| Title: | Standardize Plant Names According to World Flora Online Taxonomic Backbone |
|---|---|
| Description: | World Flora Online is an online flora of all known plants, available from <https://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013. |
| Authors: | Roeland Kindt [cre, aut]
|
| Maintainer: | Roeland Kindt <[email protected]> |
| License: | GPL-3 |
| Version: | 1.14-5 |
| Built: | 2025-01-09 06:58:15 UTC |
| Source: | CRAN |
Instead of using the taxonomic backbone data set from World Flora Online, it is possible to use matching functions of WorldFlora with alternative taxonomic backbone. The function creates new variables that correspond to key variables in the World Flora Online backbone so that matching functions WFO.match and WFO.one can be applied.
new.backbone(x, taxonID = "taxonID", scientificName = "scientificName", scientificNameAuthorship = "scientificNameAuthorship", acceptedNameUsageID = NULL, taxonomicStatus = NULL )new.backbone(x, taxonID = "taxonID", scientificName = "scientificName", scientificNameAuthorship = "scientificNameAuthorship", acceptedNameUsageID = NULL, taxonomicStatus = NULL )
x |
data.frame with the variables. |
taxonID |
name of the variable with the identification |
scientificName |
name of the variable with the full taxon name |
scientificNameAuthorship |
name of the variable with the naming authors |
acceptedNameUsageID |
ID of the record with the current (accepted) name. Should respond to an ID in the 'taxonID' column. In case the taxonomic name is current, then this field should be left blank. This field is used by function WFO.match to find the accepted name of a species. |
taxonomicStatus |
Variable that indicates whether the record is for a current name or a synonym. This variable is used by function WFO.one to discriminate situations where best matches include matches with current names and synonyms. |
This function allows a user to create a new taxonomic backbone data set that is understood by WFO.match and WFO.one.
Alternative examples with the Mammal Diversity Database (https://www.mammaldiversity.org/) and the World Checlist of Vascular Plants (https://powo.science.kew.org/about-wcvp) are provided in the Kindt 2021a,b RPubs.
The function returns a data.table that can be understood by WFO.match and WFO.one for standardizing taxonomic names.
Roeland Kindt (World Agroforestry)
Kindt, R. 2021a. Standardizing mammal species names with the Mammal Species Database via exact and fuzzy matching functions from the WorldFlora package. https://rpubs.com/Roeland-KINDT
Kindt, R. 2021b. Standardizing GlobalTreeSearch tree species names with World Flora Online and the World Checklist of Vascular Plants https://rpubs.com/Roeland-KINDT
## Not run: # load the World Flora Online taxonomic backbone WFO.remember() # get a list of Sapotaceae species Sapotaceae <- WFO.data[WFO.data$family == "Sapotaceae",] Sapotaceae <- Sapotaceae[Sapotaceae$taxonRank == "SPECIES", ] Sapotaceae <- Sapotaceae[Sapotaceae$taxonomicStatus == "Accepted", ] Sapotaceae <- Sapotaceae[, c("scientificName", "scientificNameAuthorship")] Sapotaceae <- data.frame(ID = c(1:nrow(Sapotaceae)), Sapotaceae) names(Sapotaceae)[2:3] <- c("species.name", "author") head(Sapotaceae) # create a new backbone from the GlobalTreeSearch database, # after copying locally from https://tools.bgci.org/global_tree_search.php GTS.dir <- "E://Roeland//R///World Flora Online//2021" GTS <- read.csv(paste0(GTS.dir, "//global_tree_search.csv")) GTS <- GTS[, 1:2] GTS <- data.frame(GTS.ID = paste0("GTS-", c(1:nrow(GTS))), GTS) nrow(GTS) # create the new backbone GTS.data <- new.backbone(GTS, taxonID="GTS.ID", scientificName="TaxonName", scientificNameAuthorship="Author") head(GTS.data) # Check and standardize Sapotaceae Sapotaceae.match <- WFO.one(WFO.match(Sapotaceae, WFO.data = GTS.data, spec.name = "species.name", Authorship = "author")) nrow(Sapotaceae.match[Sapotaceae.match$Fuzzy == FALSE, ] ) nrow(Sapotaceae.match[Sapotaceae.match$Fuzzy == TRUE & Sapotaceae.match$Fuzzy.dist < 4, ] ) Sapotaceae.match[Sapotaceae.match$Fuzzy == TRUE & Sapotaceae.match$Fuzzy.dist < 4, c("ID", "species.name", "Fuzzy.dist", "scientificName")] ## End(Not run)## Not run: # load the World Flora Online taxonomic backbone WFO.remember() # get a list of Sapotaceae species Sapotaceae <- WFO.data[WFO.data$family == "Sapotaceae",] Sapotaceae <- Sapotaceae[Sapotaceae$taxonRank == "SPECIES", ] Sapotaceae <- Sapotaceae[Sapotaceae$taxonomicStatus == "Accepted", ] Sapotaceae <- Sapotaceae[, c("scientificName", "scientificNameAuthorship")] Sapotaceae <- data.frame(ID = c(1:nrow(Sapotaceae)), Sapotaceae) names(Sapotaceae)[2:3] <- c("species.name", "author") head(Sapotaceae) # create a new backbone from the GlobalTreeSearch database, # after copying locally from https://tools.bgci.org/global_tree_search.php GTS.dir <- "E://Roeland//R///World Flora Online//2021" GTS <- read.csv(paste0(GTS.dir, "//global_tree_search.csv")) GTS <- GTS[, 1:2] GTS <- data.frame(GTS.ID = paste0("GTS-", c(1:nrow(GTS))), GTS) nrow(GTS) # create the new backbone GTS.data <- new.backbone(GTS, taxonID="GTS.ID", scientificName="TaxonName", scientificNameAuthorship="Author") head(GTS.data) # Check and standardize Sapotaceae Sapotaceae.match <- WFO.one(WFO.match(Sapotaceae, WFO.data = GTS.data, spec.name = "species.name", Authorship = "author")) nrow(Sapotaceae.match[Sapotaceae.match$Fuzzy == FALSE, ] ) nrow(Sapotaceae.match[Sapotaceae.match$Fuzzy == TRUE & Sapotaceae.match$Fuzzy.dist < 4, ] ) Sapotaceae.match[Sapotaceae.match$Fuzzy == TRUE & Sapotaceae.match$Fuzzy.dist < 4, c("ID", "species.name", "Fuzzy.dist", "scientificName")] ## End(Not run)
This data set lists orders for families of vascular plants (angiosperms, gymnosperms and pteridophytes). For angiosperms, information from orders and higher levels of classification correspond to the fourth update of the Angiosperm Phylogeny Group (APG IV, doi:10.1111/boj.12385). Higher levels of classification correspond to names of nodes of the consensus tree (Figure 1 in doi:10.1111/boj.12385). Orders for gymnosperms and pteridophytes were obtained from the website of Missouri Botanical Garden.
data(vascular.families)data(vascular.families)
A data frame with 476 observations on the following 10 variables.
