Read taxa_map.csv generated by create_taxa_map().
read_taxa_map(path)(character) The path to the directory containing taxa_map.csv.
(data.table; data.frame) taxa_map.csv as an R object.
mypath <- dirname(system.file("taxa_map.csv", package = "taxonomyCleanr"))
taxa_map <- read_taxa_map(mypath)
taxa_map
#> taxa_raw taxa_trimmed taxa_replacement
#> 1: Mosses <NA> <NA>
#> 2: Unsorted biomass <NA> <NA>
#> 3: Achillea millefolium(lanulosa) <NA> Achillea millefolium
#> 4: Crepis tectorum <NA> <NA>
#> 5: Cyperus sp. Cyperus <NA>
#> 6: Euphorbia glyptosperma <NA> <NA>
#> 7: Lespedeza capitata <NA> <NA>
#> 8: Achillea millefolium(lanulosaaaa) <NA> Achillea millefolium
#> 9: Achillea millefolium(lanulosabb) <NA> Achillea millefolium
#> 10: Achillea millefolium(lanulosacc) <NA> Achillea millefolium
#> 11: Lepidium densiflorum <NA> <NA>
#> 12: Poa pratensis <NA> <NA>
#> 13: Rumex acetosella <NA> <NA>
#> 14: Schizachyrium scoparium <NA> <NA>
#> 15: Bouteloua gracilis <NA> <NA>
#> 16: Koeleria cristata <NA> <NA>
#> 17: Liatris aspera <NA> <NA>
#> 18: Lupinus perennis <NA> <NA>
#> 19: Panicum virgatum <NA> <NA>
#> 20: Petalostemum purpureum <NA> <NA>
#> 21: Petalostemum villosum <NA> <NA>
#> 22: Solidago nemoralis <NA> <NA>
#> 23: Sorghastrum nutans <NA> <NA>
#> 24: Stipa spartea <NA> <NA>
#> 25: Andropogon gerardi <NA> <NA>
#> 26: Bouteloua curtipendula <NA> <NA>
#> 27: Coreopsis palmata <NA> <NA>
#> 28: Miscellaneous litter <NA> <NA>
#> 29: Petalostemum candidum <NA> <NA>
#> 30: Solidago rigida <NA> <NA>
#> 31: Sporobolus cryptandrus <NA> <NA>
#> 32: Agropyron repens <NA> <NA>
#> 33: Aristida basiramea <NA> <NA>
#> 34: Digitaria sp. Digitaria <NA>
#> 35: Erigeron canadensis <NA> <NA>
#> 36: Hedeoma hispida <NA> <NA>
#> 37: Physalis virginiana <NA> <NA>
#> 38: Taraxicum officinalis <NA> <NA>
#> 39: Agrostis scabra <NA> <NA>
#> 40: Ambrosia artemisiifolia elatior <NA> <NA>
#> 41: Eragrostis spectabilis <NA> <NA>
#> 42: Amorpha canescens <NA> <NA>
#> 43: -9999 <NA> <NA>
#> 44: Yellow Perch <NA> <NA>
#> 45: Rainbow smelt <NA> <NA>
#> 46: Large mouth bass <NA> <NA>
#> 47: Petalostemum S.p. Petalostemum <NA>
#> 48: Poa Cf. Poa <NA>
#> 49: Schizachyrium spp. Schizachyrium <NA>
#> 50: Petalostemum <NA> <NA>
#> 51: Poa cf... Poa <NA>
#> 52: Schizachyrium sPp Schizachyrium <NA>
#> 53: _Koeleria_cristata Koeleria cristata <NA>
#> 54: Lespedeza_capitata Lespedeza capitata <NA>
#> 55: _Liatris_aspera_ Liatris aspera <NA>
#> 56: <NA> <NA> <NA>
#> 57: Oncorhynchus tshawytscha <NA> <NA>
#> 58: Oncorhynchus gorbuscha <NA> <NA>
#> 59: Oncorhynchus kisutch <NA> <NA>
#> taxa_raw taxa_trimmed taxa_replacement
#> taxa_removed taxa_clean rank authority
#> 1: NA Mosses Common ITIS
#> 2: NA <NA> <NA> <NA>
#> 3: NA Achillea millefolium Species ITIS
#> 4: NA Crepis tectorum Species ITIS
#> 5: NA Cyperus Genus ITIS
#> 6: NA Euphorbia glyptosperma Species ITIS
#> 7: NA Lespedeza capitata Species ITIS
#> 8: NA Achillea millefolium Species ITIS
#> 9: NA Achillea millefolium Species ITIS
#> 10: NA Achillea millefolium Species ITIS
#> 11: NA Lepidium densiflorum Species ITIS
#> 12: NA Poa pratensis Species ITIS
#> 13: NA Rumex acetosella Species ITIS
