Resolve taxonomic conflict in the tax_table of a phyloseq object
Source:R/taxtab_modification.R
resolve_taxo_conflict.RdResolve taxonomic conflict in the tax_table of a phyloseq object
Usage
resolve_taxo_conflict(
physeq,
pattern_tax_ranks = NULL,
method = c("consensus", "rel_majority", "abs_majority", "preference", "unanimity"),
strict = FALSE,
second_method = c("consensus", "rel_majority", "abs_majority", "preference",
"unanimity"),
nb_agree_threshold = 1,
keep_tax_ranks = TRUE,
new_names = NULL,
preference_pattern = NULL,
collapse_string = "/",
replace_collapsed_rank_by_NA = FALSE
)Arguments
- physeq
(required) A phyloseq object.
- pattern_tax_ranks
(character vector, default NULL) A vector of patterns to aggregate taxonomic ranks. For example "^Genus" stands for all taxonomic ranks (columns in tax_table slot) starting with Genus.
- method
(character, default "consensus") One of "consensus", "rel_majority", "abs_majority", "preference" or "unanimity". See details in the documentation of the function
MiscMetabar::resolve_vector_ranks().- strict
(logical, default FALSE) If TRUE, NA are considered as informative in resolving conflict (i.e. NA are taken into account in vote). See details for more information.
- second_method
(character, default "consensus") One of "consensus", "rel_majority", "abs_majority", or "unanimity". Only used if method = "preference". See details.
- nb_agree_threshold
(integer, default 1) The minimum number of times a value must arise to be selected using vote. If 2, only taxonomic values present at least 2 times in the vector are kept.
- keep_tax_ranks
(logical, default TRUE) If TRUE, keep the old taxonomic ranks in the result.
- new_names
(character vector, default NULL) A vector of new names for the taxonomic columns.
- preference_pattern
(character, default NULL) A pattern to match the only column used as preferred one if method = "preference".
- collapse_string
(character, default "/") The character to collapse taxonomic names when multiple assignment is done.
- replace_collapsed_rank_by_NA
(logical, default FALSE) If TRUE, all multiple assignments (all taxonomic rank including the 'collapse_string' parameter) are replaced by NA.
Examples
data_fungi_mini_new <- assign_sintax(data_fungi_mini,
ref_fasta = system.file("extdata", "mini_UNITE_fungi.fasta.gz",
package = "MiscMetabar"
),
behavior = "add_to_phyloseq"
)
resolve_taxo_conflict(data_fungi_mini_new, pattern_tax_ranks = c("^Genus\\."), method = "consensus", new_names = "Genus_consensus")@tax_table
#> Taxonomy Table: [45 taxa by 20 taxonomic ranks]:
#> Domain Phylum.x Class.x Order.x
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Atractiellomycetes" "Atractiellales"
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" NA
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV83 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV100 "Fungi" "Basidiomycota" NA NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" "Corticiales"
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> Family.x Genus.x Species.x
#> ASV7 "Stereaceae" NA NA
#> ASV8 "Stereaceae" "Stereum" "ostrea"
#> ASV12 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV18 "Stereaceae" "Stereum" "ostrea"
#> ASV25 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV26 "Stereaceae" "Stereum" "hirsutum"
#> ASV27 "Steccherinaceae" "Antrodiella" "brasiliensis"
#> ASV29 "Exidiaceae" "Basidiodendron" "eyrei"
#> ASV32 "Cantharellales_fam_Incertae_sedis" "Sistotrema" "oblongisporum"
#> ASV34 "Entolomataceae" "Entocybe" NA
#> ASV35 "Polyporaceae" "Fomes" "fomentarius"
#> ASV41 "Tricholomataceae" "Mycena" "renati"
#> ASV42 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV46 "Atractiellales_fam_Incertae_sedis" "Helicogloea" "pellucida"
#> ASV47 "Pterulaceae" "Radulomyces" "molaris"
#> ASV48 "Aporpiaceae" "Elmerina" "caryae"
#> ASV49 "Phanerochaetaceae" "Phanerochaete" "livescens"
#> ASV50 "Russulales_fam_Incertae_sedis" "Gloeohypochnicium" "analogum"
#> ASV53 "Polyporaceae" "Fomes" "fomentarius"
#> ASV54 "Auriculariaceae" "Auricularia" NA
#> ASV58 "Polyporaceae" "Fomes" "fomentarius"
#> ASV59 "Hyphodermataceae" "Hyphoderma" "roseocremeum"
#> ASV61 "Hyphodermataceae" "Hyphoderma" "setigerum"
#> ASV62 NA NA NA
#> ASV63 NA NA NA
#> ASV64 "Polyporaceae" "Trametes" "versicolor"
#> ASV67 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV68 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV71 NA NA NA
#> ASV72 NA NA NA
#> ASV75 "Peniophoraceae" "Peniophora" "versiformis"
#> ASV77 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV82 "Exidiaceae" "Exidia" "glandulosa"
#> ASV83 NA NA NA
#> ASV85 "Hymenochaetales_fam_Incertae_sedis" "Peniophorella" "pubera"
#> ASV91 "Auriculariaceae" "Auricularia" "mesenterica"
#> ASV93 "Stereaceae" NA NA
#> ASV94 "Stereaceae" "Stereum" "ostrea"
#> ASV99 "Polyporaceae" "Fomes" "fomentarius"
#> ASV100 NA NA NA
#> ASV101 "Corticiaceae" "Marchandiomyces" "buckii"
#> ASV104 "Hericiaceae" "Hericium" "coralloides"
#> ASV105 "Schizoporaceae" "Xylodon" "flaviporus"
#> ASV107 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV108 "Exidiaceae" "Exidia" "glandulosa"
#> Trophic.Mode
#> ASV7 "Saprotroph"
#> ASV8 "Saprotroph"
#> ASV12 "Saprotroph"
#> ASV18 "Saprotroph"
#> ASV25 "Saprotroph"
#> ASV26 "Saprotroph"
#> ASV27 "Saprotroph"
#> ASV29 "Saprotroph"
#> ASV32 "Saprotroph-Symbiotroph"
#> ASV34 "Saprotroph"
#> ASV35 "Saprotroph"
#> ASV41 "Pathotroph-Saprotroph"
#> ASV42 "Saprotroph"
#> ASV46 "Saprotroph"
#> ASV47 "Saprotroph"
#> ASV48 "Saprotroph"
#> ASV49 "Saprotroph"
#> ASV50 "Saprotroph"
#> ASV53 "Saprotroph"
#> ASV54 "Saprotroph"
#> ASV58 "Saprotroph"
#> ASV59 "Saprotroph"
#> ASV61 "Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Saprotroph"
#> ASV67 "Saprotroph"
#> ASV68 "Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Pathotroph-Saprotroph"
#> ASV77 "Saprotroph"
#> ASV82 "Saprotroph-Symbiotroph"
#> ASV83 "Pathotroph-Saprotroph-Symbiotroph"
#> ASV85 "Saprotroph"
#> ASV91 "Saprotroph"
#> ASV93 "Saprotroph"
#> ASV94 "Saprotroph"
#> ASV99 "Saprotroph"
#> ASV100 "-"
#> ASV101 "Pathotroph"
#> ASV104 "Saprotroph"
#> ASV105 "Saprotroph"
#> ASV107 "Saprotroph"
#> ASV108 "Saprotroph-Symbiotroph"
#> Guild
#> ASV7 "Wood Saprotroph-Undefined Saprotroph"
#> ASV8 "Undefined Saprotroph"
#> ASV12 "Undefined Saprotroph"
#> ASV18 "Undefined Saprotroph"
#> ASV25 "Wood Saprotroph"
#> ASV26 "Undefined Saprotroph"
#> ASV27 "Wood Saprotroph"
#> ASV29 "Undefined Saprotroph"
#> ASV32 "Ectomycorrhizal-Wood Saprotroph"
#> ASV34 "Undefined Saprotroph"
#> ASV35 "Wood Saprotroph"
#> ASV41 "Leaf Saprotroph-Plant Pathogen-Undefined Saprotroph-Wood Saprotroph"
#> ASV42 "Wood Saprotroph"
#> ASV46 "Undefined Saprotroph"
#> ASV47 "Undefined Saprotroph"
#> ASV48 "Undefined Saprotroph"
#> ASV49 "Wood Saprotroph"
#> ASV50 "Undefined Saprotroph"
#> ASV53 "Wood Saprotroph"
#> ASV54 "Undefined Saprotroph"
#> ASV58 "Wood Saprotroph"
#> ASV59 "Undefined Saprotroph"
#> ASV61 "Undefined Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Wood Saprotroph"
#> ASV67 "Undefined Saprotroph"
#> ASV68 "Wood Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Plant Pathogen-Wood Saprotroph"
#> ASV77 "Wood Saprotroph"
#> ASV82 "Endophyte-Undefined Saprotroph"
#> ASV83 "Fungal Parasite-Undefined Saprotroph"
#> ASV85 "Undefined Saprotroph"
#> ASV91 "Undefined Saprotroph"
#> ASV93 "Wood Saprotroph-Undefined Saprotroph"
#> ASV94 "Undefined Saprotroph"
#> ASV99 "Wood Saprotroph"
#> ASV100 "-"
#> ASV101 "Lichen Parasite"
#> ASV104 "Undefined Saprotroph"
#> ASV105 "Undefined Saprotroph"
#> ASV107 "Undefined Saprotroph"
#> ASV108 "Endophyte-Undefined Saprotroph"
#> Trait Confidence.Ranking Genus_species
#> ASV7 "NULL" "Probable" "NA_NA"
#> ASV8 "White Rot" "Probable" "Stereum_ostrea"
#> ASV12 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV18 "White Rot" "Probable" "Stereum_ostrea"
#> ASV25 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV26 "White Rot" "Probable" "Stereum_hirsutum"
#> ASV27 "White Rot" "Highly Probable" "Antrodiella_brasiliensis"
#> ASV29 "NULL" "Probable" "Basidiodendron_eyrei"
#> ASV32 "White Rot" "Possible" "Sistotrema_oblongisporum"
#> ASV34 "NULL" "Probable" "Entocybe_NA"
#> ASV35 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV41 "NULL" "Probable" "Mycena_renati"
#> ASV42 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV46 "NULL" "Probable" "Helicogloea_pellucida"
#> ASV47 "White Rot" "Probable" "Radulomyces_molaris"
#> ASV48 "NULL" "Probable" "Elmerina_caryae"
#> ASV49 "White Rot" "Highly Probable" "Phanerochaete_livescens"
#> ASV50 "White Rot" "Probable" "Gloeohypochnicium_analogum"
#> ASV53 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV54 "NULL" "Probable" "Auricularia_NA"
#> ASV58 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV59 "White Rot" "Probable" "Hyphoderma_roseocremeum"
#> ASV61 "White Rot" "Probable" "Hyphoderma_setigerum"
#> ASV62 "-" "-" "NA_NA"
#> ASV63 "-" "-" "NA_NA"
#> ASV64 "White Rot" "Highly Probable" "Trametes_versicolor"
#> ASV67 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV68 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV71 "-" "-" "NA_NA"
#> ASV72 "-" "-" "NA_NA"
#> ASV75 "White Rot" "Probable" "Peniophora_versiformis"
#> ASV77 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV82 "NULL" "Probable" "Exidia_glandulosa"
#> ASV83 "NULL" "Possible" "NA_NA"
#> ASV85 "White Rot" "Probable" "Peniophorella_pubera"
#> ASV91 "NULL" "Probable" "Auricularia_mesenterica"
#> ASV93 "NULL" "Probable" "NA_NA"
#> ASV94 "White Rot" "Probable" "Stereum_ostrea"