GroupGroup.
Family.IDUnique ID for each family. For angiosperms, these correspond to APG IV.
FamilyName of the plant family.
Family.taxonIDtaxonID retrieved from World Flora Online.
OrderName of the plant order.
Order.taxonIDtaxonID retrieved from World Flora Online.
Node.1Name of the node in the consensus tree.
Node.2Name of the node in the consensus tree, with Node.2 nested within Node.1.
Node.3Name of the node in the consensus tree, with Node.3 nested within Node.2.
Node.4Name of the node in the consensus tree, with Node.4 nested within Node.3.
The Angiosperm Phylogeny Group, M. W. Chase, M. J. M. Christenhusz, M. F. Fay, J. W. Byng, W. S. Judd, D. E. Soltis, D. J. Mabberley, A. N. Sennikov, P. S. Soltis, P. F. Stevens, An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV, Botanical Journal of the Linnean Society 181: 1-20. doi:10.1111/boj.12385
data(vascular.families)data(vascular.families)
The function checks whether submitted and match names only differ by ending by -um, -us or -a. An extra check is done to accept differences that result from having 'ii' instead of 'i' in the submitted and matched name. An optional check ignores differences in vowels.
WFO.acceptable.match(x, spec.name="spec.name", no.vowels=FALSE)WFO.acceptable.match(x, spec.name="spec.name", no.vowels=FALSE)
x |
Output for |
spec.name |
Name of taxon submitted for matching. |
no.vowels |
Accept results if only vowels differ between submitted and matched name. |
The function was initially developed to check for changes in gender notations.
In new versions, also the following differences in species names are judged to be acceptable:
- hybrid and non-hybrid names (eg, Sorbus avonensis - Sorbus xavonensis)
- i vs. j (eg, Syzygium naiadum - Syzygium najadum)
- tt vs. t (eg, Ficus scott-elliottii - Ficus scott-elliotii)
- ll vs. l (eg, Garcinia moseleyana - Garcinia moselleyana)
- rr vs. r (eg, Hymenodictyon perrieri - Hymenodictyon perieri)
- mm vs. m (eg, Monteverdia schummaniana - Monteverdia schumanniana)
- nn vs. n (eg, Pyrus tamamschiannae - Pyrus tamamschianae)
- ff vs. f (eg, Dendropanax langsdorfii - Dendropanax langsdorffii)
- hh vs. h (eg, Gmelina leichardtii - Gmelina leichhardtii)
- dd vs. d (eg, Miconia buddlejoides - Miconia budlejoides)
- is vs. e (eg, Decarydendron ranomafanensis - Decarydendron ranomafanense)
- dt vs. d (eg, Stadtmannia acuminata - Stadmania acuminata)
The function returns a logical vector that indicates whether names could be acceptable.
Roeland Kindt (World Agroforestry)
## Not run: data(WFO.example) spec.test <- data.frame(spec.name=c("Faidherbia albida", "Acacia albida", "Faidherbia albidum", "Faidherbia albidus", "Faidherbia albiida", "Prunus africanus", "Prunos africanea", "Prunus afrocaneus", "Prunus afrocaneos")) match1 <- WFO.match.fuzzyjoin(spec.data=spec.test, WFO.data=WFO.example, fuzzydist.max = 6) match1[, c("spec.name", "scientificName")] # check for gender differences (and ii - i) WFO.acceptable.match(match1) # ignore differences in vowels WFO.acceptable.match(match1, no.vowels=TRUE) accepted.cases <- WFO.acceptable.match(match1, no.vowels=TRUE) match1.accepted <- match1[accepted.cases == TRUE, ] match1.notaccepted <- match1[accepted.cases == FALSE, ] ## End(Not run)## Not run: data(WFO.example) spec.test <- data.frame(spec.name=c("Faidherbia albida", "Acacia albida", "Faidherbia albidum", "Faidherbia albidus", "Faidherbia albiida", "Prunus africanus", "Prunos africanea", "Prunus afrocaneus", "Prunus afrocaneos")) match1 <- WFO.match.fuzzyjoin(spec.data=spec.test, WFO.data=WFO.example, fuzzydist.max = 6) match1[, c("spec.name", "scientificName")] # check for gender differences (and ii - i) WFO.acceptable.match(match1) # ignore differences in vowels WFO.acceptable.match(match1, no.vowels=TRUE) accepted.cases <- WFO.acceptable.match(match1, no.vowels=TRUE) match1.accepted <- match1[accepted.cases == TRUE, ] match1.notaccepted <- match1[accepted.cases == FALSE, ] ## End(Not run)
This data set is a subset of the World Flora Online taxonomic backbone that allows running the first set of examples. In practical applications, users should first download a static copy of the Taxonomic Backbone data from https://www.worldfloraonline.org or https://zenodo.org/doi/10.5281/zenodo.7460141 (_DwC_backbone_R.zip).
data(WFO.example)data(WFO.example)
World Flora Online. An Online Flora of All Known Plants. https://www.worldfloraonline.org
data(WFO.example)data(WFO.example)
This package checks a list of taxa (typically species) against the World Flora Online (WFO) taxonomic backbone. The user needs to first download a static copy of the Taxonomic Backbone data from https://www.worldfloraonline.org or https://zenodo.org/doi/10.5281/zenodo.7460141 (_DwC_backbone_R.zip).
