus"                  "Methanosaeta"                 
[375] "Methanosarcina"                "Methanosarcinaceae"           
[377] "Methanosphaerula"              "Methanospirillum"             
[379] "Methanothermobacter"           "Methylocella"                 
[381] "Methylococcus"                 "Methylophilaceae"             
[383] "Methylotenera"                 "Methylovorus"                 
[385] "Moraxella"                     "Mycobacterium"                
[387] "Myxococcus"                    "Nakamurella"                  
[389] "Nanoarchaeum"                  "Natranaerobius"               
[391] "Natrialba"                     "Natronomonas"                 
[393] "Nautilia"                      "Neorickettsia"                
[395] "Nitratiruptor"                 "Nitrobacter"                  
[397] "Nocardioides"                  "Nocardiopsis"                 
[399] "Novosphingobium"               "Ochrobactrum"                 
[401] "Oenococcus"                    "Orientia"                     
[403] "Parachlamydia"                 "Persephonella"                
[405] "Petrotoga"                     "Phenylobacterium"             
[407] "Phyllobacteriaceae"            "Picrophilus"                  
[409] "Pirellula"                     "Planctomyces"                 
[411] "Propionivibrio"                "Proteobacteria"               
[413] "Pseudoalteromonas"             "Psychrobacter"                
[415] "Psychromonas"                  "Pyrobaculum"                  
[417] "Pyrococcus"                    "Renibacterium"                
[419] "Rhizobiales"                   "Rhodobacter"                  
[421] "Rhodobacteraceae"              "Rhodocista"                   
[423] "Rhodocyclaceae"                "Rhodopirellula"               
[425] "Rhodopseudomonas"              "Rhodospirillaceae"            
[427] "Rhodothermus"                  "Robiginitalea"                
[429] "Roseobacter"                   "Roseomonas"                   
[431] "Rubrobacter"                   "Ruegeria"                     
[433] "Saccharomonospora"             "Saccharophagus"               
[435] "Salinibacter"                  "Salinispora"                  
[437] "Sanguibacter"                  "Sebaldella"                   
[439] "Segniliparus"                  "Silicibacter"                 
[441] "Sorangium"                     "Sphaerobacter"                
[443] "Sphingobacteriales"            "Sphingomonas"                 
[445] "Sphingopyxis"                  "Spirosoma"                    
[447] "Staphylothermus"               "Starkeya"                     
[449] "Streptosporangium"             "Sulfolobus"                   
[451] "Sulfurihydrogenibium"          "Sulfurimonas"                 
[453] "Sulfurospirillum"              "Sulfurovum"                   
[455] "Syntrophobacter"               "Teredinibacter"               
[457] "Thermoanaerobacteraceae"       "Thermobifida"                 
[459] "Thermobispora"                 "Thermococcus"                 
[461] "Thermocrinis"                  "Thermodesulfovibrio"          
[463] "Thermofilum"                   "Thermomicrobia"               
[465] "Thermomicrobium"               "Thermomonospora"              
[467] "Thermoplasma"                  "Thermoplasmatales"            
[469] "Thermoprotei"                  "Thermosipho"                  
[471] "Thermosphaera"                 "Thermotoga"                   
[473] "Thiomicrospira"                "Tropheryma"                   
[475] "Truepera"                      "Tsukamurella"                 
[477] "Ureaplasma"                    "Waddlia"                      
[479] "Wolinella"                     "Xanthobacter"                 
[481] "Xylella"                       "Zymomonas"                    
[483] "Papillibacter"                 "Anaerovorax"                  
[485] "Parasporobacterium"            "Chrysiogenes"                 
[487] "Solobacterium"                 "Sarcina"                      
[489] "Olsenella"                     "Lachnobacterium"              
[491] "Anaeroglobus"                  "Dysgonomonas"                 
[493] "Megamonas"                     "Gallicola"                    
[495] "Sneathia"                      "Victivallis"                  
[497] "Varibaculum"                   "Solirubrobacter"              
