Exploring the backbone

taxify() reads a backbone in one direction, from a name to its accepted taxon. This article shows the functions that read it in the others: the synonyms of a taxon, the species of a genus, the ranks above a species, the taxon behind an ID, the parts of a name, and common names. It ends with a taxonomy tree of a species list. Installation is covered in Get started. Every example reads the Catalogue of Life (COL); backbone names another.

List synonyms with synonyms(), and the taxa below a genus or family with children() and downstream().
Climb to the ranks above a taxon with upstream() and add_classification().
Look up IDs with id2name() and taxify_ids(), and the parts of a name with parse_name().
Translate common names with comm2sci() and sci2comm().
Compare a list with lowest_common() and class2tree().

library(taxify)

Synonyms

A species list can hold old names for a taxon. synonyms() resolves each name to its accepted taxon and lists every synonym the backbone points to it:

syn <- synonyms("Picea abies", backbone = "col", verbose = FALSE)
nrow(syn)
#> [1] 169
head(syn[, c("synonym", "authorship")])
#>                 synonym         authorship
#> 1           Abies abies         (L.) Druce
#> 2       Abies carpatica (Loudon) Ravenscr.
#> 3         Abies cinerea             Borkh.
#> 4  Abies clambrasiliana           Lavallée
#> 5 Abies clanbrassiliana           P.Lawson
#> 6    Abies coerulescens             K.Koch

The input can itself be a synonym: synonyms("Pinus abies") lists the same set, through the accepted Picea abies.

Taxa below a genus or family

To complete a checklist, the species of a genus are needed. children() lists the accepted species of a genus, or of a family:

spruces <- children("Picea", backbone = "col", verbose = FALSE)
nrow(spruces)
#> [1] 42
head(spruces[, c("name", "authorship", "rank")])
#>                    name                      authorship    rank
#> 1           Picea abies                   (L.) H.Karst. SPECIES
#> 2      Picea albertiana                           S.Br. SPECIES
#> 3      Picea alcoquiana (H.J.Veitch ex Lindl.) Carrière SPECIES
#> 4        Picea asperata                           Mast. SPECIES
#> 5      Picea aurantiaca                           Mast. SPECIES
#> 6 Picea austropanlanica                           Silba SPECIES

downstream() does the same from any higher taxon to any rank below it. The genera of the pine family:

genera <- downstream("Pinaceae", backbone = "col", downto = "genus",
                     verbose = FALSE)
genera$name
#>  [1] "Abies"       "Cathaya"     "Cedrus"      "Keteleeria"  "Larix"      
#>  [6] "Nothotsuga"  "Picea"       "Pinus"       "Pseudolarix" "Pseudotsuga"
#> [11] "Tsuga"

Both return accepted taxa only, and never the parent itself. A genus name used in two kingdoms, such as Prunella, is split with kingdom, as in taxify().

Ranks above a taxon

Grouping species by family or order needs their classification. upstream() returns the classification of one taxon, one row per rank. A synonym or misspelling is resolved first:

upstream("Pinus abies", backbone = "col", verbose = FALSE)
#>    input_name accepted_name    rank         name backbone
#> 1 Pinus abies   Picea abies kingdom      Plantae      col
#> 2 Pinus abies   Picea abies  phylum Tracheophyta      col
#> 3 Pinus abies   Picea abies   class    Pinopsida      col
#> 4 Pinus abies   Picea abies   order      Pinales      col
#> 5 Pinus abies   Picea abies  family     Pinaceae      col
#> 6 Pinus abies   Picea abies   genus        Picea      col

to = "family" returns only that rank. For a whole result, add_classification() adds kingdom, phylum, class and order as columns:

res <- taxify(c("Picea abies", "Panthera leo"), backbone = "col",
              verbose = FALSE)
cls <- add_classification(res, verbose = FALSE)
cls[, c("input_name", "kingdom", "phylum", "class", "order", "family")]
#>     input_name  kingdom       phylum     class     order   family
#> 1  Picea abies  Plantae Tracheophyta Pinopsida   Pinales Pinaceae
#> 2 Panthera leo Animalia     Chordata  Mammalia Carnivora  Felidae
#> Sources: COL 2026.09 | cite() for full citations

IDs

A table that stores only backbone IDs can be read back with id2name(), which turns backbone IDs, such as those in the taxon_id and accepted_id columns, into names, ranks and accepted names:

id2name(c("4HPZF", "KQB98"), backbone = "col", verbose = FALSE)
#>      id             name        authorship    rank is_synonym    accepted_name
#> 1 4HPZF      Picea abies     (L.) H.Karst. SPECIES      FALSE      Picea abies
#> 2 KQB98 Osphranter rufus (Desmarest, 1822) SPECIES      FALSE Osphranter rufus
#>         family      genus backbone
#> 1     Pinaceae      Picea      col
#> 2 Macropodidae Osphranter      col

An ID is meaningful only within its backbone: GBIF keys, ITIS TSNs and WoRMS AphiaIDs are read against "gbif", "itis" and "worms".

taxify_ids() lists every accepted taxon behind each matched name, one row per name and ID, with the pick marked:

pa <- taxify("Pinus abies", backbone = "col", verbose = FALSE)
ids <- taxify_ids(pa, verbose = FALSE)
ids[, c("accepted_id", "accepted_name", "family", "is_pick")]
#>   accepted_id           accepted_name       family is_pick
#> 1       4HPZF             Picea abies     Pinaceae    TRUE
#> 2        8K9Y              Abies alba     Pinaceae   FALSE
#> 3       6BRMR Cunninghamia lanceolata Cupressaceae   FALSE
#> 4       4HQ4F            Picea polita     Pinaceae   FALSE

Pinus abies was used for four species. The pick is Picea abies; How names are matched explains how it is chosen.