#> ASV99 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV100 "-" "-" "NA_NA"
#> ASV101 "NULL" "Probable" "Marchandiomyces_buckii"
#> ASV104 "White Rot" "Probable" "Hericium_coralloides"
#> ASV105 "White Rot" "Probable" "Xylodon_flaviporus"
#> ASV107 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV108 "NULL" "Probable" "Exidia_glandulosa"
#> Kingdom Phylum.y Class.y Order.y
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" "Sebacinales"
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV83 "Fungi" "Basidiomycota" NA NA
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV100 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> Family.y Genus.y
#> ASV7 NA NA
#> ASV8 NA NA
#> ASV12 NA NA
#> ASV18 NA NA
#> ASV25 "Tricholomataceae" "Tricholoma"
#> ASV26 NA NA
#> ASV27 NA NA
#> ASV29 NA NA
#> ASV32 "Hydnaceae" "Sistotrema"
#> ASV34 NA NA
#> ASV35 NA NA
#> ASV41 "Mycenaceae" "Mycena"
#> ASV42 NA NA
#> ASV46 NA NA
#> ASV47 NA NA
#> ASV48 NA NA
#> ASV49 NA NA
#> ASV50 NA NA
#> ASV53 NA NA
#> ASV54 NA NA
#> ASV58 NA NA
#> ASV59 NA NA
#> ASV61 "Hyphodermataceae" "Hyphoderma"
#> ASV62 "Serendipitaceae" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA NA
#> ASV67 NA NA
#> ASV68 "Tricholomataceae" "Tricholoma"
#> ASV71 "Tremellales_fam_Incertae_sedis" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophoraceae" "Peniophora"
#> ASV77 "Tricholomataceae" NA
#> ASV82 NA NA
#> ASV83 NA NA
#> ASV85 NA NA
#> ASV91 NA NA
#> ASV93 NA NA
#> ASV94 NA NA
#> ASV99 NA NA
#> ASV100 NA NA
#> ASV101 NA NA
#> ASV104 NA NA
#> ASV105 NA NA
#> ASV107 NA NA
#> ASV108 NA NA
#> Species.y Genus_consensus
#> ASV7 NA NA
#> ASV8 NA "Stereum"
#> ASV12 NA "Xylodon"
#> ASV18 NA "Stereum"
#> ASV25 NA "Ossicaulis/Tricholoma"
#> ASV26 NA "Stereum"
#> ASV27 NA "Antrodiella"
#> ASV29 NA "Basidiodendron"
#> ASV32 "Sistotrema_sp" "Sistotrema"
#> ASV34 NA "Entocybe"
#> ASV35 NA "Fomes"
#> ASV41 "Mycena_sp" "Mycena"
#> ASV42 NA "Ossicaulis"
#> ASV46 NA "Helicogloea"
#> ASV47 NA "Radulomyces"
#> ASV48 NA "Elmerina"
#> ASV49 NA "Phanerochaete"
#> ASV50 NA "Gloeohypochnicium"
#> ASV53 NA "Fomes"
#> ASV54 NA "Auricularia"
#> ASV58 NA "Fomes"
#> ASV59 NA "Hyphoderma"
#> ASV61 "Hyphoderma_sp" "Hyphoderma"
#> ASV62 "Serendipita_sp" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA "Trametes"
#> ASV67 NA "Xylodon"
#> ASV68 NA "Ossicaulis/Tricholoma"
#> ASV71 "Tremellales_sp" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophora_reidii" "Peniophora"
#> ASV77 NA "Ossicaulis"
#> ASV82 NA "Exidia"
#> ASV83 NA NA
#> ASV85 NA "Peniophorella"
#> ASV91 NA "Auricularia"
#> ASV93 NA NA
#> ASV94 NA "Stereum"
#> ASV99 NA "Fomes"
#> ASV100 NA NA
#> ASV101 NA "Marchandiomyces"
#> ASV104 NA "Hericium"
#> ASV105 NA "Xylodon"
#> ASV107 NA "Xylodon"
#> ASV108 NA "Exidia"
resolve_taxo_conflict(data_fungi_mini_new, pattern_tax_ranks = c("^Genus\\."), method = "consensus", new_names = "Genus_consensus", replace_collapsed_rank_by_NA = TRUE)@tax_table
#> Taxonomy Table: [45 taxa by 20 taxonomic ranks]:
#> Domain Phylum.x Class.x Order.x
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Atractiellomycetes" "Atractiellales"
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" NA
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV83 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV100 "Fungi" "Basidiomycota" NA NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" "Corticiales"
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> Family.x Genus.x Species.x
#> ASV7 "Stereaceae" NA NA
#> ASV8 "Stereaceae" "Stereum" "ostrea"
#> ASV12 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV18 "Stereaceae" "Stereum" "ostrea"
#> ASV25 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV26 "Stereaceae" "Stereum" "hirsutum"
#> ASV27 "Steccherinaceae" "Antrodiella" "brasiliensis"
#> ASV29 "Exidiaceae" "Basidiodendron" "eyrei"
#> ASV32 "Cantharellales_fam_Incertae_sedis" "Sistotrema" "oblongisporum"
#> ASV34 "Entolomataceae" "Entocybe" NA
#> ASV35 "Polyporaceae" "Fomes" "fomentarius"
#> ASV41 "Tricholomataceae" "Mycena" "renati"
#> ASV42 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV46 "Atractiellales_fam_Incertae_sedis" "Helicogloea" "pellucida"
#> ASV47 "Pterulaceae" "Radulomyces" "molaris"
#> ASV48 "Aporpiaceae" "Elmerina" "caryae"
#> ASV49 "Phanerochaetaceae" "Phanerochaete" "livescens"
#> ASV50 "Russulales_fam_Incertae_sedis" "Gloeohypochnicium" "analogum"
#> ASV53 "Polyporaceae" "Fomes" "fomentarius"
#> ASV54 "Auriculariaceae" "Auricularia" NA
#> ASV58 "Polyporaceae" "Fomes" "fomentarius"
#> ASV59 "Hyphodermataceae" "Hyphoderma" "roseocremeum"
#> ASV61 "Hyphodermataceae" "Hyphoderma" "setigerum"
#> ASV62 NA NA NA
#> ASV63 NA NA NA
#> ASV64 "Polyporaceae" "Trametes" "versicolor"
#> ASV67 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV68 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV71 NA NA NA
#> ASV72 NA NA NA
#> ASV75 "Peniophoraceae" "Peniophora" "versiformis"
#> ASV77 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV82 "Exidiaceae" "Exidia" "glandulosa"
#> ASV83 NA NA NA
#> ASV85 "Hymenochaetales_fam_Incertae_sedis" "Peniophorella" "pubera"
#> ASV91 "Auriculariaceae" "Auricularia" "mesenterica"
#> ASV93 "Stereaceae" NA NA
#> ASV94 "Stereaceae" "Stereum" "ostrea"
#> ASV99 "Polyporaceae" "Fomes" "fomentarius"
#> ASV100 NA NA NA
#> ASV101 "Corticiaceae" "Marchandiomyces" "buckii"
#> ASV104 "Hericiaceae" "Hericium" "coralloides"
#> ASV105 "Schizoporaceae" "Xylodon" "flaviporus"
#> ASV107 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV108 "Exidiaceae" "Exidia" "glandulosa"
#> Trophic.Mode
#> ASV7 "Saprotroph"
#> ASV8 "Saprotroph"
#> ASV12 "Saprotroph"
#> ASV18 "Saprotroph"
#> ASV25 "Saprotroph"
#> ASV26 "Saprotroph"
#> ASV27 "Saprotroph"
#> ASV29 "Saprotroph"
#> ASV32 "Saprotroph-Symbiotroph"
#> ASV34 "Saprotroph"
#> ASV35 "Saprotroph"
#> ASV41 "Pathotroph-Saprotroph"
#> ASV42 "Saprotroph"
#> ASV46 "Saprotroph"
#> ASV47 "Saprotroph"
#> ASV48 "Saprotroph"
#> ASV49 "Saprotroph"
#> ASV50 "Saprotroph"
#> ASV53 "Saprotroph"
#> ASV54 "Saprotroph"
#> ASV58 "Saprotroph"
#> ASV59 "Saprotroph"
#> ASV61 "Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Saprotroph"
#> ASV67 "Saprotroph"
#> ASV68 "Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Pathotroph-Saprotroph"
#> ASV77 "Saprotroph"
#> ASV82 "Saprotroph-Symbiotroph"
#> ASV83 "Pathotroph-Saprotroph-Symbiotroph"
#> ASV85 "Saprotroph"
#> ASV91 "Saprotroph"
#> ASV93 "Saprotroph"
#> ASV94 "Saprotroph"
#> ASV99 "Saprotroph"
#> ASV100 "-"
#> ASV101 "Pathotroph"
#> ASV104 "Saprotroph"
#> ASV105 "Saprotroph"
#> ASV107 "Saprotroph"
#> ASV108 "Saprotroph-Symbiotroph"
#> Guild
#> ASV7 "Wood Saprotroph-Undefined Saprotroph"
#> ASV8 "Undefined Saprotroph"
#> ASV12 "Undefined Saprotroph"
#> ASV18 "Undefined Saprotroph"
#> ASV25 "Wood Saprotroph"
#> ASV26 "Undefined Saprotroph"
#> ASV27 "Wood Saprotroph"
#> ASV29 "Undefined Saprotroph"
#> ASV32 "Ectomycorrhizal-Wood Saprotroph"
#> ASV34 "Undefined Saprotroph"
#> ASV35 "Wood Saprotroph"
#> ASV41 "Leaf Saprotroph-Plant Pathogen-Undefined Saprotroph-Wood Saprotroph"
#> ASV42 "Wood Saprotroph"
#> ASV46 "Undefined Saprotroph"
#> ASV47 "Undefined Saprotroph"
#> ASV48 "Undefined Saprotroph"
#> ASV49 "Wood Saprotroph"
#> ASV50 "Undefined Saprotroph"
#> ASV53 "Wood Saprotroph"
#> ASV54 "Undefined Saprotroph"
#> ASV58 "Wood Saprotroph"
#> ASV59 "Undefined Saprotroph"
#> ASV61 "Undefined Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Wood Saprotroph"
#> ASV67 "Undefined Saprotroph"
#> ASV68 "Wood Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Plant Pathogen-Wood Saprotroph"
#> ASV77 "Wood Saprotroph"
#> ASV82 "Endophyte-Undefined Saprotroph"
#> ASV83 "Fungal Parasite-Undefined Saprotroph"
#> ASV85 "Undefined Saprotroph"
#> ASV91 "Undefined Saprotroph"
#> ASV93 "Wood Saprotroph-Undefined Saprotroph"
#> ASV94 "Undefined Saprotroph"
#> ASV99 "Wood Saprotroph"
#> ASV100 "-"
#> ASV101 "Lichen Parasite"
#> ASV104 "Undefined Saprotroph"
#> ASV105 "Undefined Saprotroph"
#> ASV107 "Undefined Saprotroph"
#> ASV108 "Endophyte-Undefined Saprotroph"
#> Trait Confidence.Ranking Genus_species
#> ASV7 "NULL" "Probable" "NA_NA"
#> ASV8 "White Rot" "Probable" "Stereum_ostrea"
#> ASV12 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV18 "White Rot" "Probable" "Stereum_ostrea"
#> ASV25 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV26 "White Rot" "Probable" "Stereum_hirsutum"
#> ASV27 "White Rot" "Highly Probable" "Antrodiella_brasiliensis"
#> ASV29 "NULL" "Probable" "Basidiodendron_eyrei"
#> ASV32 "White Rot" "Possible" "Sistotrema_oblongisporum"
#> ASV34 "NULL" "Probable" "Entocybe_NA"
#> ASV35 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV41 "NULL" "Probable" "Mycena_renati"
#> ASV42 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV46 "NULL" "Probable" "Helicogloea_pellucida"
#> ASV47 "White Rot" "Probable" "Radulomyces_molaris"
#> ASV48 "NULL" "Probable" "Elmerina_caryae"
#> ASV49 "White Rot" "Highly Probable" "Phanerochaete_livescens"
#> ASV50 "White Rot" "Probable" "Gloeohypochnicium_analogum"
#> ASV53 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV54 "NULL" "Probable" "Auricularia_NA"
#> ASV58 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV59 "White Rot" "Probable" "Hyphoderma_roseocremeum"
#> ASV61 "White Rot" "Probable" "Hyphoderma_setigerum"
#> ASV62 "-" "-" "NA_NA"
#> ASV63 "-" "-" "NA_NA"
#> ASV64 "White Rot" "Highly Probable" "Trametes_versicolor"
#> ASV67 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV68 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV71 "-" "-" "NA_NA"