WFO.match(spec.data = NULL, WFO.file = NULL, WFO.data = NULL, no.dates = TRUE, spec.name = "spec.name", Genus = "Genus", Species = "Species", Infraspecific.rank = "Infraspecific.rank", Infraspecific = "Infraspecific", Authorship = "Authorship", First.dist = FALSE, acceptedNameUsageID.match = TRUE, Fuzzy = 0.1, Fuzzy.force = FALSE, Fuzzy.max = 250, Fuzzy.min = TRUE, Fuzzy.shortest = FALSE, Fuzzy.within = FALSE, Fuzzy.two = TRUE, Fuzzy.one = TRUE, squish = TRUE, spec.name.tolower = FALSE, spec.name.nonumber = TRUE, spec.name.nobrackets = TRUE, exclude.infraspecific = FALSE, infraspecific.excluded = c("cultivar.", "f.", "sect.", "subf.", "subg.", "subsp.", "subvar.", "var", "var.", "[infraspec.]", "fo.", "forma", "nothosubsp.", "nothovar.", "sect."), spec.name.sub = TRUE, sub.pattern=c(" sp[.] A", " sp[.] B", " sp[.] C", " sp[.]", " spp[.]", " pl[.]", " indet[.]", " ind[.]", " gen[.]", " g[.]", " fam[.]", " nov[.]", " prox[.]", " cf[.]", " aff[.]", " s[.]s[.]", " s[.]l[.]", " p[.]p[.]", " p[.] p[.]", "[?]", " inc[.]", " stet[.]", "Ca[.]", "nom[.] cons[.]", "nom[.] dub[.]", " nom[.] err[.]", " nom[.] illeg[.]", " nom[.] inval[.]", " nom[.] nov[.]", " nom[.] nud[.]", " nom[.] obl[.]", " nom[.] prot[.]", " nom[.] rej[.]", " nom[.] supp[.]", " sensu auct[.]"), verbose = TRUE, counter = 1000) WFO.url(WFO.result = NULL, browse = FALSE, browse.rows = c(1:1), ...) WFO.one(WFO.result = NULL, priority = "Accepted", spec.name = NULL, Auth.dist = NULL, Old.author.dist=NULL, First.dist = NULL, verbose = TRUE, counter = 1000) WFO.browse(taxon, WFO.file = NULL, WFO.data = NULL, accepted.only = FALSE, acceptedNameUsageID.match = TRUE, ...) WFO.synonyms(taxon, WFO.file = NULL, WFO.data = NULL, ...) WFO.family(taxon, WFO.file = NULL, WFO.data = NULL, ...)WFO.match(spec.data = NULL, WFO.file = NULL, WFO.data = NULL, no.dates = TRUE, spec.name = "spec.name", Genus = "Genus", Species = "Species", Infraspecific.rank = "Infraspecific.rank", Infraspecific = "Infraspecific", Authorship = "Authorship", First.dist = FALSE, acceptedNameUsageID.match = TRUE, Fuzzy = 0.1, Fuzzy.force = FALSE, Fuzzy.max = 250, Fuzzy.min = TRUE, Fuzzy.shortest = FALSE, Fuzzy.within = FALSE, Fuzzy.two = TRUE, Fuzzy.one = TRUE, squish = TRUE, spec.name.tolower = FALSE, spec.name.nonumber = TRUE, spec.name.nobrackets = TRUE, exclude.infraspecific = FALSE, infraspecific.excluded = c("cultivar.", "f.", "sect.", "subf.", "subg.", "subsp.", "subvar.", "var", "var.", "[infraspec.]", "fo.", "forma", "nothosubsp.", "nothovar.", "sect."), spec.name.sub = TRUE, sub.pattern=c(" sp[.] A", " sp[.] B", " sp[.] C", " sp[.]", " spp[.]", " pl[.]", " indet[.]", " ind[.]", " gen[.]", " g[.]", " fam[.]", " nov[.]", " prox[.]", " cf[.]", " aff[.]", " s[.]s[.]", " s[.]l[.]", " p[.]p[.]", " p[.] p[.]", "[?]", " inc[.]", " stet[.]", "Ca[.]", "nom[.] cons[.]", "nom[.] dub[.]", " nom[.] err[.]", " nom[.] illeg[.]", " nom[.] inval[.]", " nom[.] nov[.]", " nom[.] nud[.]", " nom[.] obl[.]", " nom[.] prot[.]", " nom[.] rej[.]", " nom[.] supp[.]", " sensu auct[.]"), verbose = TRUE, counter = 1000) WFO.url(WFO.result = NULL, browse = FALSE, browse.rows = c(1:1), ...) WFO.one(WFO.result = NULL, priority = "Accepted", spec.name = NULL, Auth.dist = NULL, Old.author.dist=NULL, First.dist = NULL, verbose = TRUE, counter = 1000) WFO.browse(taxon, WFO.file = NULL, WFO.data = NULL, accepted.only = FALSE, acceptedNameUsageID.match = TRUE, ...) WFO.synonyms(taxon, WFO.file = NULL, WFO.data = NULL, ...) WFO.family(taxon, WFO.file = NULL, WFO.data = NULL, ...)
spec.data |
A data.frame containing variables with species names. In case that a character vector is provided, then this vector will be converted to a data.frame |
WFO.file |
File name of the static copy of the Taxonomic Backbone. If not |
WFO.data |
Data set with the static copy of the Taxonomic Backbone. Ignored if |
no.dates |
Speeding up the loading of the WFO.data by not loading fields of 'created' and 'modified'. |
spec.name |
Name of the column with taxonomic names. In case that a |
Genus |
Name of the column with the genus names. |
Species |
Name of the column with the species names. |
Infraspecific.rank |
Name of the column with the infraspecific rank (such as "subsp.", "var." or "cultivar."). |
Infraspecific |
Name of the column with the infraspecific names. |
Authorship |
Name of the column with the naming authorities. |
First.dist |
If |
acceptedNameUsageID.match |
If |
Fuzzy |
If larger than 0, then attempt fuzzy matching in case an identifical taxonomic name is not found in the World Flora Online. This argument will be used as argument |
Fuzzy.force |
If |
Fuzzy.max |
Maximum number of fuzzy matches. |
Fuzzy.min |
If |
Fuzzy.shortest |
If |
Fuzzy.within |
If |
Fuzzy.two |
If |
Fuzzy.one |
If |
squish |
If |
spec.name.tolower |
If |
spec.name.nonumber |
If |
spec.name.nobrackets |
If |
exclude.infraspecific |
If |
infraspecific.excluded |
Infraspecific levels (available from column 'verbatimTaxonRank') excluded in the results. Note that levels are excluded both in direct matches and matches with the accepted name. |
spec.name.sub |
If |
sub.pattern |
Sections of the |
verbose |
Give details on the fuzzy matching process. |
counter |
Progress on the matching process is reported by multiples of this counter. |
WFO.result |
Result obtained via WFO.match. |
browse |
If |
browse.rows |
Indices of row with the urls to be browsed. |
priority |
Method of selecting the 1-to-1 matches. Option |
Auth.dist |
In case that the name of the variable with the Levenshtein distance between the authorship names is provided, then the algorithm first prioritizes records with the best match between the submitted and matched author names. |
Old.author.dist |
In case that the name of the variable with the Levenshtein distance between the authorship names for the synonym matches is provided, then the algorithm first prioritizes records with the best match between the submitted and matched author names. |
taxon |
Character string with the name of the taxon for which information will be given (for families, different genera; for genera, different specieds; for species, infraspecific levels). |
accepted.only |
If |
... |
Other arguments for browseURL ( |
The principal function (WFO.match) matches plant names. Columns retrieved from the World Flora Online are added to the provided input data.frame. In case that there are multiple matches, then rows from the input data.frame are repeated.
