library(WorldFlora)
library(data.table)
library(dplyr)The WorldFlora package (Kindt 2020) was originally designed to use the taxonomic backbone data of World Flora Online (WFO; Borsch et al. 2020; www.worldfloraonline.org).
A new function new.backbone introduced in version 1.8 of the package now allows to use alternative taxonomic backbone data sets. What is required is that the new backbone data includes a key subset of variables that correspond to variables of World Flora Online.
The example here will standardize species names via the World Checklist of Vascular Plants (version 6 of September 2021; Govaerts et al. 2021).
WCVP (2021). World Checklist of Vascular Plants, version 2.0. Facilitated by the Royal Botanic Gardens, Kew. Published on the Internet; http://wcvp.science.kew.org/ Retrieved 21 September 2021
The checklist was downloaded to a local folder and then loaded via the following script:
data.dir <- "E:\\Roeland\\R\\World Flora Online\\2021"
WCVP <- fread(paste0(data.dir, "//wcvp_v6_sep_2021.txt"),
encoding="UTF-8")
nrow(WCVP)## [1] 1196875head(WCVP)## kew_id family genus species infraspecies
## 1: 338-1 Acanthaceae Acanthodium
## 2: 44787-1 Acanthaceae Acanthodium angustum
## 3: 44788-1 Acanthaceae Acanthodium capense
## 4: 44789-1 Acanthaceae Acanthodium carduifolium
## 5: 44790-1 Acanthaceae Acanthodium delilii
## 6: 44792-1 Acanthaceae Acanthodium diversispinum
## taxon_name authors rank taxonomic_status
## 1: Acanthodium Delile GENUS Synonym
## 2: Acanthodium angustum Nees SPECIES Homotypic_Synonym
## 3: Acanthodium capense (L.f.) Nees SPECIES Homotypic_Synonym
## 4: Acanthodium carduifolium (L.f.) Nees SPECIES Homotypic_Synonym
## 5: Acanthodium delilii H.Buek SPECIES Synonym
## 6: Acanthodium diversispinum Nees SPECIES Homotypic_Synonym
## accepted_kew_id accepted_name accepted_authors parent_kew_id
## 1: 427-1 Blepharis Juss.
## 2: 46469-1 Blepharis angusta (Nees) T.Anderson
## 3: 46487-1 Blepharis capensis (L.f.) Pers.
## 4: 44830-1 Acanthopsis carduifolia (L.f.) Schinz
## 5: 46503-1 Blepharis edulis (Forssk.) Pers.
## 6: 46501-1 Blepharis diversispina (Nees) C.B.Clarke
## parent_name parent_authors reviewed
## 1: In review
## 2: In review
## 3: In review
## 4: In review
## 5: In review
## 6: In review
## publication original_name_id
## 1: Descr. Egypte, Hist. Nat. 2(Mém.): 241 (1813)
## 2: A.P.de Candolle, Prodr. 11: 273 (1847)
## 3: Linnaea 15: 361 (1841)
## 4: A.P.de Candolle, Prodr. 11: 278 (1847) 44848-1
## 5: Gen. Sp. Candoll. 3: 1 (1858)
## 6: A.P.de Candolle, Prodr. 11: 275 (1847)tail(WCVP)## kew_id family genus species infraspecies
## 1: 873720-1 Zygophyllaceae Zygophyllum waterlotii
## 2: 873721-1 Zygophyllaceae Zygophyllum webbianum
## 3: 77205534-1 Zygophyllaceae Zygophyllum xanthoxylum
## 4: 873723-1 Zygophyllaceae Zygophyllum zanthoxylum
## 5: 77184991-1 Zygophyllaceae Zygophyllum zilloides
## 6: 873724-1 Zygophyllaceae Zygophyllum zonuzensis
## taxon_name authors rank
## 1: Zygophyllum waterlotii Maire SPECIES
## 2: Zygophyllum webbianum Coss. SPECIES
## 3: Zygophyllum xanthoxylum (Bunge) Maxim. SPECIES
## 4: Zygophyllum zanthoxylum Engl. ex Dippel SPECIES
## 5: Zygophyllum zilloides (Humbert) Christenh. & Byng SPECIES
## 6: Zygophyllum zonuzensis Sabeti SPECIES
## taxonomic_status accepted_kew_id accepted_name
## 1: Homotypic_Synonym 967774-1 Zygophyllum gaetulum subsp. waterlotii
## 2: Synonym 873565-1 Zygophyllum fontanesii
## 3: Accepted
## 4: Synonym 77205534-1 Zygophyllum xanthoxylum
## 5: Accepted
## 6: Synonym
## accepted_authors parent_kew_id parent_name
## 1: (Maire) Dobignard, Jacquemoud & D.Jord.
## 2: Webb & Berthel.
## 3: 41749-1 Zygophyllum
## 4: (Bunge) Maxim.
## 5: 41749-1 Zygophyllum
## 6:
## parent_authors reviewed publication
## 1: In review Bull. Soc. Hist. Nat. Afrique N. 28: 348 (1937)
## 2: In review Bull. Soc. Bot. France 2: 365 (1855)
## 3: L. In review Fl. Tangut.: 103 (1889)
## 4: In review Handb. Laubholzk. 2: 358 (1893)
## 5: L. In review Global Fl. 4: 93 (2018)
## 6: In review Forests, Trees & Shrubs of Iran: 12 (1976)
## original_name_id
## 1:
## 2:
## 3: 873370-1
## 4:
## 5: 873235-1
## 6:In the WFO, the format for hybrid species names is ‘Fragaria ×ananassa’ instead of the format of ‘Fragaria × ananassa’ used in the WCVP. The format of WFO works better with the name matching algorithms of WorldFlora.
WCVP[WCVP$genus == "Fragaria" & WCVP$species == "ananassa", "taxon_name"]## taxon_name
## 1: Fragaria × ananassa
## 2: Fragaria × ananassa nothosubsp. cuneifoliaThe following script does the job. But this process to be very slow, so instead I made the replacement of ’ × ’ by ’ ×’ in a text editor (EditPad) and then loaded the modified text file.
# following codes is not run
# pattern1 <- paste(" ", intToUtf8(215), " ", sep="")
# pattern2 <- paste(" ", intToUtf8(215), sep="")
#for (i in 1:nrow(WCVP)) {
# if (round(i/100000) == i/100000) {cat(paste("Reached record ", i, "\n"))}
# if (grepl(pattern=pattern1, x=WCVP[i, "taxon_name"]) == TRUE) {
# WCVP[i, "taxon_name"] <- gsub(pattern=pattern1,
# replacement=pattern2,
# x=WCVP[i, "taxon_name"])
# }
#}
# read in the modified text file
WCVP <- fread(paste0(data.dir, "//wcvp_v6_sep_2021 - no spacexspace.txt"),
encoding="UTF-8")
nrow(WCVP)## [1] 1196875WCVP[WCVP$genus == "Fragaria" & WCVP$species == "ananassa", "taxon_name"]## taxon_name
## 1: Fragaria ×ananassa
## 2: Fragaria ×ananassa nothosubsp. cuneifoliaNow the WorldFlora function of new.backbone can be used to create a reference data set that can be used by WorldFlora.