#> 14: NA Schizachyrium scoparium Species ITIS
#> 15: NA Bouteloua gracilis Species ITIS
#> 16: NA Koeleria cristata Species ITIS
#> 17: NA Liatris aspera Species ITIS
#> 18: NA Lupinus perennis Species ITIS
#> 19: NA Panicum virgatum Species ITIS
#> 20: NA <NA> <NA> <NA>
#> 21: NA <NA> <NA> <NA>
#> 22: NA Solidago nemoralis Species ITIS
#> 23: NA Sorghastrum nutans Species ITIS
#> 24: TRUE Stipa spartea Species ITIS
#> 25: NA Andropogon gerardi Species ITIS
#> 26: NA Bouteloua curtipendula Species ITIS
#> 27: NA Coreopsis palmata Species ITIS
#> 28: NA <NA> <NA> <NA>
#> 29: NA <NA> <NA> <NA>
#> 30: NA Solidago rigida Species ITIS
#> 31: NA Sporobolus cryptandrus Species ITIS
#> 32: NA Agropyron repens Species ITIS
#> 33: NA Aristida basiramea Species ITIS
#> 34: NA Digitaria Genus ITIS
#> 35: NA Erigeron canadensis Species ITIS
#> 36: NA Hedeoma hispida Species ITIS
#> 37: NA Physalis virginiana Species ITIS
#> 38: NA Taraxacum officinale Species ITIS
#> 39: NA Agrostis scabra Species ITIS
#> 40: NA Ambrosia artemisiifolia elatior Infraspecies Catalogue of Life
#> 41: NA Eragrostis spectabilis Species ITIS
#> 42: NA Amorpha canescens Species ITIS
#> 43: TRUE <NA> <NA> <NA>
#> 44: NA Yellow Perch Common ITIS
#> 45: NA Rainbow smelt Common ITIS
#> 46: NA <NA> <NA> <NA>
#> 47: NA <NA> <NA> <NA>
#> 48: NA Poa Genus ITIS
#> 49: NA Schizachyrium Genus ITIS
#> 50: NA <NA> <NA> <NA>
#> 51: NA Poa Genus ITIS
#> 52: NA Schizachyrium Genus ITIS
#> 53: NA Koeleria cristata Species ITIS
#> 54: NA Lespedeza capitata Species ITIS
#> 55: NA Liatris aspera Species ITIS
#> 56: TRUE <NA> <NA> <NA>
#> 57: NA Oncorhynchus tshawytscha Species ITIS
#> 58: NA Oncorhynchus gorbuscha Species ITIS
#> 59: NA Oncorhynchus kisutch Species ITIS
#> taxa_removed taxa_clean rank authority
#> authority_id score difference
#> 1: 14189 NA NA
#> 2: <NA> NA NA
#> 3: 35423 0.988 NA
#> 4: 37212 0.988 NA
#> 5: 39882 0.750 NA
#> 6: 28074 0.988 NA
#> 7: 25897 0.988 NA
#> 8: 35423 0.988 NA
#> 9: 35423 0.988 NA
#> 10: 35423 0.988 NA
#> 11: 22960 0.988 NA
#> 12: 41088 0.988 NA
#> 13: 20934 0.988 NA
#> 14: 42076 0.988 NA
#> 15: 41493 0.988 NA
#> 16: 515476 0.988 NA
#> 17: 37909 0.988 NA
#> 18: 26091 0.988 NA
#> 19: 40913 0.988 NA
#> 20: <NA> NA NA
#> 21: <NA> NA NA
#> 22: 36281 0.988 NA
#> 23: 42102 0.988 NA
#> 24: 42166 0.988 NA
#> 25: 786156 0.988 NA
#> 26: 41500 0.988 NA
#> 27: 37148 0.988 NA
#> 28: <NA> NA NA
#> 29: <NA> NA NA
#> 30: 36297 0.988 NA
#> 31: 42132 0.988 NA
#> 32: 40382 0.988 NA
#> 33: 41412 0.988 NA
#> 34: 40603 0.750 NA
#> 35: 196266 0.988 NA
#> 36: 502890 0.988 NA
#> 37: 30612 0.988 NA
#> 38: 36213 0.750 NA
#> 39: 40424 0.988 NA
#> 40: b6b7cf5b0ace61a8272ae8d52f69de6d 0.999 NA
#> 41: 40717 0.988 NA
#> 42: 25371 0.988 NA
#> 43: <NA> NA NA
#> 44: 168469 NA NA
#> 45: 162041 NA NA
#> 46: <NA> NA NA
#> 47: <NA> NA NA
#> 48: 41074 0.750 NA
#> 49: 42069 0.750 NA
#> 50: <NA> NA NA
#> 51: 41074 0.750 NA
#> 52: 42069 0.750 NA
#> 53: 515476 0.988 NA
#> 54: 25897 0.988 NA
#> 55: 37909 0.988 NA
#> 56: <NA> NA NA
#> 57: 161980 0.988 NA
#> 58: 161975 0.988 NA
#> 59: 161977 0.988 NA
#> authority_id score difference