#> ASV72 "-" "-" "NA_NA"
#> ASV75 "White Rot" "Probable" "Peniophora_versiformis"
#> ASV77 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV82 "NULL" "Probable" "Exidia_glandulosa"
#> ASV83 "NULL" "Possible" "NA_NA"
#> ASV85 "White Rot" "Probable" "Peniophorella_pubera"
#> ASV91 "NULL" "Probable" "Auricularia_mesenterica"
#> ASV93 "NULL" "Probable" "NA_NA"
#> ASV94 "White Rot" "Probable" "Stereum_ostrea"
#> ASV99 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV100 "-" "-" "NA_NA"
#> ASV101 "NULL" "Probable" "Marchandiomyces_buckii"
#> ASV104 "White Rot" "Probable" "Hericium_coralloides"
#> ASV105 "White Rot" "Probable" "Xylodon_flaviporus"
#> ASV107 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV108 "NULL" "Probable" "Exidia_glandulosa"
#> Kingdom Phylum.y Class.y Order.y
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" "Sebacinales"
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV83 "Fungi" "Basidiomycota" NA NA
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV100 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> Family.y Genus.y
#> ASV7 NA NA
#> ASV8 NA NA
#> ASV12 NA NA
#> ASV18 NA NA
#> ASV25 "Tricholomataceae" "Tricholoma"
#> ASV26 NA NA
#> ASV27 NA NA
#> ASV29 NA NA
#> ASV32 "Hydnaceae" "Sistotrema"
#> ASV34 NA NA
#> ASV35 NA NA
#> ASV41 "Mycenaceae" "Mycena"
#> ASV42 NA NA
#> ASV46 NA NA
#> ASV47 NA NA
#> ASV48 NA NA
#> ASV49 NA NA
#> ASV50 NA NA
#> ASV53 NA NA
#> ASV54 NA NA
#> ASV58 NA NA
#> ASV59 NA NA
#> ASV61 "Hyphodermataceae" "Hyphoderma"
#> ASV62 "Serendipitaceae" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA NA
#> ASV67 NA NA
#> ASV68 "Tricholomataceae" "Tricholoma"
#> ASV71 "Tremellales_fam_Incertae_sedis" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophoraceae" "Peniophora"
#> ASV77 "Tricholomataceae" NA
#> ASV82 NA NA
#> ASV83 NA NA
#> ASV85 NA NA
#> ASV91 NA NA
#> ASV93 NA NA
#> ASV94 NA NA
#> ASV99 NA NA
#> ASV100 NA NA
#> ASV101 NA NA
#> ASV104 NA NA
#> ASV105 NA NA
#> ASV107 NA NA
#> ASV108 NA NA
#> Species.y Genus_consensus
#> ASV7 NA NA
#> ASV8 NA "Stereum"
#> ASV12 NA "Xylodon"
#> ASV18 NA "Stereum"
#> ASV25 NA NA
#> ASV26 NA "Stereum"
#> ASV27 NA "Antrodiella"
#> ASV29 NA "Basidiodendron"
#> ASV32 "Sistotrema_sp" "Sistotrema"
#> ASV34 NA "Entocybe"
#> ASV35 NA "Fomes"
#> ASV41 "Mycena_sp" "Mycena"
#> ASV42 NA "Ossicaulis"
#> ASV46 NA "Helicogloea"
#> ASV47 NA "Radulomyces"
#> ASV48 NA "Elmerina"
#> ASV49 NA "Phanerochaete"
#> ASV50 NA "Gloeohypochnicium"
#> ASV53 NA "Fomes"
#> ASV54 NA "Auricularia"
#> ASV58 NA "Fomes"
#> ASV59 NA "Hyphoderma"
#> ASV61 "Hyphoderma_sp" "Hyphoderma"
#> ASV62 "Serendipita_sp" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA "Trametes"
#> ASV67 NA "Xylodon"
#> ASV68 NA NA
#> ASV71 "Tremellales_sp" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophora_reidii" "Peniophora"
#> ASV77 NA "Ossicaulis"
#> ASV82 NA "Exidia"
#> ASV83 NA NA
#> ASV85 NA "Peniophorella"
#> ASV91 NA "Auricularia"
#> ASV93 NA NA
#> ASV94 NA "Stereum"
#> ASV99 NA "Fomes"
#> ASV100 NA NA
#> ASV101 NA "Marchandiomyces"
#> ASV104 NA "Hericium"
#> ASV105 NA "Xylodon"
#> ASV107 NA "Xylodon"
#> ASV108 NA "Exidia"
resolve_taxo_conflict(data_fungi_mini_new, pattern_tax_ranks = c("^Genus\\."), method = "preference", preference_pattern = ".x$")@tax_table
#> Taxonomy Table: [45 taxa by 20 taxonomic ranks]:
#> Domain Phylum.x Class.x Order.x
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Atractiellomycetes" "Atractiellales"
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" NA
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV83 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV100 "Fungi" "Basidiomycota" NA NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" "Corticiales"
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> Family.x Genus.x Species.x
#> ASV7 "Stereaceae" NA NA
#> ASV8 "Stereaceae" "Stereum" "ostrea"
#> ASV12 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV18 "Stereaceae" "Stereum" "ostrea"
#> ASV25 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV26 "Stereaceae" "Stereum" "hirsutum"
#> ASV27 "Steccherinaceae" "Antrodiella" "brasiliensis"
#> ASV29 "Exidiaceae" "Basidiodendron" "eyrei"
#> ASV32 "Cantharellales_fam_Incertae_sedis" "Sistotrema" "oblongisporum"
#> ASV34 "Entolomataceae" "Entocybe" NA
#> ASV35 "Polyporaceae" "Fomes" "fomentarius"
#> ASV41 "Tricholomataceae" "Mycena" "renati"
#> ASV42 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV46 "Atractiellales_fam_Incertae_sedis" "Helicogloea" "pellucida"
#> ASV47 "Pterulaceae" "Radulomyces" "molaris"
#> ASV48 "Aporpiaceae" "Elmerina" "caryae"
#> ASV49 "Phanerochaetaceae" "Phanerochaete" "livescens"
#> ASV50 "Russulales_fam_Incertae_sedis" "Gloeohypochnicium" "analogum"
#> ASV53 "Polyporaceae" "Fomes" "fomentarius"
#> ASV54 "Auriculariaceae" "Auricularia" NA
#> ASV58 "Polyporaceae" "Fomes" "fomentarius"
#> ASV59 "Hyphodermataceae" "Hyphoderma" "roseocremeum"
#> ASV61 "Hyphodermataceae" "Hyphoderma" "setigerum"
#> ASV62 NA NA NA
#> ASV63 NA NA NA
#> ASV64 "Polyporaceae" "Trametes" "versicolor"
#> ASV67 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV68 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV71 NA NA NA
#> ASV72 NA NA NA
#> ASV75 "Peniophoraceae" "Peniophora" "versiformis"
#> ASV77 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV82 "Exidiaceae" "Exidia" "glandulosa"
#> ASV83 NA NA NA
#> ASV85 "Hymenochaetales_fam_Incertae_sedis" "Peniophorella" "pubera"
#> ASV91 "Auriculariaceae" "Auricularia" "mesenterica"
#> ASV93 "Stereaceae" NA NA
#> ASV94 "Stereaceae" "Stereum" "ostrea"
#> ASV99 "Polyporaceae" "Fomes" "fomentarius"
#> ASV100 NA NA NA
#> ASV101 "Corticiaceae" "Marchandiomyces" "buckii"
#> ASV104 "Hericiaceae" "Hericium" "coralloides"
#> ASV105 "Schizoporaceae" "Xylodon" "flaviporus"
#> ASV107 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV108 "Exidiaceae" "Exidia" "glandulosa"
#> Trophic.Mode
#> ASV7 "Saprotroph"
#> ASV8 "Saprotroph"
#> ASV12 "Saprotroph"
#> ASV18 "Saprotroph"
#> ASV25 "Saprotroph"
#> ASV26 "Saprotroph"
#> ASV27 "Saprotroph"
#> ASV29 "Saprotroph"
#> ASV32 "Saprotroph-Symbiotroph"
#> ASV34 "Saprotroph"
#> ASV35 "Saprotroph"
#> ASV41 "Pathotroph-Saprotroph"
#> ASV42 "Saprotroph"
#> ASV46 "Saprotroph"
#> ASV47 "Saprotroph"
#> ASV48 "Saprotroph"
#> ASV49 "Saprotroph"
#> ASV50 "Saprotroph"
#> ASV53 "Saprotroph"
#> ASV54 "Saprotroph"
#> ASV58 "Saprotroph"
#> ASV59 "Saprotroph"
#> ASV61 "Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Saprotroph"
#> ASV67 "Saprotroph"
#> ASV68 "Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Pathotroph-Saprotroph"
#> ASV77 "Saprotroph"
#> ASV82 "Saprotroph-Symbiotroph"
#> ASV83 "Pathotroph-Saprotroph-Symbiotroph"
#> ASV85 "Saprotroph"
#> ASV91 "Saprotroph"
#> ASV93 "Saprotroph"
#> ASV94 "Saprotroph"
#> ASV99 "Saprotroph"
#> ASV100 "-"
#> ASV101 "Pathotroph"
#> ASV104 "Saprotroph"
#> ASV105 "Saprotroph"
#> ASV107 "Saprotroph"
#> ASV108 "Saprotroph-Symbiotroph"
#> Guild
#> ASV7 "Wood Saprotroph-Undefined Saprotroph"
#> ASV8 "Undefined Saprotroph"
#> ASV12 "Undefined Saprotroph"
#> ASV18 "Undefined Saprotroph"
#> ASV25 "Wood Saprotroph"
#> ASV26 "Undefined Saprotroph"
#> ASV27 "Wood Saprotroph"
#> ASV29 "Undefined Saprotroph"
#> ASV32 "Ectomycorrhizal-Wood Saprotroph"
#> ASV34 "Undefined Saprotroph"
#> ASV35 "Wood Saprotroph"
#> ASV41 "Leaf Saprotroph-Plant Pathogen-Undefined Saprotroph-Wood Saprotroph"
#> ASV42 "Wood Saprotroph"
#> ASV46 "Undefined Saprotroph"
#> ASV47 "Undefined Saprotroph"
#> ASV48 "Undefined Saprotroph"
#> ASV49 "Wood Saprotroph"
#> ASV50 "Undefined Saprotroph"
#> ASV53 "Wood Saprotroph"
#> ASV54 "Undefined Saprotroph"
#> ASV58 "Wood Saprotroph"
#> ASV59 "Undefined Saprotroph"
#> ASV61 "Undefined Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Wood Saprotroph"
#> ASV67 "Undefined Saprotroph"
#> ASV68 "Wood Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Plant Pathogen-Wood Saprotroph"
#> ASV77 "Wood Saprotroph"
#> ASV82 "Endophyte-Undefined Saprotroph"
#> ASV83 "Fungal Parasite-Undefined Saprotroph"
#> ASV85 "Undefined Saprotroph"
#> ASV91 "Undefined Saprotroph"
#> ASV93 "Wood Saprotroph-Undefined Saprotroph"
#> ASV94 "Undefined Saprotroph"
#> ASV99 "Wood Saprotroph"
#> ASV100 "-"
#> ASV101 "Lichen Parasite"
#> ASV104 "Undefined Saprotroph"
#> ASV105 "Undefined Saprotroph"
#> ASV107 "Undefined Saprotroph"
#> ASV108 "Endophyte-Undefined Saprotroph"
#> Trait Confidence.Ranking Genus_species
#> ASV7 "NULL" "Probable" "NA_NA"
#> ASV8 "White Rot" "Probable" "Stereum_ostrea"
#> ASV12 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV18 "White Rot" "Probable" "Stereum_ostrea"
#> ASV25 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV26 "White Rot" "Probable" "Stereum_hirsutum"
#> ASV27 "White Rot" "Highly Probable" "Antrodiella_brasiliensis"
#> ASV29 "NULL" "Probable" "Basidiodendron_eyrei"
#> ASV32 "White Rot" "Possible" "Sistotrema_oblongisporum"
#> ASV34 "NULL" "Probable" "Entocybe_NA"
#> ASV35 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV41 "NULL" "Probable" "Mycena_renati"
#> ASV42 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV46 "NULL" "Probable" "Helicogloea_pellucida"
#> ASV47 "White Rot" "Probable" "Radulomyces_molaris"
#> ASV48 "NULL" "Probable" "Elmerina_caryae"
#> ASV49 "White Rot" "Highly Probable" "Phanerochaete_livescens"
#> ASV50 "White Rot" "Probable" "Gloeohypochnicium_analogum"
#> ASV53 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV54 "NULL" "Probable" "Auricularia_NA"
#> ASV58 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV59 "White Rot" "Probable" "Hyphoderma_roseocremeum"