WCVP.data <- new.backbone(WCVP,
taxonID="kew_id",
scientificName="taxon_name",
scientificNameAuthorship="authors",
acceptedNameUsageID = "accepted_kew_id",
taxonomicStatus = "taxonomic_status")
head(WCVP.data)## taxonID scientificName scientificNameAuthorship
## 1: 338-1 Acanthodium Delile
## 2: 44787-1 Acanthodium angustum Nees
## 3: 44788-1 Acanthodium capense (L.f.) Nees
## 4: 44789-1 Acanthodium carduifolium (L.f.) Nees
## 5: 44790-1 Acanthodium delilii H.Buek
## 6: 44792-1 Acanthodium diversispinum Nees
## acceptedNameUsageID taxonomicStatus kew_id family genus
## 1: 427-1 Synonym 338-1 Acanthaceae Acanthodium
## 2: 46469-1 Homotypic_Synonym 44787-1 Acanthaceae Acanthodium
## 3: 46487-1 Homotypic_Synonym 44788-1 Acanthaceae Acanthodium
## 4: 44830-1 Homotypic_Synonym 44789-1 Acanthaceae Acanthodium
## 5: 46503-1 Synonym 44790-1 Acanthaceae Acanthodium
## 6: 46501-1 Homotypic_Synonym 44792-1 Acanthaceae Acanthodium
## species infraspecies taxon_name authors rank
## 1: Acanthodium Delile GENUS
## 2: angustum Acanthodium angustum Nees SPECIES
## 3: capense Acanthodium capense (L.f.) Nees SPECIES
## 4: carduifolium Acanthodium carduifolium (L.f.) Nees SPECIES
## 5: delilii Acanthodium delilii H.Buek SPECIES
## 6: diversispinum Acanthodium diversispinum Nees SPECIES
## taxonomic_status accepted_kew_id accepted_name accepted_authors
## 1: Synonym 427-1 Blepharis Juss.
## 2: Homotypic_Synonym 46469-1 Blepharis angusta (Nees) T.Anderson
## 3: Homotypic_Synonym 46487-1 Blepharis capensis (L.f.) Pers.
## 4: Homotypic_Synonym 44830-1 Acanthopsis carduifolia (L.f.) Schinz
## 5: Synonym 46503-1 Blepharis edulis (Forssk.) Pers.
## 6: Homotypic_Synonym 46501-1 Blepharis diversispina (Nees) C.B.Clarke
## parent_kew_id parent_name parent_authors reviewed
## 1: In review
## 2: In review
## 3: In review
## 4: In review
## 5: In review
## 6: In review
## publication original_name_id
## 1: Descr. Egypte, Hist. Nat. 2(Mém.): 241 (1813)
## 2: A.P.de Candolle, Prodr. 11: 273 (1847)
## 3: Linnaea 15: 361 (1841)
## 4: A.P.de Candolle, Prodr. 11: 278 (1847) 44848-1
## 5: Gen. Sp. Candoll. 3: 1 (1858)
## 6: A.P.de Candolle, Prodr. 11: 275 (1847)tail(WCVP.data)## taxonID scientificName scientificNameAuthorship
## 1: 873720-1 Zygophyllum waterlotii Maire
## 2: 873721-1 Zygophyllum webbianum Coss.
## 3: 77205534-1 Zygophyllum xanthoxylum (Bunge) Maxim.
## 4: 873723-1 Zygophyllum zanthoxylum Engl. ex Dippel
## 5: 77184991-1 Zygophyllum zilloides (Humbert) Christenh. & Byng
## 6: 873724-1 Zygophyllum zonuzensis Sabeti
## acceptedNameUsageID taxonomicStatus kew_id family genus
## 1: 967774-1 Homotypic_Synonym 873720-1 Zygophyllaceae Zygophyllum
## 2: 873565-1 Synonym 873721-1 Zygophyllaceae Zygophyllum
## 3: Accepted 77205534-1 Zygophyllaceae Zygophyllum
## 4: 77205534-1 Synonym 873723-1 Zygophyllaceae Zygophyllum
## 5: Accepted 77184991-1 Zygophyllaceae Zygophyllum
## 6: Synonym 873724-1 Zygophyllaceae Zygophyllum
## species infraspecies taxon_name authors
## 1: waterlotii Zygophyllum waterlotii Maire
## 2: webbianum Zygophyllum webbianum Coss.
## 3: xanthoxylum Zygophyllum xanthoxylum (Bunge) Maxim.
## 4: zanthoxylum Zygophyllum zanthoxylum Engl. ex Dippel
## 5: zilloides Zygophyllum zilloides (Humbert) Christenh. & Byng
## 6: zonuzensis Zygophyllum zonuzensis Sabeti
## rank taxonomic_status accepted_kew_id
## 1: SPECIES Homotypic_Synonym 967774-1
## 2: SPECIES Synonym 873565-1
## 3: SPECIES Accepted
## 4: SPECIES Synonym 77205534-1
## 5: SPECIES Accepted
## 6: SPECIES Synonym
## accepted_name
## 1: Zygophyllum gaetulum subsp. waterlotii
## 2: Zygophyllum fontanesii
## 3:
## 4: Zygophyllum xanthoxylum
## 5:
## 6:
## accepted_authors parent_kew_id parent_name
## 1: (Maire) Dobignard, Jacquemoud & D.Jord.
## 2: Webb & Berthel.
## 3: 41749-1 Zygophyllum
## 4: (Bunge) Maxim.
## 5: 41749-1 Zygophyllum
## 6:
## parent_authors reviewed publication
## 1: In review Bull. Soc. Hist. Nat. Afrique N. 28: 348 (1937)
## 2: In review Bull. Soc. Bot. France 2: 365 (1855)
## 3: L. In review Fl. Tangut.: 103 (1889)
## 4: In review Handb. Laubholzk. 2: 358 (1893)
## 5: L. In review Global Fl. 4: 93 (2018)
## 6: In review Forests, Trees & Shrubs of Iran: 12 (1976)
## original_name_id
## 1:
## 2:
## 3: 873370-1
## 4:
## 5: 873235-1
## 6:The GlobalTreeSearch database provides a global list of tree species names, compiled by a process documented in Beech et al. 2020. The version of GTS used here was version 1.5 of March 2021.
Before loading, a change was made for Monoon shendurunii to only list the first set of authors for this species.
GTS <- read.csv(paste0(data.dir, "//global_tree_search.csv"))
GTS <- GTS[, 1:2]
nrow(GTS)## [1] 58497head(GTS)## TaxonName Author
## 1 Abarema abbottii (Rose & Leonard) Barneby & J.W.Grimes
## 2 Abarema acreana (J.F.Macbr.) L.Rico
## 3 Abarema adenophora (Ducke) Barneby & J.W.Grimes
## 4 Abarema alexandri (Urb.) Barneby & J.W.Grimes
## 5 Abarema asplenifolia (Griseb.) Barneby & J.W.Grimes
## 6 Abarema auriculata (Benth.) Barneby & J.W.GrimesThe species names can now be checked via the functions of WFO.match and WFO.one of WorldFlora.