[499] "Allisonella"                   "Tepidibacter"                 
[501] "Hespellia"                     "Bryantella"                   
[503] "Mahella"                       "Ethanoligenens"               
[505] "Soehngenia"                    "Acetanaerobacterium"          
[507] "Peptococcus"                   "Carnobacterium"               
[509] "Rikenella"                     "Odoribacter"                  
[511] "Acetitomaculum"                "Phascolarctobacterium"        
[513] "Coriobacterium"                "Microbacterium"               
[515] "Acetobacterium"                "Luteococcus"                  
[517] "Geosporobacter"                "Barnesiella"                  
[519] "Zymophilus"                    "Howardella"                   
[521] "Sutterella"                    "Succiniclasticum"             
[523] "Lactonifactor"                 "Moryella"                     
[525] "Sporobacter"                   "Oscillibacter"                
[527] "Pseudobutyrivibrio"            "Cloacibacillus"               
[529] "Hallella"                      "Anaerofilum"                  
[531] "Asaccharobacter"               "Xylanibacter"                 
[533] "Escherichia"                   "Butyricimonas"                
[535] "Paraprevotella"                "Parasutterella"               
[537] "Enterorhabdus"                 "Butyricicoccus"               
[539] "Robinsoniella"                 "Hydrogenoanaerobacterium"     
[541] "Thermotalea"                   "Paraeggerthella"              
[543] "Anaerobacter"                  "Desulfocurvus"                
[545] "Fusibacter"                    "Actinobaculum"                
[547] "Asticcacaulis"                 "Succinispira"                 
[549] "Butyrivibrio"                  "Desulfonispora"               
[551] "Syntrophococcus"               "Mogibacterium"                
  [1] NA                                     
  [2] "Sulfolobaceae"                        
  [3] "SAGMA-X"                              
  [4] "Cenarchaeaceae"                       
  [5] "Nitrososphaeraceae"                   
  [6] "Halobacteriaceae"                     
  [7] "Methanosaetaceae"                     
  [8] "Methanosarcinaceae"                   
  [9] "Methanocorpusculaceae"                
 [10] "MarinegroupIII"                       
 [11] "MOB7-9"                               
 [12] "WCHD3-02"                             
 [13] "pMC2A33"                              
 [14] "MarinegroupII"                        
 [15] "WSA2"                                 
 [16] "MSBL1"                                
 [17] "Methanobacteriaceae"                  
 [18] "Propionibacteriaceae"                 
 [19] "Nocardioidaceae"                      
 [20] "Microthrixaceae"                      
 [21] "ZA3409c"                              
 [22] "TK06"                                 
 [23] "ZA3612c"                              
 [24] "ntu14"                                
 [25] "JdFBGBact"                            
 [26] "SC3-41"                               
 [27] "wb1_P06"                              
 [28] "AKIW874"                              
 [29] "Iamiaceae"                            
 [30] "CL500-29"                             
 [31] "Acidimicrobiaceae"                    
 [32] "EB1017"                               
 [33] "Euzebiaceae"                          
 [34] "Thermomonosporaceae"                  
 [35] "Nocardiopsaceae"                      
 [36] "Streptosporangiaceae"                 
 [37] "Pseudonocardiaceae"                   
 [38] "Actinosynnemataceae"                  
 [39] "Micromonosporaceae"                   
 [40] "Glycomycetaceae"                      
 [41] "Actinopolysporaceae"                  
 [42] "Catenulisporaceae"                    
 [43] "Actinospicaceae"                      
 [44] "Streptomycetaceae"                    
 [45] "ACK-M1"                               
 [46] "Frankiaceae"                          
 [47] "Sporichthyaceae"                      
 [48] "Geodermatophilaceae"                  
 [49] "Nakamurellaceae"                      
 [50] "Cryptosporangiaceae"                  
 [51] "Kineosporiaceae"                      
 [52] "Microbacteriaceae"                    
 [53] "Intrasporangiaceae"                   