#> ASV61 "White Rot" "Probable" "Hyphoderma_setigerum"
#> ASV62 "-" "-" "NA_NA"
#> ASV63 "-" "-" "NA_NA"
#> ASV64 "White Rot" "Highly Probable" "Trametes_versicolor"
#> ASV67 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV68 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV71 "-" "-" "NA_NA"
#> ASV72 "-" "-" "NA_NA"
#> ASV75 "White Rot" "Probable" "Peniophora_versiformis"
#> ASV77 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV82 "NULL" "Probable" "Exidia_glandulosa"
#> ASV83 "NULL" "Possible" "NA_NA"
#> ASV85 "White Rot" "Probable" "Peniophorella_pubera"
#> ASV91 "NULL" "Probable" "Auricularia_mesenterica"
#> ASV93 "NULL" "Probable" "NA_NA"
#> ASV94 "White Rot" "Probable" "Stereum_ostrea"
#> ASV99 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV100 "-" "-" "NA_NA"
#> ASV101 "NULL" "Probable" "Marchandiomyces_buckii"
#> ASV104 "White Rot" "Probable" "Hericium_coralloides"
#> ASV105 "White Rot" "Probable" "Xylodon_flaviporus"
#> ASV107 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV108 "NULL" "Probable" "Exidia_glandulosa"
#> Kingdom Phylum.y Class.y Order.y
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" "Sebacinales"
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV83 "Fungi" "Basidiomycota" NA NA
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV100 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> Family.y Genus.y
#> ASV7 NA NA
#> ASV8 NA NA
#> ASV12 NA NA
#> ASV18 NA NA
#> ASV25 "Tricholomataceae" "Tricholoma"
#> ASV26 NA NA
#> ASV27 NA NA
#> ASV29 NA NA
#> ASV32 "Hydnaceae" "Sistotrema"
#> ASV34 NA NA
#> ASV35 NA NA
#> ASV41 "Mycenaceae" "Mycena"
#> ASV42 NA NA
#> ASV46 NA NA
#> ASV47 NA NA
#> ASV48 NA NA
#> ASV49 NA NA
#> ASV50 NA NA
#> ASV53 NA NA
#> ASV54 NA NA
#> ASV58 NA NA
#> ASV59 NA NA
#> ASV61 "Hyphodermataceae" "Hyphoderma"
#> ASV62 "Serendipitaceae" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA NA
#> ASV67 NA NA
#> ASV68 "Tricholomataceae" "Tricholoma"
#> ASV71 "Tremellales_fam_Incertae_sedis" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophoraceae" "Peniophora"
#> ASV77 "Tricholomataceae" NA
#> ASV82 NA NA
#> ASV83 NA NA
#> ASV85 NA NA
#> ASV91 NA NA
#> ASV93 NA NA
#> ASV94 NA NA
#> ASV99 NA NA
#> ASV100 NA NA
#> ASV101 NA NA
#> ASV104 NA NA
#> ASV105 NA NA
#> ASV107 NA NA
#> ASV108 NA NA
#> Species.y ^Genus\\._preference
#> ASV7 NA NA
#> ASV8 NA "Stereum"
#> ASV12 NA "Xylodon"
#> ASV18 NA "Stereum"
#> ASV25 NA "Ossicaulis"
#> ASV26 NA "Stereum"
#> ASV27 NA "Antrodiella"
#> ASV29 NA "Basidiodendron"
#> ASV32 "Sistotrema_sp" "Sistotrema"
#> ASV34 NA "Entocybe"
#> ASV35 NA "Fomes"
#> ASV41 "Mycena_sp" "Mycena"
#> ASV42 NA "Ossicaulis"
#> ASV46 NA "Helicogloea"
#> ASV47 NA "Radulomyces"
#> ASV48 NA "Elmerina"
#> ASV49 NA "Phanerochaete"
#> ASV50 NA "Gloeohypochnicium"
#> ASV53 NA "Fomes"
#> ASV54 NA "Auricularia"
#> ASV58 NA "Fomes"
#> ASV59 NA "Hyphoderma"
#> ASV61 "Hyphoderma_sp" "Hyphoderma"
#> ASV62 "Serendipita_sp" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA "Trametes"
#> ASV67 NA "Xylodon"
#> ASV68 NA "Ossicaulis"
#> ASV71 "Tremellales_sp" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophora_reidii" "Peniophora"
#> ASV77 NA "Ossicaulis"
#> ASV82 NA "Exidia"
#> ASV83 NA NA
#> ASV85 NA "Peniophorella"
#> ASV91 NA "Auricularia"
#> ASV93 NA NA
#> ASV94 NA "Stereum"
#> ASV99 NA "Fomes"
#> ASV100 NA NA
#> ASV101 NA "Marchandiomyces"
#> ASV104 NA "Hericium"
#> ASV105 NA "Xylodon"
#> ASV107 NA "Xylodon"
#> ASV108 NA "Exidia"
resolve_taxo_conflict(data_fungi_mini_new, pattern_tax_ranks = c("^Genus\\."), method = "abs_majority")@tax_table
#> Taxonomy Table: [45 taxa by 20 taxonomic ranks]:
#> Domain Phylum.x Class.x Order.x
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Atractiellomycetes" "Atractiellales"
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" NA
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV83 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV100 "Fungi" "Basidiomycota" NA NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" "Corticiales"
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> Family.x Genus.x Species.x
#> ASV7 "Stereaceae" NA NA
#> ASV8 "Stereaceae" "Stereum" "ostrea"
#> ASV12 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV18 "Stereaceae" "Stereum" "ostrea"
#> ASV25 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV26 "Stereaceae" "Stereum" "hirsutum"
#> ASV27 "Steccherinaceae" "Antrodiella" "brasiliensis"
#> ASV29 "Exidiaceae" "Basidiodendron" "eyrei"
#> ASV32 "Cantharellales_fam_Incertae_sedis" "Sistotrema" "oblongisporum"
#> ASV34 "Entolomataceae" "Entocybe" NA
#> ASV35 "Polyporaceae" "Fomes" "fomentarius"
#> ASV41 "Tricholomataceae" "Mycena" "renati"
#> ASV42 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV46 "Atractiellales_fam_Incertae_sedis" "Helicogloea" "pellucida"
#> ASV47 "Pterulaceae" "Radulomyces" "molaris"
#> ASV48 "Aporpiaceae" "Elmerina" "caryae"
#> ASV49 "Phanerochaetaceae" "Phanerochaete" "livescens"
#> ASV50 "Russulales_fam_Incertae_sedis" "Gloeohypochnicium" "analogum"
#> ASV53 "Polyporaceae" "Fomes" "fomentarius"
#> ASV54 "Auriculariaceae" "Auricularia" NA
#> ASV58 "Polyporaceae" "Fomes" "fomentarius"
#> ASV59 "Hyphodermataceae" "Hyphoderma" "roseocremeum"
#> ASV61 "Hyphodermataceae" "Hyphoderma" "setigerum"
#> ASV62 NA NA NA
#> ASV63 NA NA NA
#> ASV64 "Polyporaceae" "Trametes" "versicolor"
#> ASV67 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV68 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV71 NA NA NA
#> ASV72 NA NA NA
#> ASV75 "Peniophoraceae" "Peniophora" "versiformis"
#> ASV77 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV82 "Exidiaceae" "Exidia" "glandulosa"
#> ASV83 NA NA NA
#> ASV85 "Hymenochaetales_fam_Incertae_sedis" "Peniophorella" "pubera"
#> ASV91 "Auriculariaceae" "Auricularia" "mesenterica"
#> ASV93 "Stereaceae" NA NA
#> ASV94 "Stereaceae" "Stereum" "ostrea"
#> ASV99 "Polyporaceae" "Fomes" "fomentarius"
#> ASV100 NA NA NA
#> ASV101 "Corticiaceae" "Marchandiomyces" "buckii"
#> ASV104 "Hericiaceae" "Hericium" "coralloides"
#> ASV105 "Schizoporaceae" "Xylodon" "flaviporus"
#> ASV107 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV108 "Exidiaceae" "Exidia" "glandulosa"
#> Trophic.Mode
#> ASV7 "Saprotroph"
#> ASV8 "Saprotroph"
#> ASV12 "Saprotroph"
#> ASV18 "Saprotroph"
#> ASV25 "Saprotroph"
#> ASV26 "Saprotroph"
#> ASV27 "Saprotroph"
#> ASV29 "Saprotroph"
#> ASV32 "Saprotroph-Symbiotroph"
#> ASV34 "Saprotroph"
#> ASV35 "Saprotroph"
#> ASV41 "Pathotroph-Saprotroph"
#> ASV42 "Saprotroph"
#> ASV46 "Saprotroph"
#> ASV47 "Saprotroph"
#> ASV48 "Saprotroph"
#> ASV49 "Saprotroph"
#> ASV50 "Saprotroph"
#> ASV53 "Saprotroph"
#> ASV54 "Saprotroph"
#> ASV58 "Saprotroph"
#> ASV59 "Saprotroph"
#> ASV61 "Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Saprotroph"
#> ASV67 "Saprotroph"
#> ASV68 "Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Pathotroph-Saprotroph"
#> ASV77 "Saprotroph"
#> ASV82 "Saprotroph-Symbiotroph"
#> ASV83 "Pathotroph-Saprotroph-Symbiotroph"
#> ASV85 "Saprotroph"
#> ASV91 "Saprotroph"
#> ASV93 "Saprotroph"
#> ASV94 "Saprotroph"
#> ASV99 "Saprotroph"
#> ASV100 "-"
#> ASV101 "Pathotroph"
#> ASV104 "Saprotroph"
#> ASV105 "Saprotroph"
#> ASV107 "Saprotroph"
#> ASV108 "Saprotroph-Symbiotroph"
#> Guild
#> ASV7 "Wood Saprotroph-Undefined Saprotroph"
#> ASV8 "Undefined Saprotroph"
#> ASV12 "Undefined Saprotroph"
#> ASV18 "Undefined Saprotroph"
#> ASV25 "Wood Saprotroph"
#> ASV26 "Undefined Saprotroph"
#> ASV27 "Wood Saprotroph"
#> ASV29 "Undefined Saprotroph"
#> ASV32 "Ectomycorrhizal-Wood Saprotroph"
#> ASV34 "Undefined Saprotroph"
#> ASV35 "Wood Saprotroph"
#> ASV41 "Leaf Saprotroph-Plant Pathogen-Undefined Saprotroph-Wood Saprotroph"
#> ASV42 "Wood Saprotroph"
#> ASV46 "Undefined Saprotroph"
#> ASV47 "Undefined Saprotroph"
#> ASV48 "Undefined Saprotroph"
#> ASV49 "Wood Saprotroph"
#> ASV50 "Undefined Saprotroph"
#> ASV53 "Wood Saprotroph"
#> ASV54 "Undefined Saprotroph"
#> ASV58 "Wood Saprotroph"
#> ASV59 "Undefined Saprotroph"
#> ASV61 "Undefined Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Wood Saprotroph"
#> ASV67 "Undefined Saprotroph"
#> ASV68 "Wood Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Plant Pathogen-Wood Saprotroph"
#> ASV77 "Wood Saprotroph"
#> ASV82 "Endophyte-Undefined Saprotroph"
#> ASV83 "Fungal Parasite-Undefined Saprotroph"
#> ASV85 "Undefined Saprotroph"
#> ASV91 "Undefined Saprotroph"
#> ASV93 "Wood Saprotroph-Undefined Saprotroph"
#> ASV94 "Undefined Saprotroph"
#> ASV99 "Wood Saprotroph"
#> ASV100 "-"
#> ASV101 "Lichen Parasite"
#> ASV104 "Undefined Saprotroph"
#> ASV105 "Undefined Saprotroph"
#> ASV107 "Undefined Saprotroph"
#> ASV108 "Endophyte-Undefined Saprotroph"
#> Trait Confidence.Ranking Genus_species
#> ASV7 "NULL" "Probable" "NA_NA"
#> ASV8 "White Rot" "Probable" "Stereum_ostrea"
#> ASV12 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV18 "White Rot" "Probable" "Stereum_ostrea"
#> ASV25 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV26 "White Rot" "Probable" "Stereum_hirsutum"
#> ASV27 "White Rot" "Highly Probable" "Antrodiella_brasiliensis"
#> ASV29 "NULL" "Probable" "Basidiodendron_eyrei"
#> ASV32 "White Rot" "Possible" "Sistotrema_oblongisporum"
#> ASV34 "NULL" "Probable" "Entocybe_NA"
#> ASV35 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV41 "NULL" "Probable" "Mycena_renati"
#> ASV42 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV46 "NULL" "Probable" "Helicogloea_pellucida"
#> ASV47 "White Rot" "Probable" "Radulomyces_molaris"
