Matching vegetation units • taxify

This article matches the names of vegetation units, such as the alliance recorded for each plot of a vegetation survey, against the EuroVegChecklist and the Czech national classification. It ends with each name resolved to its accepted unit and placed in the units above it. Installation is covered in Get started.

Parse a unit name into its parts with parse_name(code = "syntaxon").
Match the names with taxify(backbone = "evc") or backbone = "vegcz".
Roll up an association of the national classification to its European alliance and class.

library(taxify)

Names of vegetation units

A vegetation unit, or syntaxon, is a type of plant community: a class, an order, an alliance or an association. Its name follows the International Code of Phytosociological Nomenclature. The name is built from one or two plant names, and the last one carries a suffix for the rank: -etea for a class, -etalia for an order, -ion for an alliance, -enion for a suballiance and -etum for an association. The author citation carries years, as in Caricenion gracilis (Neuhäusl 1959) Oberd. et al. 1967.

parse_name() with code = "syntaxon" splits a name into these parts without matching it:

parsed <- parse_name(
  c("Caricenion gracilis (Neuhäusl 1959) Oberd. et al. 1967",
    "TDA - Arrhenatherion elatioris"),
  code = "syntaxon"
)
parsed[, c("name", "authorship", "rank", "code")]
#>                       name                         authorship        rank code
#> 1      Caricenion gracilis (Neuhäusl 1959) Oberd. et al. 1967 suballiance <NA>
#> 2 Arrhenatherion elatioris                               <NA>    alliance  TDA

The rank is read from the suffix of the last plant name. A code written in front of the name, such as the national database code TDA, goes to code and is not used for matching.

The two backbones

taxify holds two backbones of vegetation units:

evc, the EuroVegChecklist (Mucina et al. 2016) in its current version as maintained in FloraVeg.EU (Chytrý et al. 2024): the classes, orders and alliances of European vegetation, with their synonyms.
vegcz, the national classification of the Czech Republic (Chytrý 2007-2013), as published in the Pladias database (Chytrý et al. 2021): classes, alliances and associations with their synonyms. It places each association in its alliance, a level below where the EuroVegChecklist stops.

bb <- list_backbones(verbose = FALSE)
bb[bb$code == "syntaxon", c("name", "scope", "version", "n_names")]
#>     name                               scope version n_names
#> 20   evc European vegetation units (syntaxa)       4    7542
#> 21 vegcz    Czech vegetation units (syntaxa) 2026.10    2258

A backbone of vegetation units is used only when it is named in backbone. The default call reads names as taxa, and one call cannot mix the two kinds of backbone.

Matching unit names

The names below are the kind found in the header data of vegetation plots:

plots <- c(
  "Fagion sylvaticae Luquet 1926",
  "Mesobromion erecti",
  "Fagion silvaticae",
  "TDA - Arrhenatherion elatioris",
  "Cynosurion",
  "Brachypodietalia pinnata",
  "Carpinion"
)
res <- taxify(plots, backbone = "evc", verbose = FALSE)
#> Warning: 1 of 7 names resolve to more than one accepted ID (Carpinion).
#> `accepted_id` holds one and `accepted_ids` all of them; list them with
#> taxify_ids() before requesting data by ID.
res[, c("input_name", "accepted_name", "match_type", "is_synonym")]
#>                       input_name            accepted_name match_type is_synonym
#> 1  Fagion sylvaticae Luquet 1926        Fagion sylvaticae      exact      FALSE
#> 2             Mesobromion erecti           Bromion erecti short_name       TRUE
#> 3              Fagion silvaticae        Fagion sylvaticae   exact_ci      FALSE
#> 4 TDA - Arrhenatherion elatioris Arrhenatherion elatioris      exact      FALSE
#> 5                     Cynosurion      Cynosurion cristati short_name      FALSE
#> 6       Brachypodietalia pinnata Brachypodietalia pinnati      fuzzy      FALSE
#> 7                      Carpinion                     <NA>       none         NA
#> Sources: EVC 4 | cite() for full citations

Before matching, the author citation and any code written in front of a name are removed, and spelling variants of Latin, such as i and y, are made equal. A name written without its epithet, the short form, is resolved through its stem when the stem names one unit. Each row reaches its unit by one of these routes:

Fagion sylvaticae Luquet 1926 matches with its author citation removed.
Mesobromion erecti is a synonym of Bromion erecti, listed in the EuroVegChecklist without its epithet, as Mesobromion.
Fagion silvaticae is an older spelling of the epithet.
TDA - Arrhenatherion elatioris matches once the code in front is removed.
Cynosurion is the short form of Cynosurion cristati.
Brachypodietalia pinnata is misspelt and is matched by fuzzy matching.
Carpinion is the stem of three alliances, so it stays unresolved.

The candidates of an unresolved short form are listed in accepted_ids:

res[res$input_name == "Carpinion", c("input_name", "n_ids", "accepted_ids")]
#>   input_name n_ids      accepted_ids
#> 7  Carpinion     3 CA03A|CB01G|CA03C
#> Sources: EVC 4 | cite() for full citations

An author citation in the input chooses among such candidates, as in Fagion Luquet 1926.

Fuzzy matching keeps the rank, so a suballiance never matches an alliance, and it keeps the plant names a unit is named after. Vaccinio-Piceion is two letters from Vaccinio-Pinion, a different alliance, and is not matched to it.