 [54] "Dermabacteraceae"                     
 [55] "Dermatophilaceae"                     
 [56] "Dermacoccaceae"                       
 [57] "Cellulomonadaceae"                    
 [58] "Sanguibacteraceae"                    
 [59] "Promicromonosporaceae"                
 [60] "Beutenbergiaceae"                     
 [61] "Bogoriellaceae"                       
 [62] "Rarobacteraceae"                      
 [63] "Jonesiaceae"                          
 [64] "Actinomycetaceae"                     
 [65] "Brevibacteriaceae"                    
 [66] "Micrococcaceae"                       
 [67] "Yaniellaceae"                         
 [68] "Dietziaceae"                          
 [69] "Corynebacteriaceae"                   
 [70] "Nocardiaceae"                         
 [71] "Williamsiaceae"                       
 [72] "Gordoniaceae"                         
 [73] "Segniliparaceae"                      
 [74] "Tsukamurellaceae"                     
 [75] "Mycobacteriaceae"                     
 [76] "Bifidobacteriaceae"                   
 [77] "SHA-116"                              
 [78] "SHA-4"                                
 [79] "Spirochaetaceae"                      
 [80] "Leptospiraceae"                       
 [81] "Desulfohalobiaceae"                   
 [82] "Desulfonatronumaceae"                 
 [83] "Desulfovibrionaceae"                  
 [84] "Desulfomicrobiaceae"                  
 [85] "Fusobacteriaceae"                     
 [86] "Spiroplasmataceae"                    
 [87] "Entomoplasmataceae"                   
 [88] "Mycoplasmataceae"                     
 [89] "Anaeroplasmataceae"                   
 [90] "Acholeplasmataceae"                   
 [91] "Erysipelotrichaceae"                  
 [92] "vadinHA31"                            
 [93] "Chlamydomonadaceae"                   
 [94] "Mamiellaceae"                         
 [95] "Chlorarachniophyceae"                 
 [96] "Trebouxiophyceae"                     
 [97] "Acaryochloridaceae"                   
 [98] "Pseudanabaenaceae"                    
 [99] "Phormidiaceae"                        
[100] "Xenococcaceae"                        
[101] "Spirulinaceae"                        
[102] "Cyanobacteriaceae"                    
[103] "Microcystaceae"                       
[104] "Gomphosphaeriaceae"                   
[105] "Oscillatoriaceae"                     
[106] "Chamaesiphonaceae"                    
[107] "Scytonemataceae"                      
[108] "Nostocaceae"                          
[109] "Rivulariaceae"                        
[110] "Gomontiellaceae"                      
[111] "Synechococcaceae"                     
[112] "Helicobacteraceae"                    
[113] "Campylobacteraceae"                   
[114] "Mariprofundaceae"                     
[115] "Hydrogenophilaceae"                   
[116] "Burkholderiaceae"                     
[117] "Alcaligenaceae"                       
[118] "Neisseriaceae"                        
[119] "Procabacteriaceae"                    
[120] "Methylophilaceae"                     
[121] "Nitrosomonadaceae"                    
[122] "Gallionellaceae"                      
[123] "Rhodocyclaceae"                       
[124] "Oxalobacteraceae"                     
[125] "Comamonadaceae"                       
[126] "Xanthomonadaceae"                     
[127] "Cardiobacteriaceae"                   
[128] "Halothiobacillaceae"                  
[129] "Chromatiaceae"                        
[130] "Alteromonadaceae"                     
[131] "Pseudoalteromonadaceae"               
[132] "Psychromonadaceae"                    
[133] "Celerinatantimonadaceae"              
[134] "Idiomarinaceae"                       
[135] "Colwelliaceae"                        
[136] "Vibrionaceae"                         
[137] "Moritellaceae"                        
[138] "Shewanellaceae"                       
[139] "Ferrimonadaceae"                      
[140] "Aeromonadaceae"                       
[141] "Pasteurellaceae"                      
[142] "Enterobacteriaceae"                   
[143] "Succinivibrionaceae"                  
[144] "Moraxellaceae"                        
[145] "Halomonadaceae"                       
[146] "Oceanospirillaceae"                   
[147] "FCPT525"                              
[148] "SUP05"                                