#> ASV48 "NULL" "Probable" "Elmerina_caryae"
#> ASV49 "White Rot" "Highly Probable" "Phanerochaete_livescens"
#> ASV50 "White Rot" "Probable" "Gloeohypochnicium_analogum"
#> ASV53 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV54 "NULL" "Probable" "Auricularia_NA"
#> ASV58 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV59 "White Rot" "Probable" "Hyphoderma_roseocremeum"
#> ASV61 "White Rot" "Probable" "Hyphoderma_setigerum"
#> ASV62 "-" "-" "NA_NA"
#> ASV63 "-" "-" "NA_NA"
#> ASV64 "White Rot" "Highly Probable" "Trametes_versicolor"
#> ASV67 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV68 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV71 "-" "-" "NA_NA"
#> ASV72 "-" "-" "NA_NA"
#> ASV75 "White Rot" "Probable" "Peniophora_versiformis"
#> ASV77 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV82 "NULL" "Probable" "Exidia_glandulosa"
#> ASV83 "NULL" "Possible" "NA_NA"
#> ASV85 "White Rot" "Probable" "Peniophorella_pubera"
#> ASV91 "NULL" "Probable" "Auricularia_mesenterica"
#> ASV93 "NULL" "Probable" "NA_NA"
#> ASV94 "White Rot" "Probable" "Stereum_ostrea"
#> ASV99 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV100 "-" "-" "NA_NA"
#> ASV101 "NULL" "Probable" "Marchandiomyces_buckii"
#> ASV104 "White Rot" "Probable" "Hericium_coralloides"
#> ASV105 "White Rot" "Probable" "Xylodon_flaviporus"
#> ASV107 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV108 "NULL" "Probable" "Exidia_glandulosa"
#> Kingdom Phylum.y Class.y Order.y
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" "Sebacinales"
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV83 "Fungi" "Basidiomycota" NA NA
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV100 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> Family.y Genus.y
#> ASV7 NA NA
#> ASV8 NA NA
#> ASV12 NA NA
#> ASV18 NA NA
#> ASV25 "Tricholomataceae" "Tricholoma"
#> ASV26 NA NA
#> ASV27 NA NA
#> ASV29 NA NA
#> ASV32 "Hydnaceae" "Sistotrema"
#> ASV34 NA NA
#> ASV35 NA NA
#> ASV41 "Mycenaceae" "Mycena"
#> ASV42 NA NA
#> ASV46 NA NA
#> ASV47 NA NA
#> ASV48 NA NA
#> ASV49 NA NA
#> ASV50 NA NA
#> ASV53 NA NA
#> ASV54 NA NA
#> ASV58 NA NA
#> ASV59 NA NA
#> ASV61 "Hyphodermataceae" "Hyphoderma"
#> ASV62 "Serendipitaceae" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA NA
#> ASV67 NA NA
#> ASV68 "Tricholomataceae" "Tricholoma"
#> ASV71 "Tremellales_fam_Incertae_sedis" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophoraceae" "Peniophora"
#> ASV77 "Tricholomataceae" NA
#> ASV82 NA NA
#> ASV83 NA NA
#> ASV85 NA NA
#> ASV91 NA NA
#> ASV93 NA NA
#> ASV94 NA NA
#> ASV99 NA NA
#> ASV100 NA NA
#> ASV101 NA NA
#> ASV104 NA NA
#> ASV105 NA NA
#> ASV107 NA NA
#> ASV108 NA NA
#> Species.y ^Genus\\._abs_majority
#> ASV7 NA NA
#> ASV8 NA "Stereum"
#> ASV12 NA "Xylodon"
#> ASV18 NA "Stereum"
#> ASV25 NA NA
#> ASV26 NA "Stereum"
#> ASV27 NA "Antrodiella"
#> ASV29 NA "Basidiodendron"
#> ASV32 "Sistotrema_sp" "Sistotrema"
#> ASV34 NA "Entocybe"
#> ASV35 NA "Fomes"
#> ASV41 "Mycena_sp" "Mycena"
#> ASV42 NA "Ossicaulis"
#> ASV46 NA "Helicogloea"
#> ASV47 NA "Radulomyces"
#> ASV48 NA "Elmerina"
#> ASV49 NA "Phanerochaete"
#> ASV50 NA "Gloeohypochnicium"
#> ASV53 NA "Fomes"
#> ASV54 NA "Auricularia"
#> ASV58 NA "Fomes"
#> ASV59 NA "Hyphoderma"
#> ASV61 "Hyphoderma_sp" "Hyphoderma"
#> ASV62 "Serendipita_sp" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA "Trametes"
#> ASV67 NA "Xylodon"
#> ASV68 NA NA
#> ASV71 "Tremellales_sp" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophora_reidii" "Peniophora"
#> ASV77 NA "Ossicaulis"
#> ASV82 NA "Exidia"
#> ASV83 NA NA
#> ASV85 NA "Peniophorella"
#> ASV91 NA "Auricularia"
#> ASV93 NA NA
#> ASV94 NA "Stereum"
#> ASV99 NA "Fomes"
#> ASV100 NA NA
#> ASV101 NA "Marchandiomyces"
#> ASV104 NA "Hericium"
#> ASV105 NA "Xylodon"
#> ASV107 NA "Xylodon"
#> ASV108 NA "Exidia"
resolve_taxo_conflict(data_fungi_mini_new, pattern_tax_ranks = c("^Genus\\."), method = "rel_majority")@tax_table
#> Taxonomy Table: [45 taxa by 20 taxonomic ranks]:
#> Domain Phylum.x Class.x Order.x
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Atractiellomycetes" "Atractiellales"
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" NA
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV83 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV100 "Fungi" "Basidiomycota" NA NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" "Corticiales"
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> Family.x Genus.x Species.x
#> ASV7 "Stereaceae" NA NA
#> ASV8 "Stereaceae" "Stereum" "ostrea"
#> ASV12 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV18 "Stereaceae" "Stereum" "ostrea"
#> ASV25 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV26 "Stereaceae" "Stereum" "hirsutum"
#> ASV27 "Steccherinaceae" "Antrodiella" "brasiliensis"
#> ASV29 "Exidiaceae" "Basidiodendron" "eyrei"
#> ASV32 "Cantharellales_fam_Incertae_sedis" "Sistotrema" "oblongisporum"
#> ASV34 "Entolomataceae" "Entocybe" NA
#> ASV35 "Polyporaceae" "Fomes" "fomentarius"
#> ASV41 "Tricholomataceae" "Mycena" "renati"
#> ASV42 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV46 "Atractiellales_fam_Incertae_sedis" "Helicogloea" "pellucida"
#> ASV47 "Pterulaceae" "Radulomyces" "molaris"
#> ASV48 "Aporpiaceae" "Elmerina" "caryae"
#> ASV49 "Phanerochaetaceae" "Phanerochaete" "livescens"
#> ASV50 "Russulales_fam_Incertae_sedis" "Gloeohypochnicium" "analogum"
#> ASV53 "Polyporaceae" "Fomes" "fomentarius"
#> ASV54 "Auriculariaceae" "Auricularia" NA
#> ASV58 "Polyporaceae" "Fomes" "fomentarius"
#> ASV59 "Hyphodermataceae" "Hyphoderma" "roseocremeum"
#> ASV61 "Hyphodermataceae" "Hyphoderma" "setigerum"
#> ASV62 NA NA NA
#> ASV63 NA NA NA
#> ASV64 "Polyporaceae" "Trametes" "versicolor"
#> ASV67 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV68 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV71 NA NA NA
#> ASV72 NA NA NA
#> ASV75 "Peniophoraceae" "Peniophora" "versiformis"
#> ASV77 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV82 "Exidiaceae" "Exidia" "glandulosa"
#> ASV83 NA NA NA
#> ASV85 "Hymenochaetales_fam_Incertae_sedis" "Peniophorella" "pubera"
#> ASV91 "Auriculariaceae" "Auricularia" "mesenterica"
#> ASV93 "Stereaceae" NA NA
#> ASV94 "Stereaceae" "Stereum" "ostrea"
#> ASV99 "Polyporaceae" "Fomes" "fomentarius"
#> ASV100 NA NA NA
#> ASV101 "Corticiaceae" "Marchandiomyces" "buckii"
#> ASV104 "Hericiaceae" "Hericium" "coralloides"
#> ASV105 "Schizoporaceae" "Xylodon" "flaviporus"
#> ASV107 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV108 "Exidiaceae" "Exidia" "glandulosa"
#> Trophic.Mode
#> ASV7 "Saprotroph"
#> ASV8 "Saprotroph"
#> ASV12 "Saprotroph"
#> ASV18 "Saprotroph"
#> ASV25 "Saprotroph"
#> ASV26 "Saprotroph"
#> ASV27 "Saprotroph"
#> ASV29 "Saprotroph"
#> ASV32 "Saprotroph-Symbiotroph"
#> ASV34 "Saprotroph"
#> ASV35 "Saprotroph"
#> ASV41 "Pathotroph-Saprotroph"
#> ASV42 "Saprotroph"
#> ASV46 "Saprotroph"
#> ASV47 "Saprotroph"
#> ASV48 "Saprotroph"
#> ASV49 "Saprotroph"
#> ASV50 "Saprotroph"
#> ASV53 "Saprotroph"
#> ASV54 "Saprotroph"
#> ASV58 "Saprotroph"
#> ASV59 "Saprotroph"
#> ASV61 "Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Saprotroph"
#> ASV67 "Saprotroph"
#> ASV68 "Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Pathotroph-Saprotroph"
#> ASV77 "Saprotroph"
#> ASV82 "Saprotroph-Symbiotroph"
#> ASV83 "Pathotroph-Saprotroph-Symbiotroph"
#> ASV85 "Saprotroph"
#> ASV91 "Saprotroph"
#> ASV93 "Saprotroph"
#> ASV94 "Saprotroph"
#> ASV99 "Saprotroph"
#> ASV100 "-"
#> ASV101 "Pathotroph"
#> ASV104 "Saprotroph"
#> ASV105 "Saprotroph"
#> ASV107 "Saprotroph"
#> ASV108 "Saprotroph-Symbiotroph"
#> Guild
#> ASV7 "Wood Saprotroph-Undefined Saprotroph"
#> ASV8 "Undefined Saprotroph"
#> ASV12 "Undefined Saprotroph"
#> ASV18 "Undefined Saprotroph"
#> ASV25 "Wood Saprotroph"
#> ASV26 "Undefined Saprotroph"
#> ASV27 "Wood Saprotroph"
#> ASV29 "Undefined Saprotroph"
#> ASV32 "Ectomycorrhizal-Wood Saprotroph"
#> ASV34 "Undefined Saprotroph"
#> ASV35 "Wood Saprotroph"
#> ASV41 "Leaf Saprotroph-Plant Pathogen-Undefined Saprotroph-Wood Saprotroph"
#> ASV42 "Wood Saprotroph"
#> ASV46 "Undefined Saprotroph"
#> ASV47 "Undefined Saprotroph"
#> ASV48 "Undefined Saprotroph"
#> ASV49 "Wood Saprotroph"
#> ASV50 "Undefined Saprotroph"
#> ASV53 "Wood Saprotroph"
#> ASV54 "Undefined Saprotroph"
#> ASV58 "Wood Saprotroph"
#> ASV59 "Undefined Saprotroph"
#> ASV61 "Undefined Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Wood Saprotroph"
#> ASV67 "Undefined Saprotroph"
#> ASV68 "Wood Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Plant Pathogen-Wood Saprotroph"
#> ASV77 "Wood Saprotroph"
#> ASV82 "Endophyte-Undefined Saprotroph"
#> ASV83 "Fungal Parasite-Undefined Saprotroph"
#> ASV85 "Undefined Saprotroph"
#> ASV91 "Undefined Saprotroph"
#> ASV93 "Wood Saprotroph-Undefined Saprotroph"
#> ASV94 "Undefined Saprotroph"
#> ASV99 "Wood Saprotroph"
#> ASV100 "-"
#> ASV101 "Lichen Parasite"
#> ASV104 "Undefined Saprotroph"
#> ASV105 "Undefined Saprotroph"
#> ASV107 "Undefined Saprotroph"
#> ASV108 "Endophyte-Undefined Saprotroph"
#> Trait Confidence.Ranking Genus_species
#> ASV7 "NULL" "Probable" "NA_NA"
#> ASV8 "White Rot" "Probable" "Stereum_ostrea"
#> ASV12 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV18 "White Rot" "Probable" "Stereum_ostrea"
#> ASV25 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV26 "White Rot" "Probable" "Stereum_hirsutum"
#> ASV27 "White Rot" "Highly Probable" "Antrodiella_brasiliensis"
#> ASV29 "NULL" "Probable" "Basidiodendron_eyrei"
