Type:	Package
Title:	Standardize Plant Names According to World Flora Online Taxonomic Backbone
Version:	1.14-5
Date:	2024-9-9
Author:	Roeland Kindt [cre, aut]
Maintainer:	Roeland Kindt <RoelandCEKindt@gmail.com>
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.
License:	GPL-3
Depends:	R (≥ 3.5.0)
Suggests:	data.table, utils, stringr, dplyr, fuzzyjoin, stringdist
Packaged:	2024-09-10 08:15:45 UTC; RKINDT
NeedsCompilation:	no
Repository:	CRAN
Date/Publication:	2024-09-10 09:50:15 UTC

Check for fuzzy matches that can be acceptable based on gender notations

Description

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.

Usage

    WFO.acceptable.match(x, spec.name="spec.name",
      no.vowels=FALSE)

Arguments

Details

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)

Value

The function returns a logical vector that indicates whether names could be acceptable.

Author(s)

Roeland Kindt (World Agroforestry)

Examples

## 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)

World Flora Online (WFO) taxonomic backbone example data set

Description

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).

Usage

data(WFO.example)

Source

World Flora Online. An Online Flora of All Known Plants. https://www.worldfloraonline.org

Examples

data(WFO.example)

Standardize plant names according to World Flora Online taxonomic backbone

Description

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).

Usage

    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, ...)

Arguments

Details

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.

Value

The main function returns a data.set with the matched species details from the WFO.

Author(s)

Roeland Kindt (World Agroforestry, CIFOR-ICRAF)

References

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

See Also

WFO.match.fuzzyjoin

Examples

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)

Standardize plant names according to World Flora Online taxonomic backbone

Description

An alternative and typically faster method of matching records than WFO.match that allows for different methods of calculating the fuzzy distance via stringdist.

Usage

    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[.]"))

Arguments

Details

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.

Value

The main function returns a data.set with the matched species details from the WFO.

Author(s)

Roeland Kindt (World Agroforestry, CIFOR-ICRAF)

References

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

See Also

WFO.match

Examples

## 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)

Prepare a data set for analysis with WFO.match

Description

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.

Usage

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.")     
    

Arguments

Details

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).

Value

The function splits names in the botanical name and the naming authority.

Author(s)

Roeland Kindt (World Agroforestry)

Examples

## 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)

Remember the location of the Taxonomic Backbone data set

Description

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.

Usage

    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)

Arguments

Details

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.

Value

The function remembers the local location of the Taxonomic Backbone data.

Author(s)

Roeland Kindt (World Agroforestry)

Examples

## 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)

Develop a User-created Taxonomic Backbone data set

Description

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.

Usage

new.backbone(x,
    taxonID = "taxonID", scientificName = "scientificName",
    scientificNameAuthorship = "scientificNameAuthorship",
    acceptedNameUsageID = NULL, taxonomicStatus = NULL
)

Arguments

Details

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.

Value

The function returns a data.table that can be understood by WFO.match and WFO.one for standardizing taxonomic names.

Author(s)

Roeland Kindt (World Agroforestry)

References

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

See Also

WFO.match, WFO.one

Examples

## 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)

Orders and Higher Level Classifications of Vascular Plants

Description

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.

Usage

data(vascular.families)

Format

A data frame with 476 observations on the following 10 variables.

Group

Group.

Family.ID

Unique ID for each family. For angiosperms, these correspond to APG IV.

Family

Name of the plant family.

Family.taxonID

taxonID retrieved from World Flora Online.

Order

Name of the plant order.

Order.taxonID

taxonID retrieved from World Flora Online.

Node.1

Name of the node in the consensus tree.

Node.2

Name of the node in the consensus tree, with Node.2 nested within Node.1.

Node.3

Name of the node in the consensus tree, with Node.3 nested within Node.2.

Node.4

Name of the node in the consensus tree, with Node.4 nested within Node.3.

References

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

Examples

data(vascular.families)