[149] "Piscirickettsiaceae"                  
[150] "Alcanivoracaceae"                     
[151] "125ds10"                              
[152] "OM60"                                 
[153] "J115"                                 
[154] "HTCC2089"                             
[155] "ZA3412c"                              
[156] "211ds20"                              
[157] "HTCC2188"                             
[158] "Hahellaceae"                          
[159] "Litincolaceae"                        
[160] "Saccharospirillaceae"                 
[161] "Endozoicimonaceae"                    
[162] "HOC21"                                
[163] "Oleiphilaceae"                        
[164] "Pseudomonadaceae"                     
[165] "Methylococcaceae"                     
[166] "Crenotrichaceae"                      
[167] "Thiotrichaceae"                       
[168] "Coxiellaceae"                         
[169] "Legionellaceae"                       
[170] "Endoecteinascidiaceae"                
[171] "Francisellaceae"                      
[172] "Ectothiorhodospiraceae"               
[173] "Sinobacteraceae"                      
[174] "Salinisphaeraceae"                    
[175] "Rickettsiaceae"                       
[176] "Phyllobacteriaceae"                   
[177] "Rhizobiaceae"                         
[178] "Bartonellaceae"                       
[179] "Brucellaceae"                         
[180] "Aurantimonadaceae"                    
[181] "Rhodobiaceae"                         
[182] "Hyphomicrobiaceae"                    
[183] "Methylocystaceae"                     
[184] "Xanthobacteraceae"                    
[185] "Bradyrhizobiaceae"                    
[186] "Methylobacteriaceae"                  
[187] "Beijerinckiaceae"                     
[188] "Cohaesibacteraceae"                   
[189] "Rhodobacteraceae"                     
[190] "Hyphomonadaceae"                      
[191] "Caulobacteraceae"                     
[192] "Rhodospirillaceae"                    
[193] "Acetobacteraceae"                     
[194] "Sphingomonadaceae"                    
[195] "Erythrobacteraceae"                   
[196] "Kiloniellaceae"                       
[197] "Kordiimonadaceae"                     
[198] "Syntrophaceae"                        
[199] "Syntrophobacteraceae"                 
[200] "Desulfobacteraceae"                   
[201] "Desulfobulbaceae"                     
[202] "Syntrophorhabdaceae"                  
[203] "Bdellovibrionaceae"                   
[204] "Bacteriovoracaceae"                   
[205] "MND4"                                 
[206] "JTB38"                                
[207] "NB1-i"                                
[208] "Polyangiaceae"                        
[209] "Haliangiaceae"                        
[210] "Nannocystaceae"                       
[211] "Myxococcaceae"                        
[212] "Cystobacteraceae"                     
[213] "Geobacteraceae"                       
[214] "Pelobacteraceae"                      
[215] "Desulfuromonadaceae"                  
[216] "Ignavibacteriaceae"                   
[217] "Balneolaceae"                         
[218] "Flammeovirgaceae"                     
[219] "Flavobacteriaceae"                    
[220] "Blattabacteriaceae"                   
[221] "Cryomorphaceae"                       
[222] "Marinilabiaceae"                      
[223] "Porphyromonadaceae"                   
[224] "Bacteroidaceae"                       
[225] "Prevotellaceae"                       
[226] "Rikenellaceae"                        
[227] "Sphingobacteriaceae"                  
[228] "Cyclobacteriaceae"                    
[229] "Flexibacteraceae"                     
[230] "Saprospiraceae"                       
[231] "Rhodothermaceae"                      
[232] "Chlorobiaceae"                        
[233] "A714017"                              
[234] "AEGEAN_185"                           
[235] "SHAS460"                              
[236] "Thermaceae"                           
[237] "Deinococcaceae"                       
[238] "Gemmatimonadaceae"                    
[239] "Fibrobacteraceae"                     
[240] "Entotheonellaceae"                    
[241] "Elusimicrobiaceae"                    
[242] "Methylomirabiliaceae"                 
[243] "Koribacteraceae"                      