#> ASV32 "White Rot" "Possible" "Sistotrema_oblongisporum"
#> ASV34 "NULL" "Probable" "Entocybe_NA"
#> ASV35 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV41 "NULL" "Probable" "Mycena_renati"
#> ASV42 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV46 "NULL" "Probable" "Helicogloea_pellucida"
#> ASV47 "White Rot" "Probable" "Radulomyces_molaris"
#> ASV48 "NULL" "Probable" "Elmerina_caryae"
#> ASV49 "White Rot" "Highly Probable" "Phanerochaete_livescens"
#> ASV50 "White Rot" "Probable" "Gloeohypochnicium_analogum"
#> ASV53 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV54 "NULL" "Probable" "Auricularia_NA"
#> ASV58 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV59 "White Rot" "Probable" "Hyphoderma_roseocremeum"
#> ASV61 "White Rot" "Probable" "Hyphoderma_setigerum"
#> ASV62 "-" "-" "NA_NA"
#> ASV63 "-" "-" "NA_NA"
#> ASV64 "White Rot" "Highly Probable" "Trametes_versicolor"
#> ASV67 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV68 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV71 "-" "-" "NA_NA"
#> ASV72 "-" "-" "NA_NA"
#> ASV75 "White Rot" "Probable" "Peniophora_versiformis"
#> ASV77 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV82 "NULL" "Probable" "Exidia_glandulosa"
#> ASV83 "NULL" "Possible" "NA_NA"
#> ASV85 "White Rot" "Probable" "Peniophorella_pubera"
#> ASV91 "NULL" "Probable" "Auricularia_mesenterica"
#> ASV93 "NULL" "Probable" "NA_NA"
#> ASV94 "White Rot" "Probable" "Stereum_ostrea"
#> ASV99 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV100 "-" "-" "NA_NA"
#> ASV101 "NULL" "Probable" "Marchandiomyces_buckii"
#> ASV104 "White Rot" "Probable" "Hericium_coralloides"
#> ASV105 "White Rot" "Probable" "Xylodon_flaviporus"
#> ASV107 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV108 "NULL" "Probable" "Exidia_glandulosa"
#> Kingdom Phylum.y Class.y Order.y
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" "Sebacinales"
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV83 "Fungi" "Basidiomycota" NA NA
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV100 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> Family.y Genus.y
#> ASV7 NA NA
#> ASV8 NA NA
#> ASV12 NA NA
#> ASV18 NA NA
#> ASV25 "Tricholomataceae" "Tricholoma"
#> ASV26 NA NA
#> ASV27 NA NA
#> ASV29 NA NA
#> ASV32 "Hydnaceae" "Sistotrema"
#> ASV34 NA NA
#> ASV35 NA NA
#> ASV41 "Mycenaceae" "Mycena"
#> ASV42 NA NA
#> ASV46 NA NA
#> ASV47 NA NA
#> ASV48 NA NA
#> ASV49 NA NA
#> ASV50 NA NA
#> ASV53 NA NA
#> ASV54 NA NA
#> ASV58 NA NA
#> ASV59 NA NA
#> ASV61 "Hyphodermataceae" "Hyphoderma"
#> ASV62 "Serendipitaceae" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA NA
#> ASV67 NA NA
#> ASV68 "Tricholomataceae" "Tricholoma"
#> ASV71 "Tremellales_fam_Incertae_sedis" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophoraceae" "Peniophora"
#> ASV77 "Tricholomataceae" NA
#> ASV82 NA NA
#> ASV83 NA NA
#> ASV85 NA NA
#> ASV91 NA NA
#> ASV93 NA NA
#> ASV94 NA NA
#> ASV99 NA NA
#> ASV100 NA NA
#> ASV101 NA NA
#> ASV104 NA NA
#> ASV105 NA NA
#> ASV107 NA NA
#> ASV108 NA NA
#> Species.y ^Genus\\._rel_majority
#> ASV7 NA NA
#> ASV8 NA "Stereum"
#> ASV12 NA "Xylodon"
#> ASV18 NA "Stereum"
#> ASV25 NA "Ossicaulis/Tricholoma"
#> ASV26 NA "Stereum"
#> ASV27 NA "Antrodiella"
#> ASV29 NA "Basidiodendron"
#> ASV32 "Sistotrema_sp" "Sistotrema"
#> ASV34 NA "Entocybe"
#> ASV35 NA "Fomes"
#> ASV41 "Mycena_sp" "Mycena"
#> ASV42 NA "Ossicaulis"
#> ASV46 NA "Helicogloea"
#> ASV47 NA "Radulomyces"
#> ASV48 NA "Elmerina"
#> ASV49 NA "Phanerochaete"
#> ASV50 NA "Gloeohypochnicium"
#> ASV53 NA "Fomes"
#> ASV54 NA "Auricularia"
#> ASV58 NA "Fomes"
#> ASV59 NA "Hyphoderma"
#> ASV61 "Hyphoderma_sp" "Hyphoderma"
#> ASV62 "Serendipita_sp" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA "Trametes"
#> ASV67 NA "Xylodon"
#> ASV68 NA "Ossicaulis/Tricholoma"
#> ASV71 "Tremellales_sp" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophora_reidii" "Peniophora"
#> ASV77 NA "Ossicaulis"
#> ASV82 NA "Exidia"
#> ASV83 NA NA
#> ASV85 NA "Peniophorella"
#> ASV91 NA "Auricularia"
#> ASV93 NA NA
#> ASV94 NA "Stereum"
#> ASV99 NA "Fomes"
#> ASV100 NA NA
#> ASV101 NA "Marchandiomyces"
#> ASV104 NA "Hericium"
#> ASV105 NA "Xylodon"
#> ASV107 NA "Xylodon"
#> ASV108 NA "Exidia"
resolve_taxo_conflict(data_fungi_mini_new, pattern_tax_ranks = c("^Genus\\."), method = "unanimity")@tax_table
#> Taxonomy Table: [45 taxa by 20 taxonomic ranks]:
#> Domain Phylum.x Class.x Order.x
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Atractiellomycetes" "Atractiellales"
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" NA
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV83 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV100 "Fungi" "Basidiomycota" NA NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" "Corticiales"
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> Family.x Genus.x Species.x
#> ASV7 "Stereaceae" NA NA
#> ASV8 "Stereaceae" "Stereum" "ostrea"
#> ASV12 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV18 "Stereaceae" "Stereum" "ostrea"
#> ASV25 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV26 "Stereaceae" "Stereum" "hirsutum"
#> ASV27 "Steccherinaceae" "Antrodiella" "brasiliensis"
#> ASV29 "Exidiaceae" "Basidiodendron" "eyrei"
#> ASV32 "Cantharellales_fam_Incertae_sedis" "Sistotrema" "oblongisporum"
#> ASV34 "Entolomataceae" "Entocybe" NA
#> ASV35 "Polyporaceae" "Fomes" "fomentarius"
#> ASV41 "Tricholomataceae" "Mycena" "renati"
#> ASV42 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV46 "Atractiellales_fam_Incertae_sedis" "Helicogloea" "pellucida"
#> ASV47 "Pterulaceae" "Radulomyces" "molaris"
#> ASV48 "Aporpiaceae" "Elmerina" "caryae"
#> ASV49 "Phanerochaetaceae" "Phanerochaete" "livescens"
#> ASV50 "Russulales_fam_Incertae_sedis" "Gloeohypochnicium" "analogum"
#> ASV53 "Polyporaceae" "Fomes" "fomentarius"
#> ASV54 "Auriculariaceae" "Auricularia" NA
#> ASV58 "Polyporaceae" "Fomes" "fomentarius"
#> ASV59 "Hyphodermataceae" "Hyphoderma" "roseocremeum"
#> ASV61 "Hyphodermataceae" "Hyphoderma" "setigerum"
#> ASV62 NA NA NA
#> ASV63 NA NA NA
#> ASV64 "Polyporaceae" "Trametes" "versicolor"
#> ASV67 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV68 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV71 NA NA NA
#> ASV72 NA NA NA
#> ASV75 "Peniophoraceae" "Peniophora" "versiformis"
#> ASV77 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV82 "Exidiaceae" "Exidia" "glandulosa"
#> ASV83 NA NA NA
#> ASV85 "Hymenochaetales_fam_Incertae_sedis" "Peniophorella" "pubera"
#> ASV91 "Auriculariaceae" "Auricularia" "mesenterica"
#> ASV93 "Stereaceae" NA NA
#> ASV94 "Stereaceae" "Stereum" "ostrea"
#> ASV99 "Polyporaceae" "Fomes" "fomentarius"
#> ASV100 NA NA NA
#> ASV101 "Corticiaceae" "Marchandiomyces" "buckii"
#> ASV104 "Hericiaceae" "Hericium" "coralloides"
#> ASV105 "Schizoporaceae" "Xylodon" "flaviporus"
#> ASV107 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV108 "Exidiaceae" "Exidia" "glandulosa"
#> Trophic.Mode
#> ASV7 "Saprotroph"
#> ASV8 "Saprotroph"
#> ASV12 "Saprotroph"
#> ASV18 "Saprotroph"
#> ASV25 "Saprotroph"
#> ASV26 "Saprotroph"
#> ASV27 "Saprotroph"
#> ASV29 "Saprotroph"
#> ASV32 "Saprotroph-Symbiotroph"
#> ASV34 "Saprotroph"
#> ASV35 "Saprotroph"
#> ASV41 "Pathotroph-Saprotroph"
#> ASV42 "Saprotroph"
#> ASV46 "Saprotroph"
#> ASV47 "Saprotroph"
#> ASV48 "Saprotroph"
#> ASV49 "Saprotroph"
#> ASV50 "Saprotroph"
#> ASV53 "Saprotroph"
#> ASV54 "Saprotroph"
#> ASV58 "Saprotroph"
#> ASV59 "Saprotroph"
#> ASV61 "Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Saprotroph"
#> ASV67 "Saprotroph"
#> ASV68 "Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Pathotroph-Saprotroph"
#> ASV77 "Saprotroph"
#> ASV82 "Saprotroph-Symbiotroph"
#> ASV83 "Pathotroph-Saprotroph-Symbiotroph"
#> ASV85 "Saprotroph"
#> ASV91 "Saprotroph"
#> ASV93 "Saprotroph"
#> ASV94 "Saprotroph"
#> ASV99 "Saprotroph"
#> ASV100 "-"
#> ASV101 "Pathotroph"
#> ASV104 "Saprotroph"
#> ASV105 "Saprotroph"
#> ASV107 "Saprotroph"
#> ASV108 "Saprotroph-Symbiotroph"
#> Guild
#> ASV7 "Wood Saprotroph-Undefined Saprotroph"
#> ASV8 "Undefined Saprotroph"
#> ASV12 "Undefined Saprotroph"
#> ASV18 "Undefined Saprotroph"
#> ASV25 "Wood Saprotroph"
#> ASV26 "Undefined Saprotroph"
#> ASV27 "Wood Saprotroph"
#> ASV29 "Undefined Saprotroph"
#> ASV32 "Ectomycorrhizal-Wood Saprotroph"
#> ASV34 "Undefined Saprotroph"
#> ASV35 "Wood Saprotroph"
#> ASV41 "Leaf Saprotroph-Plant Pathogen-Undefined Saprotroph-Wood Saprotroph"
#> ASV42 "Wood Saprotroph"
#> ASV46 "Undefined Saprotroph"
#> ASV47 "Undefined Saprotroph"
#> ASV48 "Undefined Saprotroph"
#> ASV49 "Wood Saprotroph"
#> ASV50 "Undefined Saprotroph"
#> ASV53 "Wood Saprotroph"
#> ASV54 "Undefined Saprotroph"
#> ASV58 "Wood Saprotroph"
#> ASV59 "Undefined Saprotroph"
#> ASV61 "Undefined Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Wood Saprotroph"
#> ASV67 "Undefined Saprotroph"
#> ASV68 "Wood Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Plant Pathogen-Wood Saprotroph"
#> ASV77 "Wood Saprotroph"
#> ASV82 "Endophyte-Undefined Saprotroph"
#> ASV83 "Fungal Parasite-Undefined Saprotroph"
#> ASV85 "Undefined Saprotroph"
#> ASV91 "Undefined Saprotroph"
#> ASV93 "Wood Saprotroph-Undefined Saprotroph"
#> ASV94 "Undefined Saprotroph"
#> ASV99 "Wood Saprotroph"
#> ASV100 "-"
#> ASV101 "Lichen Parasite"
#> ASV104 "Undefined Saprotroph"
#> ASV105 "Undefined Saprotroph"
#> ASV107 "Undefined Saprotroph"
#> ASV108 "Endophyte-Undefined Saprotroph"
#> Trait Confidence.Ranking Genus_species
#> ASV7 "NULL" "Probable" "NA_NA"
#> ASV8 "White Rot" "Probable" "Stereum_ostrea"