GTS.match.test <- WFO.one(WFO.match(GTS[1:1000, ],
WFO.data = WCVP.data,
spec.name = "TaxonName",
Authorship = "Author"))## Fuzzy matches for Abarema cochliocarpos were: Abarema cochliacarpos## Fuzzy matches for Acacia macdonnellensis were: Olearia macdonnellensis, Acacia macdonnelliensis, Acacia macdonnelliensis subsp. macdonnelliensis, Acacia macdonnelliensis subsp. teretifolia## Best fuzzy matches for Acacia macdonnellensis were: Acacia macdonnelliensis## Fuzzy matches for Acropogon calcicolus were: Acropogon calcicola## Fuzzy matches for Acropogon sageniifolius were: Acropogon sageniifolia## Reached record # 1000## Fuzzy matches for Acropogon schumannianus were: Acropogon schumanniana##
## Checking new accepted IDs## Reached record # 1000## Different candidates for original record # 53, including Abies alba## Found unique non-synonym case for record # 53## Different candidates for original record # 54, including Abies lasiocarpa var. lasiocarpa## Found unique non-synonym case for record # 54## Different candidates for original record # 69, including Abies forrestii var. forrestii## Found unique non-synonym case for record # 69## Different candidates for original record # 80, including Abies grandis## Found unique non-synonym case for record # 80## Different candidates for original record # 119, including Abuta rufescens## Found unique non-synonym case for record # 119## Different candidates for original record # 149, including Acacia amoena## Found unique non-synonym case for record # 149## Different candidates for original record # 182, including Acacia binervata## Found unique non-synonym case for record # 182## Different candidates for original record # 198, including Acacia calamifolia## Found unique non-synonym case for record # 198## Different candidates for original record # 216, including Acacia conniana## Found unique non-synonym case for record # 216## Different candidates for original record # 218, including Acacia colletioides## Found unique non-synonym case for record # 218## Different candidates for original record # 249, including Acacia dealbata## Found unique non-synonym case for record # 249## Different candidates for original record # 270, including Acacia doratoxylon## Found unique non-synonym case for record # 270## Different candidates for original record # 277, including Albizia procera## Found unique non-synonym case for record # 277## Different candidates for original record # 289, including Acacia falcata## Found unique non-synonym case for record # 289## Different candidates for original record # 325, including Acacia koa## Found unique non-synonym case for record # 325## Different candidates for original record # 347, including Acacia julifera## Found unique non-synonym case for record # 347## Different candidates for original record # 359, including Acacia melanoxylon## Found unique non-synonym case for record # 359## Different candidates for original record # 374, including Acacia linearifolia## Found unique non-synonym case for record # 374## Different candidates for original record # 377, including Acacia dentifera## Found unique non-synonym case for record # 377## Different candidates for original record # 409, including Paraserianthes lophantha subsp. montana## Found unique non-synonym case for record # 409## Different candidates for original record # 410, including Senegalia montigena## Found unique non-synonym case for record # 410## Different candidates for original record # 447, including Senegalia hamulosa## Found unique non-synonym case for record # 447## Different candidates for original record # 476, including Acacia pubescens## Found unique Accepted case for record # 476## Different candidates for original record # 500, including Acacia rostellifera## Found unique non-synonym case for record # 500## Different candidates for original record # 577, including Acacia verticillata## Found unique non-synonym case for record # 577## Different candidates for original record # 616, including Acalypha glabrata## Found unique non-synonym case for record # 616## Different candidates for original record # 654, including Acalypha villosa## Found unique non-synonym case for record # 654## Different candidates for original record # 680, including Acer amoenum## Found unique Accepted case for record # 680## Different candidates for original record # 716, including Acer macrophyllum## Smallest ID candidates for 716 were: Acer campbellii subsp. flabellatum, Acer macrophyllum## Selected record with smallest ID for record # 716## Different candidates for original record # 772, including Acer palmatum## Found unique non-synonym case for record # 772## Different candidates for original record # 775, including Acer acuminatum## Found unique non-synonym case for record # 775## Different candidates for original record # 828, including Acer velutinum## Found unique non-synonym case for record # 828## Different candidates for original record # 895, including Sweetia fruticosa## Found unique non-synonym case for record # 895## Reached case # 1000When checking the full species list, details of the matching process are not shown by setting the argument of ‘verbose’ to FALSE. This is done here simply to reduce the size of the output file, but in practical applications, typically with smaller data sets, I recommend to display these details.
GTS.match <- WFO.one(WFO.match(GTS,
WFO.data = WCVP.data,
spec.name = "TaxonName",
Authorship = "Author",
verbose = FALSE,
counter = 5000),
verbose = FALSE, counter = 10000)## Reached record # 5000## Reached record # 10000## Reached record # 15000## Reached record # 20000## Reached record # 25000## Reached record # 30000## Reached record # 35000## Reached record # 40000## Reached record # 45000## Reached record # 50000## Reached record # 55000##
## Checking new accepted IDs## Reached record # 5000## Reached record # 10000## Reached record # 15000## Reached record # 20000## Reached record # 25000## Reached record # 30000## Reached record # 35000## Reached record # 40000## Reached record # 45000## Reached record # 50000## Reached record # 55000## Reached record # 60000## Reached case # 10000## Reached case # 20000## Reached case # 30000## Reached case # 40000## Reached case # 50000For the majority of GTS species, there was a direct match with a species name in WCSP.
nrow(GTS.match[GTS.match$Fuzzy == FALSE, ])## [1] 57918nrow(GTS.match[GTS.match$Fuzzy == FALSE, ]) / nrow(GTS.match)## [1] 0.9901021nrow(GTS.match[GTS.match$Fuzzy == TRUE, ])## [1] 579nrow(GTS.match[GTS.match$Fuzzy == TRUE, ]) / nrow(GTS.match)## [1] 0.009897943The following script saves copies of the matched names and details about the matching process.
GTS.m <- GTS.match[GTS.match$Fuzzy==FALSE, ]
GTS.m <- GTS.m[, c("TaxonName", "Author",
"kew_id", "family", "taxon_name", "taxonomic_status",
"authors", "Auth.dist",
"New.accepted", "Old.status")]
GTS.m.file <- paste0(data.dir, "/GTS direct match.txt")
write.table(GTS.m, file=GTS.m.file,
quote=FALSE, sep="|",
row.names=FALSE,
fileEncoding="UTF-8")
GTS.nm <- GTS.match[GTS.match$Fuzzy==TRUE, ]
GTS.nm.file <- paste0(data.dir, "/GTS fuzzy match.txt")
write.table(GTS.nm, file=GTS.nm.file,
quote=FALSE, sep="|",
row.names=FALSE,
fileEncoding="UTF-8")For two tree species, no matching names could be found. Note that ‘Fuzzy’ is documented as FALSE, indicating that fuzzy matching was not used ultimately.