The parts of a name

Names from field sheets mix authors, qualifiers and hybrid signs into one string. parse_name() splits a name into its parts without matching it against a backbone:

parse_name(c(
  "Quercus robur L.", "cf. Betula pendula Roth",
  "Abies alba subsp. borisii-regis (Mattf.) Kozuharov",
  "Mentha x piperita L."
))
#>                                           input_name   genus specific_epithet
#> 1                                   Quercus robur L. Quercus            robur
#> 2                            cf. Betula pendula Roth  Betula          pendula
#> 3 Abies alba subsp. borisii-regis (Mattf.) Kozuharov   Abies             alba
#> 4                               Mentha x piperita L.  Mentha         piperita
#>   infrasp_rank infrasp_epithet         authorship qualifier is_hybrid
#> 1         <NA>            <NA>                 L.      <NA>     FALSE
#> 2         <NA>            <NA>               Roth       cf.     FALSE
#> 3       subsp.   borisii-regis (Mattf.) Kozuharov      <NA>     FALSE
#> 4         <NA>            <NA>                 L.      <NA>      TRUE
#>    hybrid_type         rank                       canonical
#> 1         <NA>      species                   Quercus robur
#> 2         <NA>      species                  Betula pendula
#> 3         <NA> infraspecies Abies alba subsp. borisii-regis
#> 4 nothospecies      species                 Mentha piperita

canonical is the cleaned name that taxify() matches. parse_name(code = "syntaxon") parses the names of vegetation units, as shown in Matching vegetation units.

Common names

sci2comm() returns the common names of each taxon, from the vernacular names that GBIF, NCBI and the Open Tree of Life publish. lang takes two-letter language codes, and name_rank orders the names of a language by how many sources give them:

cn <- sci2comm("Picea abies", lang = c("en", "de"), backbone = "col",
               verbose = FALSE)
cn[cn$name_rank <= 2, c("common_name", "lang", "name_rank")]
#>          common_name lang name_rank
#> 1     Gemeine Fichte   de         1
#> 2 Gewöhnliche Fichte   de         2
#> 5      Norway Spruce   en         1
#> 6       White Spruce   en         2

comm2sci() goes the other way, with capitals ignored. A common name is often given to several taxa, so it returns every scientific name that carries it:

sp <- comm2sci("Norway spruce", lang = "en", verbose = FALSE)
nrow(sp)
#> [1] 31
head(sp$accepted_name)
#> [1] "Abies dicksonii"                 "Abies excelsa var. attenuata"   
#> [3] "Abies excelsa var. aurea"        "Abies excelsa var. brevifolia"  
#> [5] "Abies excelsa var. eremita"      "Abies excelsa var. finedonensis"

With output = "result", the names are matched with taxify(), and query_common keeps the common name of each row:

sp_res <- comm2sci("Norway spruce", lang = "en", output = "result",
                   backbone = "col", verbose = FALSE)
table(sp_res$accepted_name)
#> 
#>                          Abies alba Abies sachalinensis var. nemorensis 
#>                                   2                                   1 
#>                         Picea abies              Picea abies var. abies 
#>                                  19                                   6 
#>          Picea abies var. acuminata 
#>                                   2

Of the 31 names that carry “Norway spruce”, 30 match COL, and 27 of those resolve to Picea abies or one of its varieties. The other three resolve to Abies alba and Abies sachalinensis var. nemorensis, so a common-name lookup gives candidates to check rather than one answer. add_common_names() attaches the first common name of each language as columns of a result.

Comparing a list

How closely the species of a list are related is the lowest rank they share, which lowest_common() returns:

conifers <- c("Picea abies", "Pinus sylvestris", "Abies alba")
lowest_common(conifers, backbone = "col", verbose = FALSE)
#>     rank     name n_taxa
#> 1 family Pinaceae      3
lowest_common(c("Picea abies", "Quercus robur"), backbone = "col",
              verbose = FALSE)
#>     rank         name n_taxa
#> 1 phylum Tracheophyta      2

class2tree() builds a taxonomy tree from the classifications, as a Newick string, and as a phylo object when the ape package is installed:

trees <- c(conifers, "Quercus robur", "Fagus sylvatica")
tree <- class2tree(trees, backbone = "col", verbose = FALSE)
tree$newick
#> [1] "(((((((Picea_abies)Picea,(Pinus_sylvestris)Pinus,(Abies_alba)Abies)Pinaceae)Pinales)Pinopsida,((((Quercus_robur)Quercus,(Fagus_sylvatica)Fagus)Fagaceae)Fagales)Magnoliopsida)Tracheophyta)Plantae)root;"

The tree follows the ranks of the backbone’s classification; it is not a phylogeny, and branch lengths carry no meaning.

Where next

How names are matched: the forward direction, from a name to its accepted taxon.
Requesting GBIF data for a species list: taxify_ids() in a download of occurrence records.