taxocheck: Provide taxonomic status of a tree names list

In frmunoz/TreeGhats: Taxonomic name resolution and phylogeny generator for Western Ghats trees

Provide taxonomic status of a tree names list

Description

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.

Usage

taxocheck(names, otherinfo = T,  max.distance = 2, phylo = F)

Arguments

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, taxocheck selects the first column named "names" or "binome" (case insensitive). This column should include taxon names following the same format as presented above.
otherinfo	logical. If 'TRUE' (default), the biogeographic origin, the habit, the phenology and the IUCN status are provided for the taxon names found in TreeGhatsData.
max.distance	maximum distance allowed in spelling correction with agrep function.
phylo	if 'TRUE', the function will return an object of class phylo with the phylogenetic tree. Default is 'FALSE'.

Details

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.

Value

If phylo = F (default), the function returns an object of class data.frame with the following components:

FoundName	taxon names as found in TreeGhatsData or in TPL. Orthographic errors are corrected. The taxon names provided by the user is kept in the rownames of the return object. 'IncompleteName' is return when the user provide a name without species epithet, or including a number. NA indicates taxon names found neither in TreeGhatsData nor in TPL.
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 Foundname column, while the spelling provided by the user is kept as row name.
Status_TPL	taxonomic status found in The Plant List, either 'Accepted', 'Synonym', 'Unresolved', or 'Misapplied' (see http://www.theplantlist.org/1.1/about/#status). NA indicates taxon names not found in TPL. 'SeveralHomonyms' indicates that there are several homonyms in TPL for the taxon name provided.
ReferenceName_TPL	the reference taxon name extracted from TPL.
ReferenceAuthority_TPL	authority of ReferenceName_TPL.
Status_TBGRI	taxonomic status according to TBGRI and extracted from TreeGhatsData, either 'Absent', 'Accepted', 'Synonym'. 'Absent' indicates taxon names not found in TBGRI.
ReferenceName_TBGRI	the reference taxon name according to TBGRI extracted from TreeGhatsData.
ReferenceAuthorithy_TBGRI	authority of ReferenceName_TBGRI.
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 ReferenceName_proposed.
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 otherinfo = T, the biogegraphical origin of the reference taxon proposed. The information is extracted from TreeGhatsData, and is either 'exotic', 'endemic WG' for endemic of Western Ghats, 'endemic India' or 'native'. NA indicates that the reference taxon proposed is absent from TreeGhatsData.
Habit	if otherinfo = T, the habit of the reference taxon proposed. It is extracted from from TreeGhatsData, and is either 'climbing shrub', 'liana', 'shrub', 'straggling shrub', 'straggling tree', 'tree', 'twining shrub', 'unknown' or any combination of the terms. NA indicates that the reference taxon proposed is absent from TreeGhatsData.
Phenology	if otherinfo = T, the leaf phenology of the reference taxon proposed. It is extracted from TreeGhatsData, and is either 'evergreen' or 'deciduous'. NA indicates unkown phenology.
IUCN	if otherinfo = T, the IUCN status, either 'CR', 'DD', 'EN', 'EX', 'LC', 'LR/cd', 'LR/lc', 'LR/nt', 'NE', 'VU' for the reference taxon proposed. When the taxon name is not present in TreeGhatsData or not evaluated by IUCN, the function returns NA.

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.

Note

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.

Author(s)

V. Raevel & F. Munoz

References

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.

See Also

TreeGhatsData, the database used by the function. TPLck TPLck2

Examples

## 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)

frmunoz/TreeGhats documentation built on July 29, 2022, 5:21 a.m.