GTS.match[GTS.match$Matched == FALSE, ]## TaxonName Author TaxonName.ORIG Squished
## 24080 Gea crassifolia Achille Gea crassifolia FALSE
## 24531 Glycomosis superba B.C.Stone Glycomosis superba FALSE
## Brackets.detected Number.detected Unique Matched Fuzzy Fuzzy.toomany
## 24080 FALSE FALSE TRUE FALSE FALSE 585
## 24531 FALSE FALSE TRUE FALSE FALSE 0
## Fuzzy.two Fuzzy.one Fuzzy.dist Auth.dist OriSeq Subseq taxonID
## 24080 FALSE FALSE NA 7 24080 1
## 24531 FALSE TRUE NA 9 24531 1
## scientificName scientificNameAuthorship acceptedNameUsageID
## 24080
## 24531
## taxonomicStatus kew_id family genus species infraspecies taxon_name
## 24080
## 24531
## authors rank taxonomic_status accepted_kew_id accepted_name
## 24080
## 24531
## accepted_authors parent_kew_id parent_name parent_authors reviewed
## 24080
## 24531
## publication original_name_id Hybrid New.accepted Old.status Old.ID
## 24080 FALSE
## 24531 FALSE
## Old.name Old.author Old.author.dist One.Reason
## 24080
## 24531Over 3000 tree species were directly matched with a synonym.
nrow(GTS.m[GTS.m$New.accepted == TRUE, ])## [1] 3052GTS.m[GTS.m$New.accepted == TRUE, c("TaxonName", "taxon_name",
