taxocheck | R Documentation |
Check the taxonomic status of a vector of taxon names, according to the Tropical Botanic Garden and Research Institute of India (TBGRI) and The Plant List (TPL), from the TreeGhatsData
database. The function corrects orthographical errors in taxon names and provides the taxonomic status and the reference names according to TBGRI and TPL. From these information a status, a reference name and authority are proposed. For the reference taxon proposed, the family name according to APGIII is provided. The biogeographic origin, the habit, the phenology and the IUCN status are also provided, if otherinfo = TRUE
and if the taxon name is present in TreeGhatsData
. A phylogenetic tree of the data is provided if phylo = TRUE
.
taxocheck(names, otherinfo = T, max.distance = 2, phylo = F)
names |
typically a vector of taxon names, each element including a genus, a specific epithet and, additionally, an infraspecific rank and an infraspecific epithet. The elements must be separated with a space. The authority of the taxon name should not be included.
If the user instead provides a data frame, |
otherinfo |
logical. If 'TRUE' (default), the biogeographic origin, the habit, the phenology and the IUCN status are provided for the taxon names found in |
max.distance |
maximum distance allowed in spelling correction with |
phylo |
if 'TRUE', the function will return an object of class |
First, the function standardizes the taxon names by removing unnecessary spaces and homogenising the abbreviations of intraspecific rank. It identifies incomplete names, i.e. names without species epithet or including a number or 'sp' instead of a species epithet. Second, the function searches the taxon names in the database TreeGhatsData
and provides their taxonomic status according to TPL and TBGRI. Typos can be detected depending on the arguments max.distance
and the correct spelling is provided in FoundName
. Orthographic errors can be corrected only in specific epithets. max.distance
should not be too large, to avoid incorrect matching. Third, for taxon names absent from TreeGhatsData
, the function provides taxonomic status according to TPL, by using a modified version of the function TPLck
(see TPLck2
). The modified version indicates if several homonyms are present in TPL (i.e., names with identical spelling but decribed by different authorities, thus corresponding to different taxa).
Based on the statuses found in TPL and TBGRI, a status, a reference name and authority are proposed, with the following rules: if a taxon name is absent from TreeGhatsData
, we retain information given by TPL, and otherwise we retain the taxonomic status poposed in TreeGhatsData
. For taxon names with several homonyms in TPL or incomplete, the function returns 'SeveralHomonyms' and 'IncompleteName' as the status, respectively, and NA
as reference name and authority. For a taxon name provided by the user at species level, if only one infrataxon is present in TreeGhatsData
, the function returns the information concerning this infrataxon, otherwise the function returns the information concerning the species level and includes 'SeveralInfrataxa' in the Infrataxon_info column. In the later case, the infrataxon level cannot be identified.
If otherinfo = T
, the biogeographic origin, the habit, the phenology and the IUCN status of the reference taxon proposed are extracted from the TreeGhatsData
.
If phylo = F
(default), the function returns an object of class data.frame
with the following components:
FoundName |
taxon names as found in |
Typo |
logical. If 'TRUE', there was a spelling error in the taxon name provided by the user. The correct spelling can be found in the |
Status_TPL |
taxonomic status found in The Plant List, either 'Accepted', 'Synonym', 'Unresolved', or 'Misapplied' (see http://www.theplantlist.org/1.1/about/#status). |
ReferenceName_TPL |
the reference taxon name extracted from TPL. |
ReferenceAuthority_TPL |
authority of |
Status_TBGRI |
taxonomic status according to TBGRI and extracted from |
ReferenceName_TBGRI |
the reference taxon name according to TBGRI extracted from |
ReferenceAuthorithy_TBGRI |
authority of |
Status_proposed |
proposed taxonomic status, either 'Accepted', 'Synonym', 'Unresolved', 'IncompleteName' or 'SeveralHomonyms'. 'IncompleteName' indicates incomplete taxon names provided by the user. 'SeveralHomonyms' indicates that there are several homonyms in TPL. |
ReferenceName_proposed |
the taxon name proposed. |
ReferenceAuthorithy_proposed |
authority of |
Infrataxon_info |
indicates if a taxon name given at specific level by the user includes one ('OneInfrataxon'), or several infrataxa ('SeveralInfrataxa') in the Western Ghats according to TBGRI. If it is not the case for any taxon, the field is absent. |
Family_APGIII |
family name according to APGIII for the reference taxon proposed. |
Genus |
genus of reference taxon proposed. |
Species |
specific epithet of reference taxon proposed. |
InfrataxonRank |
infraspecific rank of reference taxon proposed. If there is no infrataxon in the result, this field is absent. |
InfrataxonName |
infraspecific epithet of reference taxon proposed. If there is no infrataxon in the result, this field is absent. |
Origin |
if |
Habit |
if |
Phenology |
if |
IUCN |
if |
If phylo = T
, the function returns a list with the same data frame as above in $tab
, plus an object of class phylo
in $phylo
providing the phylogenetic tree of the requested taxa.
The function relies on the database TreeGhatsData
included in the package, which will be updated regularly.
The running time of the function depends on the length of the taxon names vector.
An internet connection is needed to check names in TPL.
TPLck2
is a modified version of TPLck
, which allows handling homonyms.
V. Raevel & F. Munoz
Cayuela, L., Granzow-de la Cerda, I., Albuquerque, F.S. and Golicher, J.D. 2012. Taxonstand: An R package for species names standardisation in vegetation databases. Methods in Ecology and Evolution, 3(6): 1078-1083.
Kalwij, J.M. 2012. Review of 'The Plant List, a working list of all plant species'. Journal of Vegetation Science, 23(5): 998-1002.http://www.theplantlist.org/
Nayar, T., Rasiya Beegam, A. & Sibi, M. 2015. Flowering plants of the Western Ghats, India, Volume 1 Dicots; Volume 2 Monocots. Jawaharlal Nehru Tropical Botanic Garden and Research Insitute.
Nayar, T.S., Beegam, A.R. & Sibi, M. 2014. Flowering Plants of the Western Ghats, India: Dicots. Jawaharlal Nehru Tropical Botanic Garden and Research Institute.
TreeGhatsData
, the database used by the function.
TPLck
TPLck2
## Not run: example <- c("Dipterocarpus indicus","Michelia champaca","Drypetes roxburghii", "Corypha umbraculifera") result <- taxocheck(example) # Tree species from the Uppangala permanent forest plot test <- taxocheck(UPSP_Species, phylo = TRUE) plot(test$phylo) ## End(Not run)
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