The units above each name

A result for vegetation units has the columns of a result for taxa except those only a taxon has: family, genus, epithet, the genus register’s columns and the hybrid and aggregate columns. In their place it carries the hierarchy of the accepted unit, class, order, alliance and association:

res[, c("accepted_name", "class", "order", "alliance")]
#>              accepted_name                      class
#> 1        Fagion sylvaticae Carpino-Fagetea sylvaticae
#> 2           Bromion erecti           Festuco-Brometea
#> 3        Fagion sylvaticae Carpino-Fagetea sylvaticae
#> 4 Arrhenatherion elatioris    Molinio-Arrhenatheretea
#> 5      Cynosurion cristati    Molinio-Arrhenatheretea
#> 6 Brachypodietalia pinnati           Festuco-Brometea
#> 7                     <NA>                       <NA>
#>                         order                 alliance
#> 1        Fagetalia sylvaticae        Fagion sylvaticae
#> 2    Brachypodietalia pinnati           Bromion erecti
#> 3        Fagetalia sylvaticae        Fagion sylvaticae
#> 4 Arrhenatheretalia elatioris Arrhenatherion elatioris
#> 5 Arrhenatheretalia elatioris      Cynosurion cristati
#> 6    Brachypodietalia pinnati                     <NA>
#> 7                        <NA>                     <NA>
#> Sources: EVC 4 | cite() for full citations

Every matched name, synonym or not, is placed in the ranks above it.

From a national association to a European alliance

Plot data from the Czech Republic often record an association, a rank the EuroVegChecklist does not cover. The national classification places each association in an alliance. Arrhenatheretum elatioris is a synonym of two associations, under Braun 1915 and under Scherrer 1925, so an author citation in the input chooses between them:

cz <- taxify(
  c("Pastinaco sativae-Arrhenatheretum elatioris",
    "Arrhenatheretum elatioris Braun 1915"),
  backbone = "vegcz", verbose = FALSE
)
#> Warning: 1 of 2 names resolve to more than one accepted ID (Arrhenatheretum
#> elatioris Braun 1915). `accepted_id` holds one and `accepted_ids` all of them;
#> list them with taxify_ids() before requesting data by ID.
cz[, c("input_name", "accepted_name", "alliance", "accepted_ids")]
#>                                    input_name
#> 1 Pastinaco sativae-Arrhenatheretum elatioris
#> 2        Arrhenatheretum elatioris Braun 1915
#>                                 accepted_name                 alliance
#> 1 Pastinaco sativae-Arrhenatheretum elatioris Arrhenatherion elatioris
#> 2 Pastinaco sativae-Arrhenatheretum elatioris Arrhenatherion elatioris
#> Sources: VEGCZ 2026.10 | cite() for full citations

The second name, cited with Braun 1915, resolves to that author’s association, which is listed first in accepted_ids; the other association stays listed, so the warning names the row.

The alliance then resolves against the EuroVegChecklist:

eu <- taxify(cz$alliance, backbone = "evc", verbose = FALSE)
eu[, c("input_name", "accepted_name", "order", "class")]
#>                 input_name            accepted_name                       order
#> 1 Arrhenatherion elatioris Arrhenatherion elatioris Arrhenatheretalia elatioris
#> 2 Arrhenatherion elatioris Arrhenatherion elatioris Arrhenatheretalia elatioris
#>                     class
#> 1 Molinio-Arrhenatheretea
#> 2 Molinio-Arrhenatheretea
#> Sources: EVC 4 | cite() for full citations

The two backbones can also form a fallback chain, backbone = c("vegcz", "evc"), so that each name is resolved by the national classification where it holds the name and by the EuroVegChecklist otherwise.

Mixing taxa and vegetation units

A call that names a backbone of taxa and one of vegetation units stops with an error, since the two follow different codes of nomenclature:

taxify("Fagion sylvaticae", backbone = c("evc", "col"))
#> Error:
#> ! Backbones of different nomenclature codes cannot be combined: evc (syntaxon), col (taxon). Match taxon names and syntaxon names in separate calls.

How the backbones were built

evc is built from the FloraVeg.EU list of European vegetation units (version 4, 2025-06-17) and the synonyms on each unit’s FloraVeg.EU nomenclature page. A few dozen of those pages fail partway through; for those units the synonym lists printed in Mucina et al. (2016), published under CC BY 4.0, supply the missing entries.

vegcz is built from the Pladias list of the vegetation units of the Czech Republic and the synonyms on each unit’s Pladias nomenclature page. Pladias data are free for research, teaching and conservation; commercial use needs the approval of the Pladias board.

A name either source cites in another author’s sense (sensu, auct.) is kept with taxonomic_status = "MISAPPLIED", and ranks below the synonyms when a name points to more than one unit.

Where next

How names are matched: the match stages and the fuzzy threshold.
Choosing and combining backbones: fallback chains and backbone versions.

References

Chytrý M (ed.) (2007-2013). Vegetace České republiky 1-4 [Vegetation of the Czech Republic 1-4]. Academia, Praha.

Chytrý M, Danihelka J, Kaplan Z, Wild J, Holubová D, Novotný P, et al. (2021). Pladias Database of the Czech Flora and Vegetation. Preslia 93: 1-87. https://doi.org/10.23855/preslia.2021.001

Chytrý M, Řezníčková M, Novotný P, Holubová D, Preislerová Z, Attorre F, et al. (2024). FloraVeg.EU: an online database of European vegetation, habitats and flora. Applied Vegetation Science 27: e12798. https://doi.org/10.1111/avsc.12798

Mucina L, Bültmann H, Dierßen K, Theurillat J-P, Raus T, Čarni A, et al. (2016). Vegetation of Europe: hierarchical floristic classification system of vascular plant, bryophyte, lichen, and algal communities. Applied Vegetation Science 19 (Suppl. 1): 3-264. https://doi.org/10.1111/avsc.12257