Column 'Unique' shows whether there was a unique match (or not match) in the WFO.
Column 'Matched' shows whether there was a match in the WFO.
Column 'Fuzzy' shows whether matching was done by the fuzzy method.
Column 'Fuzzy.dist' gives the Levenshtein distance calculated between submitted and matched plant names adist.
Column 'Auth.dist' gives the Levenshtein distance calculated between submitted and matched authorship names, if the former were provided adist.
Column 'Subseq' gives different numbers for different matches for the same plant name.
Column 'Hybrid' shows whether there was a hybrid character in the scientificName.
Column 'New.accepted' shows whether the species details correspond to the current accepted name.
Column 'Old.status' gives the taxonomic status of the first match with the non-blank acceptedNameUsageID.
Column 'Old.ID' gives the ID of the first match with the non-blank acceptedNameUsageID.
Column 'Old.name' gives the name of the first match with the non-blank acceptedNameUsageID.
The function was inspired on the Taxonstand package that matches plant names against The Plant List. Note that The Plant List has been static since 2013, but was used as the starting point for the Taxonomic Backbone of the World Flora Online.
Function WFO.one finds one unique matching name for each submitted name. Via priority = "Accepted", it first limits candidates to accepted names, with a possible second step of eliminating accepted names that are synonyms. Via priority = "Synonym", it first limits candidates to those that are not synonyms, with a possible second step of eliminating names that are not accepted. When the number of matches is larger than one after these steps, a third algorithm picks the candidate with the smallest taxonID. When a spec.name is given to WFO.one, the original submitted name is inserted for the scientificName.
When the user specifies the column with the Auth.dist, documenting the Levenshtein
distance between the submitted and matched authorities, then WFO.one first prioritizes records with best match between Authorities.
Function WFO.browse lists all the genera for a family, all species for a genus or all infraspecific levels for a species.
Function WFO.synonyms gives all records with the acceptedNameUsageID equal to the matched accepted species shown in the first row.
Function WFO.family provides information on the order of vascular plants, based on information available from vascular.families. Based on an internal list of bryophyte families, when the submitted plant name is a bryophyte, the function returns 'bryophyte' instead.
The main function returns a data.set with the matched species details from the WFO.
Roeland Kindt (World Agroforestry, CIFOR-ICRAF)
World Flora Online. An Online Flora of All Known Plants. https://www.worldfloraonline.org
Sigovini M, Keppel E, Tagliapietra. 2016. Open Nomenclature in the biodiversity era. Methods in Ecology and Evolution 7: 1217-1225.
Kindt, R. 2020. WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data. Applications in Plant Sciences 8(9): e11388
data(WFO.example) spec.test <- data.frame(spec.name=c("Faidherbia albida", "Acacia albida", "Omalanthus populneus", "Pygeum afric")) WFO.match(spec.data=spec.test, WFO.data=WFO.example, counter=1, verbose=TRUE) # Also calculate the Levenshtein distance for the genus WFO.match(spec.data=spec.test, WFO.data=WFO.example, First.dist=TRUE, counter=1, verbose=TRUE) # Show all the fuzzy matches, which included those at infraspecifc level e1 <- WFO.match(spec.data=spec.test, WFO.data=WFO.example, counter=1, Fuzzy.min=FALSE, Fuzzy.shortest=FALSE, verbose=TRUE) e1 # Use function WFO.one for a 1-to-1 match between submitted and matched names WFO.one(e1) # Hybrid species WFO.match("Arabis divaricarpa", WFO.data=WFO.example) WFO.match("Arabis x divaricarpa", WFO.data=WFO.example) # Convert capitals to lower case WFO.match("FAIDHERBIA ALBIDA", WFO.data=WFO.example, spec.name.tolower=TRUE) # Remove sections of plant names that are equal to ' sp.' or ' indet. ' WFO.match("Prunus sp.", WFO.data=WFO.example, spec.name.sub=TRUE) # Get urls, but do not open any e2 <- WFO.match(spec.data=spec.test, WFO.data=WFO.example, counter=1, verbose=TRUE) WFO.url(e2, browse=FALSE, browse.rows=c(1:nrow(e2))) # Include input species names where no matches were found # This happens when the name with original species names is provided to WFO.one x1 <- WFO.match("World agroforestry", WFO.data=WFO.example) WFO.one(x1, spec.name="spec.name") ## Not run: # Cross-check with Taxonstand results library(Taxonstand) data(bryophytes) # Give the file with the static copy of the Taxonomic Backbone data ('classification.txt') # that was downloaded from \url{https://www.worldfloraonline.org/downloadData}. # Possibly first use unzip(file.choose()) for the downloaded WFO_Backbone.zip WFO.file.RK <- file.choose() # check species name w1 <- WFO.match(bryophytes[1:20, ], WFO.file=WFO.file.RK, spec.name="Full.name", counter=1) w1 # check species name from list of names w1 <- WFO.match(bryophytes$Full.name[1:20], WFO.file=WFO.file.RK, counter=1) # re-check species names obtained via Taxonstand # note that Taxonstand did not match some infraspecific names ('Higher.level') r1 <- Taxonstand::TPL(bryophytes$Full.name[1:20], corr = TRUE) w2 <- WFO.match(r1, WFO.file=WFO.file.RK, Genus="New.Genus", Species="New.Species", Infraspecific.rank="New.Infraspecific.rank", Infraspecific="New.Infraspecific", counter=1) w2 # only check genus and species # specify different names for infraspecific columns as default to Taxonstand w3 <- WFO.match(r1, WFO.file=WFO.file.RK, Genus="New.Genus", Species="New.Species", Infraspecific.rank="none", Infraspecific="none", counter=1) # note that the method above also retrieved infraspecific levels # to only retrieve at the species level, match infraspecific levels with an empty column r1$empty <- rep("", nrow(r1)) w4 <- WFO.match(r1, WFO.file=WFO.file.RK, Genus="New.Genus", Species="New.Species", Infraspecific.rank="empty", Infraspecific="empty", counter=1) # as an alternative to the method above, exclude all documented infraspecific levels # from the results w5 <- WFO.match(r1, WFO.file=WFO.file.RK, Genus="New.Genus", Species="New.Species", exclude.infraspecific=TRUE, counter=1) # save results to file # utils::write.table(w4, quote=F, sep="\t", row.names=F, append=FALSE) # limit the fuzzy matches to those that contain a shortened version of a species name w6 <- WFO.match("Acacia caes", WFO.file=WFO.file.RK, Fuzzy=0.01, Fuzzy.within=TRUE, verbose=TRUE) # show all the matches for a genus spec.test1 <- data.frame(Genus=c("Casimiroa")) w8 <- WFO.match(spec.test1, WFO.file=WFO.file.RK, exclude.infraspecific=TRUE, verbose=TRUE) # show all listings at a next hierarchical level WFO.data1 <- data.table::fread(WFO.file.RK, encoding="UTF-8") WFO.browse("Pinaceae", WFO.data=WFO.data1) WFO.browse("Pinaceae", WFO.data=WFO.data1, accepted.only=T) WFO.browse("Tsuga", WFO.data=WFO.data1) WFO.browse("Tsuga", WFO.data=WFO.data1, accepted.only=T) WFO.browse("Olea europaea", WFO.data=WFO.data1) WFO.browse("Olea europaea", WFO.data=WFO.data1, accepted.only=T) # browsing only works at family, genus and species levels # for orders, however, information is given from vascular.families WFO.browse("Polypodiales", WFO.data=WFO.data1) # submitting no name results in a list of all families WFO.browse(, WFO.data=WFO.data1) # give synonyms WFO.synonyms("Olea europaea", WFO.data=WFO.data1) # give order and other higher levels from family WFO.family("Olea europaea", WFO.data=WFO.data1) ## End(Not run)data(WFO.example) spec.test <- data.frame(spec.name=c("Faidherbia albida", "Acacia albida", "Omalanthus populneus", "Pygeum afric")) WFO.match(spec.data=spec.test, WFO.data=WFO.example, counter=1, verbose=TRUE) # Also calculate the Levenshtein distance for the genus WFO.match(spec.data=spec.test, WFO.data=WFO.example, First.dist=TRUE, counter=1, verbose=TRUE) # Show all the fuzzy matches, which included those at infraspecifc level e1 <- WFO.match(spec.data=spec.test, WFO.data=WFO.example, counter=1, Fuzzy.min=FALSE, Fuzzy.shortest=FALSE, verbose=TRUE) e1 # Use function WFO.one for a 1-to-1 match between submitted and matched names WFO.one(e1) # Hybrid species WFO.match("Arabis divaricarpa", WFO.data=WFO.example) WFO.match("Arabis x divaricarpa", WFO.data=WFO.example) # Convert capitals to lower case WFO.match("FAIDHERBIA ALBIDA", WFO.data=WFO.example, spec.name.tolower=TRUE) # Remove sections of plant names that are equal to ' sp.' or ' indet. ' WFO.match("Prunus sp.", WFO.data=WFO.example, spec.name.sub=TRUE) # Get urls, but do not open any e2 <- WFO.match(spec.data=spec.test, WFO.data=WFO.example, counter=1, verbose=TRUE) WFO.url(e2, browse=FALSE, browse.rows=c(1:nrow(e2))) # Include input species names where no matches were found # This happens when the name with original species names is provided to WFO.one x1 <- WFO.match("World agroforestry", WFO.data=WFO.example) WFO.one(x1, spec.name="spec.name") ## Not run: # Cross-check with Taxonstand results library(Taxonstand) data(bryophytes) # Give the file with the static copy of the Taxonomic Backbone data ('classification.txt') # that was downloaded from \url{https://www.worldfloraonline.org/downloadData}. # Possibly first use unzip(file.choose()) for the downloaded WFO_Backbone.zip WFO.file.RK <- file.choose() # check species name w1 <- WFO.match(bryophytes[1:20, ], WFO.file=WFO.file.RK, spec.name="Full.name", counter=1) w1 # check species name from list of names w1 <- WFO.match(bryophytes$Full.name[1:20], WFO.file=WFO.file.RK, counter=1) # re-check species names obtained via Taxonstand # note that Taxonstand did not match some infraspecific names ('Higher.level') r1 <- Taxonstand::TPL(bryophytes$Full.name[1:20], corr = TRUE) w2 <- WFO.match(r1, WFO.file=WFO.file.RK, Genus="New.Genus", Species="New.Species", Infraspecific.rank="New.Infraspecific.rank", Infraspecific="New.Infraspecific", counter=1) w2 # only check genus and species # specify different names for infraspecific columns as default to Taxonstand w3 <- WFO.match(r1, WFO.file=WFO.file.RK, Genus="New.Genus", Species="New.Species", Infraspecific.rank="none", Infraspecific="none", counter=1) # note that the method above also retrieved infraspecific levels # to only retrieve at the species level, match infraspecific levels with an empty column r1$empty <- rep("", nrow(r1)) w4 <- WFO.match(r1, WFO.file=WFO.file.RK, Genus="New.Genus", Species="New.Species", Infraspecific.rank="empty", Infraspecific="empty", counter=1) # as an alternative to the method above, exclude