"taxonomic_status", "Old.status")][1:50, ]## TaxonName taxon_name
## 2 Abarema acreana Hydrochorea acreana
## 40 Abarema obovata Abarema brachystachya
## 129 Abutilon peruvianum Callianthe peruviana
## 130 Abutilon purpusii Callianthe purpusii
## 430 Acacia oliveri Senegalia senegal
## 440 Acacia ouyrarema Mimosa ouyrarema
## 456 Acacia pennivenia Vachellia pennivenia
## 602 Acalypha benensis Acalypha stricta
## 629 Acalypha multiflora Acalypha flagellata
## 652 Acalypha suirenbiensis Acalypha cardiophylla
## 675 Acca sellowiana Feijoa sellowiana
## 680.1 Acer amoenum Acer paihengii
## 682 Acer anhweiense Acer robustum
## 709 Acer divergens Acer cappadocicum subsp. divergens
## 716 Acer flabellatum Acer macrophyllum
## 717 Acer floridanum Acer saccharum subsp. floridanum
## 727 Acer heptaphlebium Acer campbellii subsp. flabellatum
## 729 Acer hookeri Acer sikkimense
## 734 Acer kawakamii Acer caudatifolium
## 744 Acer leucoderme Acer saccharum subsp. leucoderme
## 745 Acer lobelii Acer cappadocicum subsp. lobelii
## 756 Acer miaotaiense Acer miyabei subsp. miaotaiense
## 762 Acer nigrum Acer saccharum subsp. nigrum
## 766 Acer okamotoanum Acer pictum subsp. mono
## 770 Acer osmastonii Acer calcaratum
## 790 Acer rubescens Acer morrisonense
## 812 Acer takesimense Acer pseudosieboldianum
## 824 Acer turkestanicum Acer platanoides subsp. turkestanicum
## 860 Achuaria hirsuta Raputia hirsuta
## 886 Acnistus arborescens Iochroma arborescens
## 961 Acronychia porteri Maclurodendron porteri
## 1036 Actinodaphne cuspidata Actinodaphne notabilis
## 1052 Actinodaphne gullavara Actinodaphne angustifolia
## 1100 Actinodaphne philippinensis Litsea whitfordii
## 1161 Adelobotrys antioquiensis Meriania hoyosii
## 1397 Aequatorium cajamarcense Nordenstamia cajamarcensis
## 1398 Aequatorium carpishense Nordenstamia carpishensis
## 1401 Aequatorium limonense Nordenstamia limonensis
## 1403 Aequatorium rimachianum Nordenstamia rimachiana
## 1404 Aequatorium stellatopilosum Nordenstamia stellatopilosa
## 1406 Aeschrion cubensis Picrasma cubensis
## 1425 Aesculus wangii Aesculus assamica
## 1461 Afzelia coriacea Sindora coriacea
## 1474 Agapetes pilifera Vaccinium piliferum
## 1531 Aglaia bourdillonii Aglaia elaeagnoidea
## 1546 Aglaia dasyclada Aglaia spectabilis
## 1568 Aglaia iloilo Aglaia argentea
## 1705 Aiouea costaricensis Ocotea insularis
## 1716 Aiouea guatemalensis Damburneya guatemalensis
## 1741 Aiouea parvissima Damburneya parvissima
## taxonomic_status Old.status
## 2 Accepted Homotypic_Synonym
## 40 Accepted Synonym
## 129 Accepted Homotypic_Synonym
## 130 Accepted Homotypic_Synonym
## 430 Accepted Synonym
## 440 Unplaced Synonym
## 456 Accepted Homotypic_Synonym
## 602 Accepted Synonym
## 629 Accepted Synonym
## 652 Accepted Synonym
## 675 Accepted Homotypic_Synonym
## 680.1 Accepted Synonym
## 682 Accepted Synonym
## 709 Accepted Homotypic_Synonym
## 716 Accepted Synonym
## 717 Accepted Homotypic_Synonym
## 727 Accepted Synonym
## 729 Accepted Synonym
## 734 Accepted Synonym
## 744 Accepted Homotypic_Synonym
## 745 Accepted Homotypic_Synonym
## 756 Accepted Homotypic_Synonym
## 762 Accepted Homotypic_Synonym
## 766 Accepted Synonym
## 770 Accepted Synonym
## 790 Accepted Synonym
## 812 Accepted Synonym
## 824 Accepted Homotypic_Synonym
## 860 Accepted Homotypic_Synonym
## 886 Accepted Homotypic_Synonym
## 961 Accepted Homotypic_Synonym
## 1036 Accepted Synonym
## 1052 Accepted Synonym
## 1100 Accepted Homotypic_Synonym
## 1161 Accepted Synonym
## 1397 Accepted Homotypic_Synonym
## 1398 Accepted Homotypic_Synonym
## 1401 Accepted Homotypic_Synonym
## 1403 Accepted Homotypic_Synonym
## 1404 Accepted Synonym
## 1406 Accepted Homotypic_Synonym
## 1425 Accepted Synonym
## 1461 Accepted Homotypic_Synonym
## 1474 Accepted Homotypic_Synonym
## 1531 Accepted Synonym
## 1546 Accepted Synonym
## 1568 Accepted Synonym
## 1705 Accepted Synonym
## 1716 Accepted Homotypic_Synonym
## 1741 Accepted Homotypic_Synonym32 tree species were matched with a name of a hybrid species.
nrow(GTS.nm[GTS.nm$Hybrid == "×", ])## [1] 32GTS.nm[GTS.nm$Hybrid == "×", c("TaxonName", "taxon_name",
"taxonomic_status", "Old.status")]## TaxonName taxon_name taxonomic_status
## 1176 Adenanthos sericeus Adenanthos ×sericeus Accepted
## 5926 Betula murrayana Betula ×purpusii Accepted
## 6744 Bruguiera hainesii Bruguiera ×hainesii Accepted
## 8568 Carramboa rodriguezii Espeletia ×rodriguezii Accepted
## 13234 Crataegus anamesa Crataegus ×anamesa Accepted
## 13283 Crataegus disperma Crataegus ×disperma Accepted
## 13284 Crataegus dispessa Crataegus ×dispessa Accepted
## 13308 Crataegus grandis Crataegus ×disperma Accepted
## 13311 Crataegus harveyana Crataegus ×rupicola Accepted
## 13328 Crataegus knieskerniana Crataegus ×knieskerniana Accepted
## 13410 Crataegus rufula Crataegus ×rufula Accepted
## 13425 Crataegus stenosepala Crataegus ×stenosepala Accepted
## 13438 Crataegus vailiae Crataegus ×vailiae Accepted
## 18957 Elizabetha grahamiae Paloue ×grahamiae Accepted
## 19109 Endiandra monothyra Endiandra ×monothyra Accepted
## 23726 Garcinia guacopary Garcinia ×guacopary Accepted
## 28309 Inga andersonii Inga ×andersonii Accepted
## 32128 Machaerium salvadorense Machaerium ×salvadorense Accepted
## 33105 Malus floribunda Malus ×floribunda Accepted
## 33116 Malus micromalus Malus ×micromalus Synonym
## 34442 Mespilus canescens × Crataemespilus canescens Accepted
## 40926 Paulownia taiwaniana Paulownia ×taiwaniana Accepted
## 42790 Pittosporum obcordatum Pittosporum ×obcordatum Accepted
## 43311 Plumeria trouinensis Plumeria ×stenopetala Accepted
## 44465 Prosopis vinalillo Prosopis ×vinalillo Accepted
## 46011 Pyrus anatolica Pyrus ×michauxii Accepted
## 46059 Pyrus sinkiangensis Pyrus ×sinkiangensis Accepted
## 47374 Rhododendron wilhelminae Rhododendron ×wilhelminae Accepted
## 48255 Salix heteromera Salix ×heteromera Unplaced
## 50789 Sonneratia hainanensis Sonneratia ×hainanensis Accepted
## 50948 Sorbus leptophylla Aria ×leptophylla Accepted
## 58179 Yucca rigida Yucca ×rigida Synonym
## Old.status
## 1176
## 5926 Synonym
## 6744
## 8568 Homotypic_Synonym
## 13234
## 13283
## 13284
## 13308 Synonym
## 13311 Synonym
## 13328
## 13410
## 13425
## 13438
## 18957 Homotypic_Synonym
## 19109
## 23726
## 28309
## 32128
## 33105
## 33116
## 34442 Homotypic_Synonym
## 40926
## 42790
## 43311 Synonym
## 44465
## 46011 Synonym
## 46059
## 47374
## 48255
## 50789
## 50948 Homotypic_Synonym
## 58179In the majority of cases where fuzzy matching was done, the Levenshtein distance was 1 or 2.
nrow(GTS.nm[GTS.nm$Fuzzy.dist == 1, ])## [1] 259nrow(GTS.nm[GTS.nm$Fuzzy.dist == 1, ]) / nrow(GTS.match[GTS.match$Fuzzy == TRUE, ])## [1] 0.447323nrow(GTS.nm[GTS.nm$Fuzzy.dist < 3, ])## [1] 423nrow(GTS.nm[GTS.nm$Fuzzy.dist < 3, ]) / nrow(GTS.match[GTS.match$Fuzzy == TRUE, ])## [1] 0.7305699Where the Levenshtein distance was larger than 10, typically only a matching genus name could be found.
nrow(GTS.nm[GTS.nm$Fuzzy.dist > 10, ])## [1] 64nrow(GTS.nm[GTS.nm$Fuzzy.dist > 10, ]) / nrow(GTS.match[GTS.match$Fuzzy == TRUE, ])## [1] 0.1105354GTS.nm[GTS.nm$Fuzzy.dist > 10, c("TaxonName", "taxon_name",
"taxonomic_status", "rank", "Old.status")]## TaxonName taxon_name taxonomic_status