#> ASV12 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV18 "White Rot" "Probable" "Stereum_ostrea"
#> ASV25 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV26 "White Rot" "Probable" "Stereum_hirsutum"
#> ASV27 "White Rot" "Highly Probable" "Antrodiella_brasiliensis"
#> ASV29 "NULL" "Probable" "Basidiodendron_eyrei"
#> ASV32 "White Rot" "Possible" "Sistotrema_oblongisporum"
#> ASV34 "NULL" "Probable" "Entocybe_NA"
#> ASV35 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV41 "NULL" "Probable" "Mycena_renati"
#> ASV42 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV46 "NULL" "Probable" "Helicogloea_pellucida"
#> ASV47 "White Rot" "Probable" "Radulomyces_molaris"
#> ASV48 "NULL" "Probable" "Elmerina_caryae"
#> ASV49 "White Rot" "Highly Probable" "Phanerochaete_livescens"
#> ASV50 "White Rot" "Probable" "Gloeohypochnicium_analogum"
#> ASV53 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV54 "NULL" "Probable" "Auricularia_NA"
#> ASV58 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV59 "White Rot" "Probable" "Hyphoderma_roseocremeum"
#> ASV61 "White Rot" "Probable" "Hyphoderma_setigerum"
#> ASV62 "-" "-" "NA_NA"
#> ASV63 "-" "-" "NA_NA"
#> ASV64 "White Rot" "Highly Probable" "Trametes_versicolor"
#> ASV67 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV68 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV71 "-" "-" "NA_NA"
#> ASV72 "-" "-" "NA_NA"
#> ASV75 "White Rot" "Probable" "Peniophora_versiformis"
#> ASV77 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV82 "NULL" "Probable" "Exidia_glandulosa"
#> ASV83 "NULL" "Possible" "NA_NA"
#> ASV85 "White Rot" "Probable" "Peniophorella_pubera"
#> ASV91 "NULL" "Probable" "Auricularia_mesenterica"
#> ASV93 "NULL" "Probable" "NA_NA"
#> ASV94 "White Rot" "Probable" "Stereum_ostrea"
#> ASV99 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV100 "-" "-" "NA_NA"
#> ASV101 "NULL" "Probable" "Marchandiomyces_buckii"
#> ASV104 "White Rot" "Probable" "Hericium_coralloides"
#> ASV105 "White Rot" "Probable" "Xylodon_flaviporus"
#> ASV107 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV108 "NULL" "Probable" "Exidia_glandulosa"
#> Kingdom Phylum.y Class.y Order.y
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" "Sebacinales"
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV83 "Fungi" "Basidiomycota" NA NA
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV100 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> Family.y Genus.y
#> ASV7 NA NA
#> ASV8 NA NA
#> ASV12 NA NA
#> ASV18 NA NA
#> ASV25 "Tricholomataceae" "Tricholoma"
#> ASV26 NA NA
#> ASV27 NA NA
#> ASV29 NA NA
#> ASV32 "Hydnaceae" "Sistotrema"
#> ASV34 NA NA
#> ASV35 NA NA
#> ASV41 "Mycenaceae" "Mycena"
#> ASV42 NA NA
#> ASV46 NA NA
#> ASV47 NA NA
#> ASV48 NA NA
#> ASV49 NA NA
#> ASV50 NA NA
#> ASV53 NA NA
#> ASV54 NA NA
#> ASV58 NA NA
#> ASV59 NA NA
#> ASV61 "Hyphodermataceae" "Hyphoderma"
#> ASV62 "Serendipitaceae" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA NA
#> ASV67 NA NA
#> ASV68 "Tricholomataceae" "Tricholoma"
#> ASV71 "Tremellales_fam_Incertae_sedis" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophoraceae" "Peniophora"
#> ASV77 "Tricholomataceae" NA
#> ASV82 NA NA
#> ASV83 NA NA
#> ASV85 NA NA
#> ASV91 NA NA
#> ASV93 NA NA
#> ASV94 NA NA
#> ASV99 NA NA
#> ASV100 NA NA
#> ASV101 NA NA
#> ASV104 NA NA
#> ASV105 NA NA
#> ASV107 NA NA
#> ASV108 NA NA
#> Species.y ^Genus\\._unanimity
#> ASV7 NA NA
#> ASV8 NA "Stereum"
#> ASV12 NA "Xylodon"
#> ASV18 NA "Stereum"
#> ASV25 NA NA
#> ASV26 NA "Stereum"
#> ASV27 NA "Antrodiella"
#> ASV29 NA "Basidiodendron"
#> ASV32 "Sistotrema_sp" "Sistotrema"
#> ASV34 NA "Entocybe"
#> ASV35 NA "Fomes"
#> ASV41 "Mycena_sp" "Mycena"
#> ASV42 NA "Ossicaulis"
#> ASV46 NA "Helicogloea"
#> ASV47 NA "Radulomyces"
#> ASV48 NA "Elmerina"
#> ASV49 NA "Phanerochaete"
#> ASV50 NA "Gloeohypochnicium"
#> ASV53 NA "Fomes"
#> ASV54 NA "Auricularia"
#> ASV58 NA "Fomes"
#> ASV59 NA "Hyphoderma"
#> ASV61 "Hyphoderma_sp" "Hyphoderma"
#> ASV62 "Serendipita_sp" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA "Trametes"
#> ASV67 NA "Xylodon"
#> ASV68 NA NA
#> ASV71 "Tremellales_sp" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophora_reidii" "Peniophora"
#> ASV77 NA "Ossicaulis"
#> ASV82 NA "Exidia"
#> ASV83 NA NA
#> ASV85 NA "Peniophorella"
#> ASV91 NA "Auricularia"
#> ASV93 NA NA
#> ASV94 NA "Stereum"
#> ASV99 NA "Fomes"
#> ASV100 NA NA
#> ASV101 NA "Marchandiomyces"
#> ASV104 NA "Hericium"
#> ASV105 NA "Xylodon"
#> ASV107 NA "Xylodon"
#> ASV108 NA "Exidia"
resolve_taxo_conflict(data_fungi_mini_new, pattern_tax_ranks = c("^Genus\\.", "^Family\\.", "^Species\\."), method = "consensus")@tax_table
#> Taxonomy Table: [45 taxa by 22 taxonomic ranks]:
#> Domain Phylum.x Class.x Order.x
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Atractiellomycetes" "Atractiellales"
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" NA
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV83 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV100 "Fungi" "Basidiomycota" NA NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" "Corticiales"
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Hymenochaetales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Auriculariales"
#> Family.x Genus.x Species.x
#> ASV7 "Stereaceae" NA NA
#> ASV8 "Stereaceae" "Stereum" "ostrea"
#> ASV12 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV18 "Stereaceae" "Stereum" "ostrea"
#> ASV25 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV26 "Stereaceae" "Stereum" "hirsutum"
#> ASV27 "Steccherinaceae" "Antrodiella" "brasiliensis"
#> ASV29 "Exidiaceae" "Basidiodendron" "eyrei"
#> ASV32 "Cantharellales_fam_Incertae_sedis" "Sistotrema" "oblongisporum"
#> ASV34 "Entolomataceae" "Entocybe" NA
#> ASV35 "Polyporaceae" "Fomes" "fomentarius"
#> ASV41 "Tricholomataceae" "Mycena" "renati"
#> ASV42 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV46 "Atractiellales_fam_Incertae_sedis" "Helicogloea" "pellucida"
#> ASV47 "Pterulaceae" "Radulomyces" "molaris"
#> ASV48 "Aporpiaceae" "Elmerina" "caryae"
#> ASV49 "Phanerochaetaceae" "Phanerochaete" "livescens"
#> ASV50 "Russulales_fam_Incertae_sedis" "Gloeohypochnicium" "analogum"
#> ASV53 "Polyporaceae" "Fomes" "fomentarius"
#> ASV54 "Auriculariaceae" "Auricularia" NA
#> ASV58 "Polyporaceae" "Fomes" "fomentarius"
#> ASV59 "Hyphodermataceae" "Hyphoderma" "roseocremeum"
#> ASV61 "Hyphodermataceae" "Hyphoderma" "setigerum"
#> ASV62 NA NA NA
#> ASV63 NA NA NA
#> ASV64 "Polyporaceae" "Trametes" "versicolor"
#> ASV67 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV68 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV71 NA NA NA
#> ASV72 NA NA NA
#> ASV75 "Peniophoraceae" "Peniophora" "versiformis"
#> ASV77 "Lyophyllaceae" "Ossicaulis" "lachnopus"
#> ASV82 "Exidiaceae" "Exidia" "glandulosa"
#> ASV83 NA NA NA
#> ASV85 "Hymenochaetales_fam_Incertae_sedis" "Peniophorella" "pubera"
#> ASV91 "Auriculariaceae" "Auricularia" "mesenterica"
#> ASV93 "Stereaceae" NA NA
#> ASV94 "Stereaceae" "Stereum" "ostrea"
#> ASV99 "Polyporaceae" "Fomes" "fomentarius"
#> ASV100 NA NA NA
#> ASV101 "Corticiaceae" "Marchandiomyces" "buckii"
#> ASV104 "Hericiaceae" "Hericium" "coralloides"
#> ASV105 "Schizoporaceae" "Xylodon" "flaviporus"
#> ASV107 "Schizoporaceae" "Xylodon" "raduloides"
#> ASV108 "Exidiaceae" "Exidia" "glandulosa"
#> Trophic.Mode
#> ASV7 "Saprotroph"
#> ASV8 "Saprotroph"
#> ASV12 "Saprotroph"
#> ASV18 "Saprotroph"
#> ASV25 "Saprotroph"
#> ASV26 "Saprotroph"
#> ASV27 "Saprotroph"
#> ASV29 "Saprotroph"
#> ASV32 "Saprotroph-Symbiotroph"
#> ASV34 "Saprotroph"
#> ASV35 "Saprotroph"
#> ASV41 "Pathotroph-Saprotroph"
#> ASV42 "Saprotroph"
#> ASV46 "Saprotroph"
#> ASV47 "Saprotroph"
#> ASV48 "Saprotroph"
#> ASV49 "Saprotroph"
#> ASV50 "Saprotroph"
#> ASV53 "Saprotroph"
#> ASV54 "Saprotroph"
#> ASV58 "Saprotroph"
#> ASV59 "Saprotroph"
#> ASV61 "Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Saprotroph"
#> ASV67 "Saprotroph"
#> ASV68 "Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Pathotroph-Saprotroph"
#> ASV77 "Saprotroph"
#> ASV82 "Saprotroph-Symbiotroph"
#> ASV83 "Pathotroph-Saprotroph-Symbiotroph"
#> ASV85 "Saprotroph"
#> ASV91 "Saprotroph"
#> ASV93 "Saprotroph"
#> ASV94 "Saprotroph"
#> ASV99 "Saprotroph"
#> ASV100 "-"
#> ASV101 "Pathotroph"
#> ASV104 "Saprotroph"
#> ASV105 "Saprotroph"
#> ASV107 "Saprotroph"
#> ASV108 "Saprotroph-Symbiotroph"
#> Guild
#> ASV7 "Wood Saprotroph-Undefined Saprotroph"
#> ASV8 "Undefined Saprotroph"
#> ASV12 "Undefined Saprotroph"
#> ASV18 "Undefined Saprotroph"
#> ASV25 "Wood Saprotroph"
#> ASV26 "Undefined Saprotroph"
#> ASV27 "Wood Saprotroph"
#> ASV29 "Undefined Saprotroph"
#> ASV32 "Ectomycorrhizal-Wood Saprotroph"
#> ASV34 "Undefined Saprotroph"
#> ASV35 "Wood Saprotroph"
#> ASV41 "Leaf Saprotroph-Plant Pathogen-Undefined Saprotroph-Wood Saprotroph"
#> ASV42 "Wood Saprotroph"
#> ASV46 "Undefined Saprotroph"
#> ASV47 "Undefined Saprotroph"
#> ASV48 "Undefined Saprotroph"
#> ASV49 "Wood Saprotroph"
#> ASV50 "Undefined Saprotroph"
#> ASV53 "Wood Saprotroph"
#> ASV54 "Undefined Saprotroph"
#> ASV58 "Wood Saprotroph"
#> ASV59 "Undefined Saprotroph"
#> ASV61 "Undefined Saprotroph"
#> ASV62 "-"
#> ASV63 "-"
#> ASV64 "Wood Saprotroph"
#> ASV67 "Undefined Saprotroph"
#> ASV68 "Wood Saprotroph"
#> ASV71 "-"
#> ASV72 "-"
#> ASV75 "Plant Pathogen-Wood Saprotroph"
#> ASV77 "Wood Saprotroph"
#> ASV82 "Endophyte-Undefined Saprotroph"
#> ASV83 "Fungal Parasite-Undefined Saprotroph"
#> ASV85 "Undefined Saprotroph"