[244] "Acidobacteriaceae"                    
[245] "Solibacteraceae"                      
[246] "Holophagaceae"                        
[247] "Thermodesulfovibrionaceae"            
[248] "Nitrospiraceae"                       
[249] "FW"                                   
[250] "Nitrospinaceae"                       
[251] "PRR-10"                               
[252] "Puniceicoccaceae"                     
[253] "Opitutaceae"                          
[254] "Methylacidiphilaceae"                 
[255] "LD19"                                 
[256] "Verrucomicrobiaceae"                  
[257] "Spartobacteriaceae"                   
[258] "Verrucomicrobiasubdivision3"          
[259] "Victivallaceae"                       
[260] "Lentisphaeraceae"                     
[261] "Waddliaceae"                          
[262] "Parachlamydiaceae"                    
[263] "Simkaniaceae"                         
[264] "Rhabdochlamydiaceae"                  
[265] "kpj58rc"                              
[266] "Kueneniaceae"                         
[267] "Pirellulaceae"                        
[268] "Planctomycetaceae"                    
[269] "Gemmataceae"                          
[270] "Isosphaeraceae"                       
[271] "Phycisphaeraceae"                     
[272] "At425_EubF1"                          
[273] "Coriobacteriaceae"                    
[274] "Solirubrobacteraceae"                 
[275] "Patulibacteraceae"                    
[276] "Rubrobacteraceae"                     
[277] "Halobacteroidaceae"                   
[278] "Halanaerobiaceae"                     
[279] "Chthonomonadaceae"                    
[280] "Armatimonadaceae"                     
[281] "WD294"                                
[282] "F16"                                  
[283] "Oscillochloridaceae"                  
[284] "Kouleothrixaceae"                     
[285] "AKYH910"                              
[286] "FFCH4570"                             
[287] "5B-12"                                
[288] "Dolo_23"                              
[289] "Dehalococcoidaceae"                   
[290] "Caldilineaceae"                       
[291] "S47"                                  
[292] "KNA6-EB22"                            
[293] "Anaerolinaceae"                       
[294] "SHA-31"                               
[295] "Clostridiaceae"                       
[296] "Eubacteriaceae"                       
[297] "Peptostreptococcaceae"                
[298] "ClostridialesFamilyXIII.IncertaeSedis"
[299] "ClostridialesFamilyXII.IncertaeSedis" 
[300] "ClostridialesFamilyXI.IncertaeSedis"  
[301] "Catabacteriaceae"                     
[302] "Ruminococcaceae"                      
[303] "Lachnospiraceae"                      
[304] "Symbiobacteriaceae"                   
[305] "Thermoanaerobacteraceae"              
[306] "Thermicanaceae"                       
[307] "Paenibacillaceae"                     
[308] "Bacillaceae"                          
[309] "Sporolactobacillaceae"                
[310] "Planococcaceae"                       
[311] "Listeriaceae"                         
[312] "Gemellaceae"                          
[313] "Turicibacteraceae"                    
[314] "Haloplasmataceae"                     
[315] "Carnobacteriaceae"                    
[316] "Enterococcaceae"                      
[317] "Aerococcaceae"                        
[318] "Leuconostocaceae"                     
[319] "Streptococcaceae"                     
[320] "Lactobacillaceae"                     
[321] "Staphylococcaceae"                    
[322] "Exiguobacteraceae"                    
[323] "Pasteuriaceae"                        
[324] "Thermoactinomycetaceae"               
[325] "Alicyclobacillaceae"                  
[326] "Syntrophomonadaceae"                  
[327] "Desulfitobacteraceae"                 
[328] "BSV43"                                
[329] "Veillonellaceae"                      
[330] "Peptococcaceae"                       
[331] "Dehalobacteriaceae"                   
[332] "Thermotogaceae"                       
[333] "Synergistaceae"                       
[334] "Dethiosulfovibrionaceae"              
[335] "Thermodesulfobiaceae"                 
Warning message:
system call failed: Cannot allocate memory 

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.