## 806 Acer sosnowskyi Acer Accepted
## 3094 Annona penicillata Annona Accepted
## 5642 Beilschmiedia tisseranti Beilschmiedia Accepted
## 6249 Boscia mazzocchii Boscia Accepted
## 6294 Bougainvillea fasciculata Bougainvillea Accepted
## 7966 Camellia hengchunensis Camellia Accepted
## 8987 Castanopsis damingshanensis Castanopsis Accepted
## 9010 Castanopsis globigemmata Castanopsis Accepted
## 9047 Castanopsis nigrescens Castanopsis Accepted
## 9078 Castanopsis subuliformis Castanopsis Accepted
## 10197 Cinnadenia liyuyingii Cinnadenia Accepted
## 12947 Cotoneaster ellipticus Cotoneaster Accepted
## 14375 Cryptocarya sheikelmudiyana Cryptocarya Accepted
## 14457 Ctenodon molliculus Ctenodon Accepted
## 14459 Ctenodon mucronulatus Ctenodon Accepted
## 15907 Desmopsis colombiana Desmopsis Accepted
## 19237 Englerodaphne ovalifolia Englerodaphne Accepted
## 23415 Freziera caesariata Freziera Accepted
## 23418 Freziera campanulata Freziera Accepted
## 23436 Freziera glabrescens Freziera Accepted
## 23713 Garcinia erythrosepala Garcinia Accepted
## 24891 Gordonia singaporeana Gordonia Accepted
## 25069 Grewia delphinensis Grewia Accepted
## 25113 Grewia mansouriana Grewia Accepted
## 27276 Hopea quisumbingiana Hopea Accepted
## 28130 Ilex qingyuanensis Ilex Accepted
## 32418 Madhuca chia-ananii Madhuca Accepted
## 33223 Mangifera salomonensis Mangifera Accepted
## 37300 Myrsine perpauciflora Myrsine Accepted
## 38153 Nototrichium sandwicense Nototrichium Accepted
## 38278 Ochrosia tahitensis Ochrosia Accepted
## 38482 Ocotea javitensis Ocotea Accepted
## 39210 Ormosia boluoensis Ormosia Accepted
## 40235 Paloue guianensis Paloue Accepted
## 40962 Pausinystalia brachythyrsum Corynanthe Accepted
## 42164 Piliocalyx ignambiensis Syzygium Accepted
## 42873 Plagioscyphus calciphilus Plagioscyphus Accepted
## 42875 Plagioscyphus danguyanus Plagioscyphus Accepted
## 42879 Plagioscyphus meridionalis Plagioscyphus Accepted
## 42880 Plagioscyphus unijugatus Plagioscyphus Accepted
## 43006 Plathymenia foliolosa Plathymenia reticulata Accepted
## 43131 Plerandra letocartiorum Plerandra Accepted
## 43132 Plerandra longistyla Plerandra Accepted
## 43134 Plerandra memaoyaensis Plerandra Accepted
## 43145 Plerandra pouemboutensis Plerandra Accepted
## 43152 Plerandra tronchetii Plerandra Accepted
## 43850 Populus minhoensis Populus Accepted
## 46054 Pyrus sachokiana Pyrus Accepted
## 46265 Quercus centenaria Quercus Accepted
## 47240 Rhododendron laojunshanense Rhododendron Accepted
## 47885 Ruagea parvifructa Ruagea Accepted
## 48794 Scaphium scaphigerum Scaphium Accepted
## 49474 Scyphostegia borneensis Scyphostelma Accepted
## 49564 Seguieria paraguayensis Seguieria Accepted
## 50973 Sorbus obtusifolia Sorbus Accepted
## 51545 Sterculia multiovula Sterculia Accepted
## 51572 Sterculia scortechinii Sterculia Accepted
## 51824 Stryphnodendron racemiferum Stryphnodendron Accepted
## 54123 Tapiscia yunnanensis Tapiscia Accepted
## 55621 Trilepisium gymnandrum Trilepisium Accepted
## 56275 Vachellia ormocarpoides Vachellia Accepted
## 56615 Vepris robertsoniae Vepris Accepted
## 57242.1 Volkameria emirnensis Volkameria Accepted
## 57473 Weinmannia turckheimii Weinmannia Accepted
## rank Old.status
## 806 GENUS
## 3094 GENUS
## 5642 GENUS
## 6249 GENUS
## 6294 GENUS
## 7966 GENUS
## 8987 GENUS
## 9010 GENUS
## 9047 GENUS
## 9078 GENUS
## 10197 GENUS
## 12947 GENUS
## 14375 GENUS
## 14457 GENUS
## 14459 GENUS
## 15907 GENUS
## 19237 GENUS
## 23415 GENUS
## 23418 GENUS
## 23436 GENUS
## 23713 GENUS
## 24891 GENUS
## 25069 GENUS
## 25113 GENUS
## 27276 GENUS
## 28130 GENUS
## 32418 GENUS
## 33223 GENUS
## 37300 GENUS
## 38153 GENUS
## 38278 GENUS
## 38482 GENUS
## 39210 GENUS
## 40235 GENUS
## 40962 GENUS Synonym
## 42164 GENUS Synonym
## 42873 GENUS
## 42875 GENUS
## 42879 GENUS
## 42880 GENUS
## 43006 SPECIES Synonym
## 43131 GENUS
## 43132 GENUS
## 43134 GENUS
## 43145 GENUS
## 43152 GENUS
## 43850 GENUS
## 46054 GENUS
## 46265 GENUS
## 47240 GENUS
## 47885 GENUS
## 48794 GENUS
## 49474 GENUS
## 49564 GENUS
## 50973 GENUS
## 51545 GENUS
## 51572 GENUS
## 51824 GENUS
## 54123 GENUS
## 55621 GENUS
## 56275 GENUS
## 56615 GENUS
## 57242.1 GENUS
## 57473 GENUSnrow(GTS.nm[GTS.nm$Fuzzy.one == TRUE, ])## [1] 127nrow(GTS.nm[GTS.nm$Fuzzy.one == TRUE, ]) / nrow(GTS.match[GTS.match$Fuzzy == TRUE, ])## [1] 0.2193437For those species that could not be matched directly with the WCVP, we now try matching those names with World Flora Online. Afterwards a comparison will be made between matches of WCVP and WFO.
Selecting species names that were not matched directly with the WCVP:
GTS.recheck1 <- GTS.nm[, c("TaxonName", "Author")]
GTS.recheck2 <- GTS.match[GTS.match$Matched == FALSE, c("TaxonName", "Author")]
GTS.recheck <- rbind(GTS.recheck1, GTS.recheck2)Loading the World Flora Online taxonomic backbone:
WFO.remember()## Data sourced from: C:\R-3.6.1\bin\x64\classification.txt (Wed Sep 22 14:00:37 2021)## Reading WFO data## Warning in data.table::fread(WFO.file1, encoding = "UTF-8"): Found and resolved
## improper quoting out-of-sample. First healed line 118: <<wfo-0000000117
## Hieracium onosmoides subsp. sphaerianthum SUBSPECIES wfo-0000034880 (Arv.-
## Touv.) Zahn Asteraceae Hieracium onosmoides sphaerianthum subsp. "Zahn, in
## Engler, Pflanzenr. 82. 1923." 1676 1923 Accepted 2012-02-11 2012-02-11 http://
## www.theplantlist.org/tpl1.1/record/gcc-10011>>. If the fields are not quoted
## (e.g. field separator does not appear within any field), try quote="" to avoid
## this warning.## The WFO data is now available from WFO.dataGTS.WFO <- WFO.one(WFO.match(GTS.recheck,
WFO.data = WFO.data,
spec.name = "TaxonName",
Authorship = "Author",
verbose = FALSE,
counter = 100),
verbose = FALSE, counter = 100)## Reached record # 100## Reached record # 200## Reached record # 300## Reached record # 400## Reached record # 500##
## Checking new accepted IDs## Reached record # 100## Reached record # 200## Reached record # 300## Reached record # 400## Reached record # 500## Reached case # 100## Reached case # 200## Reached case # 300## Reached case # 400## Reached case # 500The majority of species that could not be directly matched by the WCVP could be matched by WFO.
nrow(GTS.WFO[GTS.WFO$Fuzzy == FALSE, ])## [1] 478nrow(GTS.WFO[GTS.WFO$Fuzzy == FALSE, ]) / nrow(GTS.WFO)## [1] 0.8227194nrow(GTS.WFO[GTS.WFO$Fuzzy == TRUE, ])## [1] 103nrow(GTS.WFO[GTS.WFO$Fuzzy == TRUE, ]) / nrow(GTS.WFO)## [1] 0.1772806Saving the results locally:
GTS.m2 <- GTS.WFO[GTS.WFO$Fuzzy==FALSE, ]
GTS.m2 <- GTS.m2[, c("TaxonName", "Author",
"taxonID", "family", "scientificName", "taxonomicStatus",
"scientificNameAuthorship", "Auth.dist",
"New.accepted", "Old.status")]
GTS.m2.file <- paste0(data.dir, "/WFO direct match.txt")
write.table(GTS.m2, file=GTS.m2.file,
quote=FALSE, sep="|",
row.names=FALSE,
fileEncoding="UTF-8")
GTS.nm2 <- GTS.WFO[GTS.WFO$Fuzzy==TRUE, ]
GTS.nm2.file <- paste0(data.dir, "/WFO fuzzy match.txt")
write.table(GTS.nm2, file=GTS.nm2.file,
quote=FALSE, sep="|",
row.names=FALSE,
fileEncoding="UTF-8")WFO includes species names for many instances where the WCVP could only be matched at the genus level.