all documented infraspecific levels # from the results w5 <- WFO.match(r1, WFO.file=WFO.file.RK, Genus="New.Genus", Species="New.Species", exclude.infraspecific=TRUE, counter=1) # save results to file # utils::write.table(w4, quote=F, sep="\t", row.names=F, append=FALSE) # limit the fuzzy matches to those that contain a shortened version of a species name w6 <- WFO.match("Acacia caes", WFO.file=WFO.file.RK, Fuzzy=0.01, Fuzzy.within=TRUE, verbose=TRUE) # show all the matches for a genus spec.test1 <- data.frame(Genus=c("Casimiroa")) w8 <- WFO.match(spec.test1, WFO.file=WFO.file.RK, exclude.infraspecific=TRUE, verbose=TRUE) # show all listings at a next hierarchical level WFO.data1 <- data.table::fread(WFO.file.RK, encoding="UTF-8") WFO.browse("Pinaceae", WFO.data=WFO.data1) WFO.browse("Pinaceae", WFO.data=WFO.data1, accepted.only=T) WFO.browse("Tsuga", WFO.data=WFO.data1) WFO.browse("Tsuga", WFO.data=WFO.data1, accepted.only=T) WFO.browse("Olea europaea", WFO.data=WFO.data1) WFO.browse("Olea europaea", WFO.data=WFO.data1, accepted.only=T) # browsing only works at family, genus and species levels # for orders, however, information is given from vascular.families WFO.browse("Polypodiales", WFO.data=WFO.data1) # submitting no name results in a list of all families WFO.browse(, WFO.data=WFO.data1) # give synonyms WFO.synonyms("Olea europaea", WFO.data=WFO.data1) # give order and other higher levels from family WFO.family("Olea europaea", WFO.data=WFO.data1) ## End(Not run)
An alternative and typically faster method of matching records than WFO.match that allows for different methods of calculating the fuzzy distance via stringdist.
WFO.match.fuzzyjoin(spec.data = NULL, WFO.file = NULL, WFO.data = NULL, no.dates = TRUE, spec.name = "spec.name", Authorship = "Authorship", stringdist.method = "lv", fuzzydist.max = 4, Fuzzy.min = TRUE, acceptedNameUsageID.match = TRUE, squish = TRUE, spec.name.tolower = FALSE, spec.name.nonumber = TRUE, spec.name.nobrackets = TRUE, spec.name.sub = TRUE, sub.pattern=c(" sp[.] A", " sp[.] B", " sp[.] C", " sp[.]", " spp[.]", " pl[.]", " indet[.]", " ind[.]", " gen[.]", " g[.]", " fam[.]", " nov[.]", " prox[.]", " cf[.]", " aff[.]", " s[.]s[.]", " s[.]l[.]", " p[.]p[.]", " p[.] p[.]", "[?]", " inc[.]", " stet[.]", "Ca[.]", "nom[.] cons[.]", "nom[.] dub[.]", " nom[.] err[.]", " nom[.] illeg[.]", " nom[.] inval[.]", " nom[.] nov[.]", " nom[.] nud[.]", " nom[.] obl[.]", " nom[.] prot[.]", " nom[.] rej[.]", " nom[.] supp[.]", " sensu auct[.]"))WFO.match.fuzzyjoin(spec.data = NULL, WFO.file = NULL, WFO.data = NULL, no.dates = TRUE, spec.name = "spec.name", Authorship = "Authorship", stringdist.method = "lv", fuzzydist.max = 4, Fuzzy.min = TRUE, acceptedNameUsageID.match = TRUE, squish = TRUE, spec.name.tolower = FALSE, spec.name.nonumber = TRUE, spec.name.nobrackets = TRUE, spec.name.sub = TRUE, sub.pattern=c(" sp[.] A", " sp[.] B", " sp[.] C", " sp[.]", " spp[.]", " pl[.]", " indet[.]", " ind[.]", " gen[.]", " g[.]", " fam[.]", " nov[.]", " prox[.]", " cf[.]", " aff[.]", " s[.]s[.]", " s[.]l[.]", " p[.]p[.]", " p[.] p[.]", "[?]", " inc[.]", " stet[.]", "Ca[.]", "nom[.] cons[.]", "nom[.] dub[.]", " nom[.] err[.]", " nom[.] illeg[.]", " nom[.] inval[.]", " nom[.] nov[.]", " nom[.] nud[.]", " nom[.] obl[.]", " nom[.] prot[.]", " nom[.] rej[.]", " nom[.] supp[.]", " sensu auct[.]"))
spec.data |
A data.frame containing variables with species names. In case that a character vector is provided, then this vector will be converted to a data.frame |
WFO.file |
File name of the static copy of the Taxonomic Backbone. If not |
WFO.data |
Data set with the static copy of the Taxonomic Backbone. Ignored if |
no.dates |
Speeding up the loading of the WFO.data by not loading fields of 'created' and 'modified'. |
spec.name |
Name of the column with taxonomic names. |
Authorship |
Name of the column with the naming authorities. |
stringdist.method |
Method used to calculate the fuzzy distance as used by in the internally called |
fuzzydist.max |
Maximum distance used for joining as in |
Fuzzy.min |
Limit the results of fuzzy matching to those with the smallest distance. |
acceptedNameUsageID.match |
If |
squish |
If |
spec.name.tolower |
If |
spec.name.nonumber |
If |
spec.name.nobrackets |
If |
spec.name.sub |
If |
sub.pattern |
Sections of the |
This function matches plant names by using the stringdist_left_join function internally. The results are provided in a similar formatto those from WFO.match; therefore the WFO.one function can be used in a next step of the analysis.
For large data sets the function may fail due to memory limits. A solution is to analyse different subsets of large data, as for example shown by Kindt (2023).
Column 'Unique' shows whether there was a unique match (or not match) in the WFO.
Column 'Matched' shows whether there was a match in the WFO.
Column 'Fuzzy' shows whether matching was done by the fuzzy method.
Column 'Fuzzy.dist' gives the fuzzy distance calculated between submitted and matched plant names, calculated internally with stringdist_left_join.
Column 'Auth.dist' gives the Levenshtein distance calculated between submitted and matched authorship names, if the former were provided. This distance is calculated in the same way as for the WFO.match function via adist.
