2. Extracting a species list from a vegetation table
2.1 Example data
One of the main tasks of taxlist is to structure taxonomic information for a further linkage to biodiversity records. This structure have to be on the one side consistent with taxonomic issues (e.g. synonyms, hierarchies, etc.), on the other side have to be flexible for containing different depth of information availability (from plain species lists to hierarchical structures).
In this guide, we will work with a species list from phytosociological relevés collected at the borderline between the Democratic Republic of the Congo and Rwanda (Mullenders 1953 Vegetatio 4(2): 73–83).
The digitized data can be loaded by following command:
The data is formatted as data.frame in R, including the names of the species in the first column:
## TaxonName 3094 3093 3092 3095 3096 3097 3098
## 1 Eragrostis tenuifolia + <NA> <NA> <NA> <NA> <NA> <NA>
## 2 Cyperus sublimis <NA> + <NA> <NA> <NA> <NA> <NA>
## 3 Digitaria abyssinica + 1 2 2 2 3 1
## 4 Hyparrhenia filipendula <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5 Erigeron floribundus + 1 <NA> <NA> <NA> <NA> <NA>
## 6 Aerva lanata + 1 <NA> <NA> <NA> <NA> <NA>2.2 From plain list to taxlist
As already mentioned, the first column in the cross table contains the names of the species occurring in the observed plots. Thus, we can use this character vector to construct a taxlist object. This can be achieved through the function df2taxlist.
## object size: 8.5 Kb
## validation of 'taxlist' object: TRUE
##
## number of names: 35
## number of concepts: 35
## trait entries: 0
## number of trait variables: 0
## reference entries: 0Note that the function summary provides a quick overview in the content of the resulting object. This function can be also applied to a specific taxon:
## ------------------------------
## concept ID: 5
## view ID: none
## level: none
## parent: none
##
## # accepted name:
## 5 Erigeron floribundus
## ------------------------------2.3 Resolving taxonomic names with taxize
One of the main concerns is to resolve nomenclatorial issues, especially when working with historical data or combining data from different sources. For this purpose, taxlist implements a method for the function tnrs (package taxize):
## object size: 8.5 Kb
## validation of 'taxlist' object: TRUE
##
## number of names: 35
## number of concepts: 35
## trait entries: 0
## number of trait variables: 0
## reference entries: 0## object size: 14.6 Kb
## validation of 'taxlist' object: TRUE
##
## number of names: 45
## number of concepts: 35
## trait entries: 0
## number of trait variables: 0
## reference entries: 0While after this procedure, the number of taxa remained as 35, the number of taxon names increased, indicating that some of the names in the original source are currently considered as synonyms. This is for example the case of Erigeron floribundus:
## ------------------------------
## concept ID: 5
## view ID: none
## level: none
## parent: none
##
## # accepted name:
## 36 Conyza sumatrensis var. leiotheca (S.F. Blake) Pruski & G. Sancho
##
## # synonyms (1):
## 5 Erigeron floribundus
## ------------------------------At this point it is important to mention that while most resolvers are offering ways to replace names by accepted ones, in taxlist objects both, accepted names and synonyms are preserved. Only typographical errors and names of authors will be changed in the object. This is important in the compilation of diversity records (i.e. vegetation plot databases), where the stored data have to be faithful to the source. Thus data connected to a taxon name can be automatically assigned to the correspondent taxon concept without to modify the record’s entry. An overview to the accepted names and possible changes can be displayed as follows:
## TaxonConceptID TaxonUsageID TaxonName
## 1 1 1 Eragrostis tenuifolia
## 2 2 2 Cyperus sublimis
## 3 3 3 Digitaria abyssinica
## 4 4 4 Hyparrhenia filipendula
## 5 5 36 Conyza sumatrensis var. leiotheca
## AuthorName
## 1 (A. Rich.) Hochst. ex Steud.
## 2 (C.B. Clarke) Dandy
## 3 (Hochst. ex A. Rich.) Stapf
## 4 (Hochst.) Stapf
## 5 (S.F. Blake) Pruski & G. Sancho