GTS.comb <- dplyr::right_join(GTS.m2[, c("TaxonName", "scientificName")],
GTS.nm[, c("TaxonName", "taxon_name", "Fuzzy.dist")],
by="TaxonName")
GTS.comb[GTS.comb$Fuzzy.dist > 10, ]## TaxonName scientificName
## 3 Acer sosnowskyi Acer sosnowskyi
## 29 Beilschmiedia tisseranti Beilschmiedia tisseranti
## 33 Boscia mazzocchii Boscia mazzocchii
## 34 Bougainvillea fasciculata Bougainvillea fasciculata
## 43 Camellia hengchunensis Camellia brevistyla
## 53 Castanopsis damingshanensis Castanopsis damingshanensis
## 54 Castanopsis globigemmata Castanopsis globigemmata
## 55 Castanopsis nigrescens Castanopsis nigrescens
## 56 Castanopsis subuliformis Castanopsis subuliformis
## 83 Cotoneaster ellipticus Cotoneaster ellipticus
## 126 Englerodaphne ovalifolia Englerodaphne ovalifolia
## 139 Freziera campanulata Freziera campanulata
## 140 Freziera glabrescens Freziera glabrescens
## 145 Garcinia erythrosepala Garcinia erythrosepala
## 156 Gordonia singaporeana Gordonia singaporeana
## 161 Grewia delphinensis Grewia delphinensis
## 183 Ilex qingyuanensis Ilex qingyuanensis
## 212 Madhuca chia-ananii Madhuca chia-ananii
## 222 Mangifera salomonensis Mangifera salomonensis
## 253 Myrsine perpauciflora Myrsine perpauciflora
## 261 Nototrichium sandwicense Nototrichium sandwicense
## 262 Ochrosia tahitensis Ochrosia tahitensis
## 264 Ocotea javitensis Ocotea javitensis
## 271 Ormosia boluoensis Ormosia boluoensis
## 274 Paloue guianensis Paloue guianensis
## 285 Pausinystalia brachythyrsum Pausinystalia brachythyrsum
## 304 Plagioscyphus calciphilus Plagioscyphus calciphilus
## 305 Plagioscyphus danguyanus Plagioscyphus danguyanus
## 307 Plagioscyphus meridionalis Plagioscyphus meridionalis
## 308 Plagioscyphus unijugatus Plagioscyphus unijugatus
## 310 Plathymenia foliolosa Plathymenia foliolosa
## 314 Plerandra letocartiorum Plerandra letocartiorum
## 315 Plerandra longistyla Plerandra longistyla
## 317 Plerandra memaoyaensis Plerandra memaoyaensis
## 320 Plerandra pouemboutensis Plerandra pouemboutensis
## 322 Plerandra tronchetii Plerandra tronchetii
## 331 Populus minhoensis Populus minhoensis
## 368 Pyrus sachokiana Pyrus sachokiana
## 378 Rhododendron laojunshanense Rhododendron laojunshanense
## 397 Scaphium scaphigerum Scaphium scaphigerum
## 410 Scyphostegia borneensis Scyphostegia borneensis
## 411 Seguieria paraguayensis Seguieria paraguayensis
## 420 Sorbus obtusifolia Sorbus graeca
## 425 Sterculia multiovula Sterculia multiovula
## 429 Stryphnodendron racemiferum Stryphnodendron racemiferum
## 442 Tapiscia yunnanensis Tapiscia yunnanensis
## 459 Vepris robertsoniae Vepris robertsoniae
## 467 Weinmannia turckheimii Weinmannia turckheimii
## 484 Annona penicillata <NA>
## 495 Cinnadenia liyuyingii <NA>
## 499 Cryptocarya sheikelmudiyana <NA>
## 500 Ctenodon molliculus <NA>
## 502 Ctenodon mucronulatus <NA>
## 508 Desmopsis colombiana <NA>
## 519 Freziera caesariata <NA>
## 525 Grewia mansouriana <NA>
## 529 Hopea quisumbingiana <NA>
## 548 Piliocalyx ignambiensis <NA>
## 554 Quercus centenaria <NA>
## 559 Ruagea parvifructa <NA>
## 569 Sterculia scortechinii <NA>
## 574 Trilepisium gymnandrum <NA>
## 575 Vachellia ormocarpoides <NA>
## 577 Volkameria emirnensis <NA>
## taxon_name Fuzzy.dist
## 3 Acer 11
## 29 Beilschmiedia 11
## 33 Boscia 11
## 34 Bougainvillea 12
## 43 Camellia 14
## 53 Castanopsis 16
## 54 Castanopsis 13
## 55 Castanopsis 11
## 56 Castanopsis 13
## 83 Cotoneaster 11
## 126 Englerodaphne 11
## 139 Freziera 12
## 140 Freziera 12
## 145 Garcinia 14
## 156 Gordonia 13
## 161 Grewia 13
## 183 Ilex 14
## 212 Madhuca 12
## 222 Mangifera 13
## 253 Myrsine 14
## 261 Nototrichium 12
## 262 Ochrosia 11
## 264 Ocotea 11
## 271 Ormosia 11
## 274 Paloue 11
## 285 Corynanthe 14
## 304 Plagioscyphus 12
## 305 Plagioscyphus 11
## 307 Plagioscyphus 13
## 308 Plagioscyphus 11
## 310 Plathymenia reticulata 20
## 314 Plerandra 14
## 315 Plerandra 11
## 317 Plerandra 13
## 320 Plerandra 15
## 322 Plerandra 11
## 331 Populus 11
## 368 Pyrus 11
## 378 Rhododendron 15
## 397 Scaphium 12
## 410 Scyphostelma 13
## 411 Seguieria 14
## 420 Sorbus 12
## 425 Sterculia 11
## 429 Stryphnodendron 12
## 442 Tapiscia 12
## 459 Vepris 13
## 467 Weinmannia 12
## 484 Annona 12
## 495 Cinnadenia 11
## 499 Cryptocarya 16
## 500 Ctenodon 11
## 502 Ctenodon 13
## 508 Desmopsis 11
## 519 Freziera 11
## 525 Grewia 12
## 529 Hopea 15
## 548 Syzygium 13
## 554 Quercus 11
## 559 Ruagea 12
## 569 Sterculia 13
## 574 Trilepisium 11
## 575 Vachellia 14
## 577 Volkameria 11Since the number of species that are neither directly matched by the WCVP and the WFO is relatively small, it becomes possible now to manually check for potentially correct species names.