Column 'Subseq' gives different numbers for different matches for the same plant name.
Column 'Hybrid' shows whether there was a hybrid character in the scientificName.
Column 'New.accepted' shows whether the species details correspond to the current accepted name.
Column 'Old.status' gives the taxonomic status of the first match with the non-blank acceptedNameUsageID.
Column 'Old.ID' gives the ID of the first match with the non-blank acceptedNameUsageID.
Column 'Old.name' gives the name of the first match with the non-blank acceptedNameUsageID.
The main function returns a data.set with the matched species details from the WFO.
Roeland Kindt (World Agroforestry, CIFOR-ICRAF)
World Flora Online. An Online Flora of All Known Plants. https://www.worldfloraonline.org
Sigovini M, Keppel E, Tagliapietra. 2016. Open Nomenclature in the biodiversity era. Methods in Ecology and Evolution 7: 1217-1225.
Kindt, R. 2020. WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data. Applications in Plant Sciences 8(9): e11388
Kindt, R. 2023. Standardizing tree species names of GlobalTreeSearch with WorldFlora while testing the faster matching function of WFO.match.fuzzyjoin. https://rpubs.com/Roeland-KINDT/996500
## Not run: data(WFO.example) library(fuzzyjoin) spec.test <- data.frame(spec.name=c("Faidherbia albida", "Acacia albida", "Faidherbia albiad", "Omalanthus populneus", "Pygeum afric")) WFO.match.fuzzyjoin(spec.data=spec.test, WFO.data=WFO.example) # Using the Damerau-Levenshtein distance WFO.match.fuzzyjoin(spec.data=spec.test, WFO.data=WFO.example, stringdist.method="dl") ## End(Not run)## Not run: data(WFO.example) library(fuzzyjoin) spec.test <- data.frame(spec.name=c("Faidherbia albida", "Acacia albida", "Faidherbia albiad", "Omalanthus populneus", "Pygeum afric")) WFO.match.fuzzyjoin(spec.data=spec.test, WFO.data=WFO.example) # Using the Damerau-Levenshtein distance WFO.match.fuzzyjoin(spec.data=spec.test, WFO.data=WFO.example, stringdist.method="dl") ## End(Not run)
The main function of WFO.prepare attempts to split a list of species names with naming authorities in different fields of botanical names and authorities.
WFO.prepare(spec.data = NULL, spec.full="spec.full", squish = TRUE, spec.name.nonumber = TRUE, spec.name.sub = TRUE, sub.pattern = c(" sp[.] A", " sp[.] B", " sp[.] C", " sp[.]", " spp[.]", " pl[.]", " indet[.]", " ind[.]", " gen[.]", " g[.]", " fam[.]", " nov[.]", " prox[.]", " cf[.]", " aff[.]", " s[.]s[.]", " s[.]l[.]", " p[.]p[.]", " p[.] p[.]", "[?]", " inc[.]", " stet[.]", "Ca[.]", "nom[.] cons[.]", "nom[.] dub[.]", " nom[.] err[.]", " nom[.] illeg[.]", " nom[.] inval[.]", " nom[.] nov[.]", " nom[.] nud[.]", " nom[.] obl[.]", " nom[.] prot[.]", " nom[.] rej[.]", " nom[.] supp[.]", " sensu auct[.]"), genus.2.flag = TRUE, species.2.flag = TRUE, punctuation.flag = TRUE, pointless.flag = TRUE, trinomial = c("cultivar.", "f.", "sect.", "subf.", "subg.", "subsp.", "subvar.", "var.", "CULTIVAR.", "SECT.", "SUBF.", "SUBG.", "SUBSP.", "SUBVAR.", "VAR."), authors.ending.f=c("Aiton f.", "Baker f.", "Bak. f.", "Burm. f.", "Cheng f.", "Chrtek f.", "De Marco f.", "Fang f.", "Ferry f.", "Forsyth f.", "Forster f.", "Fraser f.", "G.Don f.", "Haller f.", "Hallier f.", "Hook. f.", "Hooker f.", "Hsueh f.", "J.Kickx f.", "J. Kickx f.", "Keng f.", "Kickx f.", "Klokov f.", "Koster f.", "Liou f.", "L. f.", "Ma f.", "Mikan f.", "Occhioni f.", "Rchb. f.", "Schultes f.", "Schult. f.", "Stapf f."), verbose = TRUE, counter = 1000) WFO.preprepare(spec.data=NULL, spec.full="spec.full", trinomial.first="subsp.", trinomial.second="var.")WFO.prepare(spec.data = NULL, spec.full="spec.full", squish = TRUE, spec.name.nonumber = TRUE, spec.name.sub = TRUE, sub.pattern = c(" sp[.] A", " sp[.] B", " sp[.] C", " sp[.]", " spp[.]", " pl[.]", " indet[.]", " ind[.]", " gen[.]", " g[.]", " fam[.]", " nov[.]", " prox[.]", " cf[.]", " aff[.]", " s[.]s[.]", " s[.]l[.]", " p[.]p[.]", " p[.] p[.]", "[?]", " inc[.]", " stet[.]", "Ca[.]", "nom[.] cons[.]", "nom[.] dub[.]", " nom[.] err[.]", " nom[.] illeg[.]", " nom[.] inval[.]", " nom[.] nov[.]", " nom[.] nud[.]", " nom[.] obl[.]", " nom[.] prot[.]", " nom[.] rej[.]", " nom[.] supp[.]", " sensu auct[.]"), genus.2.flag = TRUE, species.2.flag = TRUE, punctuation.flag = TRUE, pointless.flag = TRUE, trinomial = c("cultivar.", "f.", "sect.", "subf.", "subg.", "subsp.", "subvar.", "var.", "CULTIVAR.", "SECT.", "SUBF.", "SUBG.", "SUBSP.", "SUBVAR.", "VAR."), authors.ending.f=c("Aiton f.", "Baker f.", "Bak. f.", "Burm. f.", "Cheng f.", "Chrtek f.", "De Marco f.", "Fang f.", "Ferry f.", "Forsyth f.", "Forster f.", "Fraser f.", "G.Don f.", "Haller f.", "Hallier f.", "Hook. f.", "Hooker f.", "Hsueh f.", "J.Kickx f.", "J. Kickx f.", "Keng f.", "Kickx f.", "Klokov f.", "Koster f.", "Liou f.", "L. f.", "Ma f.", "Mikan f.", "Occhioni f.", "Rchb. f.", "Schultes f.", "Schult. f.", "Stapf f."), verbose = TRUE, counter = 1000) WFO.preprepare(spec.data=NULL, spec.full="spec.full", trinomial.first="subsp.", trinomial.second="var.")
