U.Taxonstand is an R Package for Standardizing and Harmonizing Scientific Names of Plants and Animals. This package can standardize and harmonize scientific names in plant and animal species lists at a fast execution speed and at a high rate of matching success. It works with all taxonomic databases, as long as they are properly formatted.
NOTE: An online version of U.Taxonstand is now available: https://ecoinfor.shinyapps.io/UTaxonstandOnline. Only some basic functions are included in the web application.
This package can be installed in R as follows,
# github (requires `remotes` or `devtools`)
devtools::install_github("ecoinfor/U.Taxonstand")library(U.Taxonstand)
# load the example database (you can creat your own database for specific taxomic groups)
data(databaseExample)
# The input names as a character vector
sps <- c("Syntoma comosum (L.) Dalla Torre & Sarnth.", "Turczaninowia fastigiata (Fisch.) DC.",
"Zizyphora abd-el-asisii Hand.-Mazz.")
nameMatch(spList=sps, spSource=databaseExample, author = TRUE, max.distance= 1)
# The input as a dataframe with the columns "SPECIES", "AUTHOR" and/or "RANK"
data(spExample)
res <- nameMatch(spList=spExample, spSource=databaseExample, author = TRUE, max.distance= 1)
head(res)
# The current default only keeps the first 'best' matching result for each taxon name. If you want to check all the matched results, please change the option 'matchFirst=FALSE'.
res <- nameMatch(spList=spExample, spSource=databaseExample, author = TRUE, max.distance= 1, matchFirst=FALSE)
dim(res)
# Using the additional data of genus pairs for fuzzy matching of genus names
data(spExample)
data(genusPairs_Plants)
res <- nameMatch(spList=spExample, spSource=databaseExample, author = TRUE, max.distance= 1,
genusPairs=genusPairs_Plants)
head(res)
#------------------ The R package also works for other taxomic groups. The below is an exmaple for birds
# load the formatted ITIS Aves database; the formatted database can be downloaded here:
# https://github.com/nameMatch/Database
#--- load the xlsx datafile
# require(openxlsx)
# database <- read.xlsx("Birds_ITIS_database.xlsx")
#--- load the rdata file
load("Birds.rdadta")
spAves <- c("Hieraaetus fasciata","Merops leschenaultia","Egretta sacra","Sturnia philippensis","Phoenicurus caeruleocephala","Enicurus maculates","Orthotomus cucullatus","Phalacrocorax carbo")
nameMatch(spList=spAves,spSource=database, author = FALSE, max.distance= 1)
#------------------ You can use the function "nameSplit" to format your species name list
sps <- c("Syntoma comosum (L.) Dalla Torre & Sarnth.","Eupatorium betoniciforme f. alternifolium Hicken","Turczaninowia fastigiata (Fisch.) DC.","Zizyphora abd-el-asisii Hand.-Mazz.","Baccharis X paulopolitana I.L.Teodoro & W.Hoehne","Accipiter albogularis woodfordi (Sharpe, 1888)")
(splist <- nameSplit(splist=sps))
#------------------ You can use the function "synSearch" to find all the synonyms and accepted names.
data(databaseExample)
synSearch(splist="Isoetes tenella", spSource=databaseExample)
synSearch(splist=c("Isoetes tenella","Isoetes echinospora","Isoetes underwoodii L.F. Hend. Isoetes"), spSource=databaseExample)
#------------------ You can use the function "familyMatch" to find all the accepted family names for taxon names.
# genus names
familyMatch(genuslist=c("Aa","Pinus","Humbertodendron"), taxon="plant")
familyMatch(genuslist = c("Acanthocharax","Agosia","Alticorpus"),taxon="fish")
# species names
familyMatch(splist=c("Aa xyz","Pinus xyz","Humbertodendron xyz"), taxon="plant")
familyMatch(splist = c("Acanthocharax xyz","Agosia xyz","Alticorpus xyz"),taxon="fish")If you use this package, please cite it.
Zhang, J. & Qian, H. (2023). U.Taxonstand: An R package for standardizing scientific names of plants and animals. Plant Diversity, 45(1): 1-5. DOI: 10.1016/j.pld.2022.09.001
Zhang, J., Qian, H., Wang, X. (2024). An online version and some updates of R package U.Taxonstand for standardizing scientific names in plant and animal species. Plant Diversity, DOI: 10.1016/j.pld.2024.09.005
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Huang, Xing-Zhao, et al. Are allometric model parameters of aboveground biomass for trees phylogenetically constrained? Plant Diversity (2022). https://doi.org/10.1016/j.pld.2022.11.005
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