#> ASV91 "Undefined Saprotroph"
#> ASV93 "Wood Saprotroph-Undefined Saprotroph"
#> ASV94 "Undefined Saprotroph"
#> ASV99 "Wood Saprotroph"
#> ASV100 "-"
#> ASV101 "Lichen Parasite"
#> ASV104 "Undefined Saprotroph"
#> ASV105 "Undefined Saprotroph"
#> ASV107 "Undefined Saprotroph"
#> ASV108 "Endophyte-Undefined Saprotroph"
#> Trait Confidence.Ranking Genus_species
#> ASV7 "NULL" "Probable" "NA_NA"
#> ASV8 "White Rot" "Probable" "Stereum_ostrea"
#> ASV12 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV18 "White Rot" "Probable" "Stereum_ostrea"
#> ASV25 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV26 "White Rot" "Probable" "Stereum_hirsutum"
#> ASV27 "White Rot" "Highly Probable" "Antrodiella_brasiliensis"
#> ASV29 "NULL" "Probable" "Basidiodendron_eyrei"
#> ASV32 "White Rot" "Possible" "Sistotrema_oblongisporum"
#> ASV34 "NULL" "Probable" "Entocybe_NA"
#> ASV35 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV41 "NULL" "Probable" "Mycena_renati"
#> ASV42 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV46 "NULL" "Probable" "Helicogloea_pellucida"
#> ASV47 "White Rot" "Probable" "Radulomyces_molaris"
#> ASV48 "NULL" "Probable" "Elmerina_caryae"
#> ASV49 "White Rot" "Highly Probable" "Phanerochaete_livescens"
#> ASV50 "White Rot" "Probable" "Gloeohypochnicium_analogum"
#> ASV53 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV54 "NULL" "Probable" "Auricularia_NA"
#> ASV58 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV59 "White Rot" "Probable" "Hyphoderma_roseocremeum"
#> ASV61 "White Rot" "Probable" "Hyphoderma_setigerum"
#> ASV62 "-" "-" "NA_NA"
#> ASV63 "-" "-" "NA_NA"
#> ASV64 "White Rot" "Highly Probable" "Trametes_versicolor"
#> ASV67 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV68 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV71 "-" "-" "NA_NA"
#> ASV72 "-" "-" "NA_NA"
#> ASV75 "White Rot" "Probable" "Peniophora_versiformis"
#> ASV77 "Brown Rot" "Probable" "Ossicaulis_lachnopus"
#> ASV82 "NULL" "Probable" "Exidia_glandulosa"
#> ASV83 "NULL" "Possible" "NA_NA"
#> ASV85 "White Rot" "Probable" "Peniophorella_pubera"
#> ASV91 "NULL" "Probable" "Auricularia_mesenterica"
#> ASV93 "NULL" "Probable" "NA_NA"
#> ASV94 "White Rot" "Probable" "Stereum_ostrea"
#> ASV99 "Brown Rot-White Rot" "Probable" "Fomes_fomentarius"
#> ASV100 "-" "-" "NA_NA"
#> ASV101 "NULL" "Probable" "Marchandiomyces_buckii"
#> ASV104 "White Rot" "Probable" "Hericium_coralloides"
#> ASV105 "White Rot" "Probable" "Xylodon_flaviporus"
#> ASV107 "White Rot" "Probable" "Xylodon_raduloides"
#> ASV108 "NULL" "Probable" "Exidia_glandulosa"
#> Kingdom Phylum.y Class.y Order.y
#> ASV7 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV8 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV12 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV18 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV25 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV26 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV27 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV29 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV32 "Fungi" "Basidiomycota" "Agaricomycetes" "Cantharellales"
#> ASV34 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV35 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV41 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV42 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV46 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV47 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV48 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV49 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV50 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV53 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV54 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV58 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV59 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV61 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV62 "Fungi" "Basidiomycota" "Agaricomycetes" "Sebacinales"
#> ASV63 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV64 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV67 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV68 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV71 "Fungi" "Basidiomycota" "Tremellomycetes" "Tremellales"
#> ASV72 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV75 "Fungi" "Basidiomycota" "Agaricomycetes" "Russulales"
#> ASV77 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV82 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV83 "Fungi" "Basidiomycota" NA NA
#> ASV85 "Fungi" "Basidiomycota" "Agaricomycetes" "Polyporales"
#> ASV91 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV93 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV94 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV99 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV100 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV101 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV104 "Fungi" "Basidiomycota" "Agaricomycetes" NA
#> ASV105 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV107 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> ASV108 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"
#> Family.y Genus.y
#> ASV7 NA NA
#> ASV8 NA NA
#> ASV12 NA NA
#> ASV18 NA NA
#> ASV25 "Tricholomataceae" "Tricholoma"
#> ASV26 NA NA
#> ASV27 NA NA
#> ASV29 NA NA
#> ASV32 "Hydnaceae" "Sistotrema"
#> ASV34 NA NA
#> ASV35 NA NA
#> ASV41 "Mycenaceae" "Mycena"
#> ASV42 NA NA
#> ASV46 NA NA
#> ASV47 NA NA
#> ASV48 NA NA
#> ASV49 NA NA
#> ASV50 NA NA
#> ASV53 NA NA
#> ASV54 NA NA
#> ASV58 NA NA
#> ASV59 NA NA
#> ASV61 "Hyphodermataceae" "Hyphoderma"
#> ASV62 "Serendipitaceae" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA NA
#> ASV67 NA NA
#> ASV68 "Tricholomataceae" "Tricholoma"
#> ASV71 "Tremellales_fam_Incertae_sedis" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophoraceae" "Peniophora"
#> ASV77 "Tricholomataceae" NA
#> ASV82 NA NA
#> ASV83 NA NA
#> ASV85 NA NA
#> ASV91 NA NA
#> ASV93 NA NA
#> ASV94 NA NA
#> ASV99 NA NA
#> ASV100 NA NA
#> ASV101 NA NA
#> ASV104 NA NA
#> ASV105 NA NA
#> ASV107 NA NA
#> ASV108 NA NA
#> Species.y ^Genus\\._consensus
#> ASV7 NA NA
#> ASV8 NA "Stereum"
#> ASV12 NA "Xylodon"
#> ASV18 NA "Stereum"
#> ASV25 NA "Ossicaulis/Tricholoma"
#> ASV26 NA "Stereum"
#> ASV27 NA "Antrodiella"
#> ASV29 NA "Basidiodendron"
#> ASV32 "Sistotrema_sp" "Sistotrema"
#> ASV34 NA "Entocybe"
#> ASV35 NA "Fomes"
#> ASV41 "Mycena_sp" "Mycena"
#> ASV42 NA "Ossicaulis"
#> ASV46 NA "Helicogloea"
#> ASV47 NA "Radulomyces"
#> ASV48 NA "Elmerina"
#> ASV49 NA "Phanerochaete"
#> ASV50 NA "Gloeohypochnicium"
#> ASV53 NA "Fomes"
#> ASV54 NA "Auricularia"
#> ASV58 NA "Fomes"
#> ASV59 NA "Hyphoderma"
#> ASV61 "Hyphoderma_sp" "Hyphoderma"
#> ASV62 "Serendipita_sp" "Serendipita"
#> ASV63 NA NA
#> ASV64 NA "Trametes"
#> ASV67 NA "Xylodon"
#> ASV68 NA "Ossicaulis/Tricholoma"
#> ASV71 "Tremellales_sp" "Tremellales_gen_Incertae_sedis"
#> ASV72 NA NA
#> ASV75 "Peniophora_reidii" "Peniophora"
#> ASV77 NA "Ossicaulis"
#> ASV82 NA "Exidia"
#> ASV83 NA NA
#> ASV85 NA "Peniophorella"
#> ASV91 NA "Auricularia"
#> ASV93 NA NA
#> ASV94 NA "Stereum"
#> ASV99 NA "Fomes"
#> ASV100 NA NA
#> ASV101 NA "Marchandiomyces"
#> ASV104 NA "Hericium"
#> ASV105 NA "Xylodon"
#> ASV107 NA "Xylodon"
#> ASV108 NA "Exidia"
#> ^Family\\._consensus
#> ASV7 "Stereaceae"
#> ASV8 "Stereaceae"
#> ASV12 "Schizoporaceae"
#> ASV18 "Stereaceae"
#> ASV25 "Lyophyllaceae/Tricholomataceae"
#> ASV26 "Stereaceae"
#> ASV27 "Steccherinaceae"
#> ASV29 "Exidiaceae"
#> ASV32 "Cantharellales_fam_Incertae_sedis/Hydnaceae"
#> ASV34 "Entolomataceae"
#> ASV35 "Polyporaceae"
#> ASV41 "Tricholomataceae/Mycenaceae"
#> ASV42 "Lyophyllaceae"
#> ASV46 "Atractiellales_fam_Incertae_sedis"
#> ASV47 "Pterulaceae"
#> ASV48 "Aporpiaceae"
#> ASV49 "Phanerochaetaceae"
#> ASV50 "Russulales_fam_Incertae_sedis"
#> ASV53 "Polyporaceae"
#> ASV54 "Auriculariaceae"
#> ASV58 "Polyporaceae"
#> ASV59 "Hyphodermataceae"
#> ASV61 "Hyphodermataceae"
#> ASV62 "Serendipitaceae"
#> ASV63 NA
#> ASV64 "Polyporaceae"
#> ASV67 "Schizoporaceae"
#> ASV68 "Lyophyllaceae/Tricholomataceae"
#> ASV71 "Tremellales_fam_Incertae_sedis"
#> ASV72 NA
#> ASV75 "Peniophoraceae"
#> ASV77 "Lyophyllaceae/Tricholomataceae"
#> ASV82 "Exidiaceae"
#> ASV83 NA
#> ASV85 "Hymenochaetales_fam_Incertae_sedis"
#> ASV91 "Auriculariaceae"
#> ASV93 "Stereaceae"
#> ASV94 "Stereaceae"
#> ASV99 "Polyporaceae"
#> ASV100 NA
#> ASV101 "Corticiaceae"
#> ASV104 "Hericiaceae"
#> ASV105 "Schizoporaceae"
#> ASV107 "Schizoporaceae"
#> ASV108 "Exidiaceae"
#> ^Species\\._consensus
#> ASV7 NA
#> ASV8 "ostrea"
#> ASV12 "raduloides"
#> ASV18 "ostrea"
#> ASV25 "lachnopus"
#> ASV26 "hirsutum"
#> ASV27 "brasiliensis"
#> ASV29 "eyrei"
#> ASV32 "oblongisporum/Sistotrema_sp"
#> ASV34 NA
#> ASV35 "fomentarius"
#> ASV41 "renati/Mycena_sp"
#> ASV42 "lachnopus"
#> ASV46 "pellucida"
#> ASV47 "molaris"
#> ASV48 "caryae"
#> ASV49 "livescens"
#> ASV50 "analogum"
#> ASV53 "fomentarius"
#> ASV54 NA
#> ASV58 "fomentarius"
#> ASV59 "roseocremeum"
#> ASV61 "setigerum/Hyphoderma_sp"
#> ASV62 "Serendipita_sp"
#> ASV63 NA
#> ASV64 "versicolor"
#> ASV67 "raduloides"
#> ASV68 "lachnopus"
#> ASV71 "Tremellales_sp"
#> ASV72 NA
#> ASV75 "versiformis/Peniophora_reidii"
#> ASV77 "lachnopus"
#> ASV82 "glandulosa"
#> ASV83 NA
#> ASV85 "pubera"
#> ASV91 "mesenterica"
#> ASV93 NA
#> ASV94 "ostrea"
#> ASV99 "fomentarius"
#> ASV100 NA
#> ASV101 "buckii"
#> ASV104 "coralloides"
#> ASV105 "flaviporus"
#> ASV107 "raduloides"
#> ASV108 "glandulosa"