spec.data |
A data.frame containing variables with species names. In case that a character vector is provided, then this vector will be converted to a data.frame |
spec.full |
Name of the column with full taxonomic names. |
squish |
If |
spec.name.nonumber |
If |
spec.name.sub |
If |
sub.pattern |
Sections of the |
genus.2.flag |
Flag first part of the names with only 2 characters. |
species.2.flag |
Flag second part of the names with only 2 characters. |
punctuation.flag |
Flag if the retained plant name has punctuation characters. |
pointless.flag |
Flag if the retained plant name has sub.pattern without the point. |
trinomial |
Descriptors for trinomial names. In case a trinomial name is expected, the species name will be obtained from the first two words and the two words starting with the trinomial descriptor. |
authors.ending.f |
Author names that end with ' f.', not confuse the function about trinomials with 'f.', indicating 'filius' ('son of'). |
verbose |
Give details on the process. |
counter |
Progress on the process is reported by multiples of this counter. |
trinomial.first |
Pattern to split species name in different columns. |
trinomial.second |
Second pattern to split species name in different columns. |
Function WFO.prepare splits submitted names into the botanical name ('spec.name') and the naming authority ('Authorship'). When the submitted name contains section between brackets that are not at the beginning of the naming authority, these sections will be removed. Function WFO.preprepare was designed to deal with situations where author names are given at species and infra-specific levels (see examples).
The function splits names in the botanical name and the naming authority.
Roeland Kindt (World Agroforestry)
## Not run: WFO.prepare("Terminalia superba Engl. & Diels (**) (In review)") WFO.prepare("Sorbus aucuparia subsp. praemorsa (Guss.) Nyman") WFO.prepare("Ormosia aff. coarctata Jackson") WFO.prepare("Ormosia aff coarctata Jackson") WFO.prepare("Ormosia /coarctata Jackson") WFO.prepare("Qualea TMG 148 Aubl.") # Note that the sub.pattern is ' cf.' WFO.prepare("cf Myrcia M1") # Dealing with author names that end with ' f.' ('filius') WFO.prepare("Malveopsis scabrosum Stapf f.") # Using preprepare to deal with authorities at multiple levels WFO.preprepare("Agave deserti Engelm. subsp. simplex Gentry") WFO.preprepare("Zoysia matrella (L.) Merr. var. pacifica Goudsw.") test.name <- paste0("Agastache pallidiflora (A. Heller) Rydb.", " subsp. neomexicana (Briq.) Lint & Epling", " var. havardii (A. Gray) R.W. Sanders") WFO.preprepare(test.name) ## End(Not run)## Not run: WFO.prepare("Terminalia superba Engl. & Diels (**) (In review)") WFO.prepare("Sorbus aucuparia subsp. praemorsa (Guss.) Nyman") WFO.prepare("Ormosia aff. coarctata Jackson") WFO.prepare("Ormosia aff coarctata Jackson") WFO.prepare("Ormosia /coarctata Jackson") WFO.prepare("Qualea TMG 148 Aubl.") # Note that the sub.pattern is ' cf.' WFO.prepare("cf Myrcia M1") # Dealing with author names that end with ' f.' ('filius') WFO.prepare("Malveopsis scabrosum Stapf f.") # Using preprepare to deal with authorities at multiple levels WFO.preprepare("Agave deserti Engelm. subsp. simplex Gentry") WFO.preprepare("Zoysia matrella (L.) Merr. var. pacifica Goudsw.") test.name <- paste0("Agastache pallidiflora (A. Heller) Rydb.", " subsp. neomexicana (Briq.) Lint & Epling", " var. havardii (A. Gray) R.W. Sanders") WFO.preprepare(test.name) ## End(Not run)
The function remembers where the Taxonomic Backbone data was downloaded to. In case that no arguments are specified, then data.frame WFO.data will contain the previously specified Taxonomic Backbone data.
WFO.download(WFO.url = paste0("https://files.worldfloraonline.org/files/WFO_Backbone/", "_WFOCompleteBackbone/WFO_Backbone.zip"), save.dir = getwd(), WFO.remember = TRUE, timeout = 500, ...) WFO.remember(WFO.file = NULL, WFO.data = "WFO.data", WFO.pos = 1)WFO.download(WFO.url = paste0("https://files.worldfloraonline.org/files/WFO_Backbone/", "_WFOCompleteBackbone/WFO_Backbone.zip"), save.dir = getwd(), WFO.remember = TRUE, timeout = 500, ...) WFO.remember(WFO.file = NULL, WFO.data = "WFO.data", WFO.pos = 1)
WFO.url |
Hyperlink to the download from the World Flora Online. |
save.dir |
Directory where the file will be downloaded and unzipped. |
WFO.remember |
Remember the location of the file for |
timeout |
Timeout in seconds for some internet operations, to be modified among Options Settings. |
... |
Other arguments for download.file. |
WFO.file |
File path to the Taxonomic Backbone data ('classification.txt'). |
WFO.data |
Name of data set to be used by other WorldFlora functions. |
WFO.pos |
Argument pos as in assign. |
These functions avoid that a user needs to reload and re-specify the location of the Taxonomic Backbone data that was previously downloaded from the World Flora Online website. The location is saved in a text file in the 'etc' directory of the WorldFlora directory.
The function remembers the local location of the Taxonomic Backbone data.
Roeland Kindt (World Agroforestry)
## Not run: # change the working directory setwd(choose.dir()) # download the Taxonomic Backbone data WFO.download() # remember the previous download and avail the data as 'WFO.data' WFO.remember() # check WFO.match("Faidherbia albida", WFO.data=WFO.data) ## End(Not run)## Not run: # change the working directory setwd(choose.dir()) # download the Taxonomic Backbone data WFO.download() # remember the previous download and avail the data as 'WFO.data' WFO.remember() # check WFO.match("Faidherbia albida", WFO.data=WFO.data) ## End(Not run)