GTS.comb <- dplyr::left_join(GTS.nm2[, c("TaxonName", "scientificName")],
GTS.nm[, c("TaxonName", "taxon_name", "Fuzzy.dist")],
by="TaxonName")
GTS.comb[GTS.comb$Fuzzy.dist == 1, ]## TaxonName scientificName
## 4 Aldina aquae-nigrae Aldina aquae-negrae
## 12 Athenaea wettesteiniana Athenaea
## 13 Bathysa mendoncaei Bathysa mendoncae
## 14 Betula murrayana Betula ×murrayana
## 18 Celtis orthacanthos Celtis orthocanthos
## 20 Citharexylum mocinnoi Citharexylum mocinoi
## 22 Crataegus jonesiae Crataegus jonesae
## 28 Cynometra dwyerii Cynometra
## 31 Dalbergia entadioides Dalbergia entadoides
## 34 Diospyros apeibacarpos Diospyros apeibocarpos
## 35 Diospyros martinii Diospyros martini
## 39 Eucalyptus gregoryensis Eucalyptus gregoriensis
## 40 Eugenia marchiana Eugenia marshiana
## 45 Freziera monzonensis Freziera monsonensis
## 46 Garcinia martini Garcinia murtonii
## 48 Gigasiphon humblotianus Gigasiphon humblotianum
## 51 Guettarda prenleloupii Guettarda preneloupii
## 54 Ixora richard-longii Ixora
## 55 Lebrunia bushaie Lebrunia busbaie
## 57 Machaerium robsonnianum Machaerium
## 59 Macrolobium longiracemosum Macrolobium longeracemosum
## 62 Memecylon plebeium Memecylon plebejum
## 63 Mezoneuron kavaiense Caesalpinia kauaiensis
## 64 Miconia doniana Miconia doriana
## 67 Myrciaria vismiifolia Myrciaria vismeifolia
## 70 Pavieasia annamensis Pavieasia anamensis
## 71 Peltophorum dasyrachis Peltophorum dasyrrhachis
## 73 Plumeria trouinensis Plumeria ×trouinenais
## 84 Schefflera le-ratii Schefflera le-rati
## 85 Schefflera longepetiolata Schefflera longipetiolata
## 87 Sonneratia hainanensis Sonneratia ×hainanensis
## 88 Sorbus arvonensis Sorbus arranensis
## 89 Sorbus pseudosemiincisa Sorbus ×pseudosemi-incisa
## 90 Sorbus semiincisa Sorbus semi-incisa
## 91 Sorbus yondeensis Sorbus
## 92 Stenostomum albobruneum Stenostomum albobrunneum
## 96 Tabernaemontana mocquerysii Tabernaemontana mocquerysi
## 100 Vitex carvalhi Vitex mossambicensis
## 103 Waltheria cinerascens Waltheria cinerescens
## taxon_name Fuzzy.dist
## 4 Aldina macrophylla 1
## 12 Athenaea wettsteiniana 1
## 13 Bathysa mendoncae 1
## 14 Betula ×purpusii 1
## 18 Celtis orthocanthos 1
## 20 Citharexylum mocinoi 1
## 22 Crataegus jonesae 1
## 28 Cynometra dwyeri 1
## 31 Dalbergia entadoides 1
## 34 Diospyros apeibocarpos 1
## 35 Diospyros martini 1
## 39 Eucalyptus gregoriensis 1
## 40 Eugenia marshiana 1
## 45 Freziera monsonensis 1
## 46 Garcinia martinii 1
## 48 Gigasiphon humblotianum 1
## 51 Guettarda preneloupii 1
## 54 Ixora richardi-longii 1
## 55 Lebrunia busbaie 1
## 57 Machaerium robsonianum 1
## 59 Macrolobium longeracemosum 1
## 62 Memecylon plebejum 1
## 63 Mezoneuron kauaiense 1
## 64 Miconia doriana 1
## 67 Myrciaria vismeifolia 1
## 70 Pavieasia anamensis 1
## 71 Peltophorum dasyrhachis 1
## 73 Plumeria ×stenopetala 1
## 84 Schefflera leratii 1
## 85 Didymopanax longe-petiolatus 1
## 87 Sonneratia ×hainanensis 1
## 88 Aria avonensis 1
## 89 Karpatiosorbus pseudosemi-incisa 1
## 90 Karpatiosorbus semi-incisa 1
## 91 Griffitharia yongdeensis 1
## 92 Stenostomum albobrunneum 1
## 96 Tabernaemontana mocquerysi 1
## 100 Vitex mossambicensis 1
## 103 Waltheria cinerescens 1GTS.comb[GTS.comb$Fuzzy.dist == 2, ]## TaxonName scientificName taxon_name
## 1 Acropogon calcicolus Acropogon calcicola Acropogon calcicola
## 2 Acropogon sageniifolius Acropogon sageniifolia Acropogon sageniifolia
## 3 Acropogon schumannianus Acropogon schumanniana Acropogon schumanniana
## 9 Archidendron oblonga Archidendropsis oblonga Archidendropsis oblonga
## 11 Aspidostemon triantherus Aspidostemon trianthera Aspidostemon trianthera
## 16 Canarium subsidiarum Canarium subsidarium Canarium subsidarium
## 17 Catostemma digitatum Catostemma digitata Catostemma digitata
## 27 Cupania castaneaefolia Cupania racemosa Cupania castaneifolia
## 29 Dalbergia acarantha Dalbergia acariiantha Dalbergia acariiantha
## 30 Dalbergia annamensis Dalbergia andapensis Dalbergia andapensis
## 41 Eugenia poroensis Eugenia pardensis Eugenia pardensis
## 47 Garnieria spathulaefolia Garnieria spathulifolia Garnieria spathulifolia
## 52 Guettarda wayaensis Guettarda wagapensis Guettarda wagapensis
## 61 Memecylon arnhemensis Memecylon arnhemense Memecylon arnhemense
## 65 Monteverdia gonoclada Maytenus buxifolia Maytenus gonoclados
## 66 Monteverdia schummaniana Maytenus buxifolia Maytenus schumanniana
## 68 Omalanthus stokesii Homalanthus stokesii Homalanthus stokesii
## 69 Pandanus callmanderianus Pandanus callmanderiana Pandanus callmanderiana
## 74 Priogymnanthus saxicolus Priogymnanthus Priogymnanthus saxicola
## 76 Psychotria volii Psychotria bonii Psychotria bonii
## 77 Psydrax glabra Psydrax Canthiumera glabra
## 79 Quercus mexiae Quercus gambelii Quercus gambelii
## 80 Rhododendron suoilenhensis Rhododendron Rhododendron suoilenhense
## 86 Semecarpus calcicolus Semecarpus calcicola Semecarpus calcicola
## 95 Syzygium trukensis Syzygium Syzygium trukense
## Fuzzy.dist
## 1 2
## 2 2
## 3 2
## 9 2
## 11 2
## 16 2
## 17 2
## 27 2
## 29 2
## 30 2
## 41 2
## 47 2
## 52 2
## 61 2
## 65 2
## 66 2
## 68 2
## 69 2
## 74 2
## 76 2
## 77 2
## 79 2
## 80 2
## 86 2
## 95 2GTS.comb[GTS.comb$Fuzzy.dist > 2, ]## TaxonName scientificName taxon_name
## 5 Alseis sertaneja Alseis Alseis
## 6 Amphitecna fonceti Amphitecna Amphitecna
## 7 Annona imparilis Annona Annona
## 8 Annona penicillata Annona Annona
## 10 Artocarpus bergii Artocarpus Artocarpus
## 15 Bursera zapoteca Bursera Bursera
## 19 Cinnadenia liyuyingii Cinnadenia Cinnadenia
## 21 Conchocarpus rubrus Conchocarpus Conchocarpus
## 23 Cryptocarya sheikelmudiyana Cryptocarya Cryptocarya
## 24 Ctenodon molliculus Stenodon Ctenodon
## 25 Ctenodon monteiroi Stenodon Ctenodon
## 26 Ctenodon mucronulatus Stenodon Ctenodon
## 32 Desmopsis colombiana Desmopsis Desmopsis
## 33 Desmopsis confusa Desmopsis Desmopsis
## 36 Drypetes louisii Drypetes Drypetes
## 37 Englerodendron libassum Englerodendron Englerodendron
## 38 Eucalyptus alatissima Eucalyptus plenissima Eucalyptus plenissima
## 42 Flindersia bennettii Flindersia bennettiana Flindersia bennettiana
## 43 Freziera caesariata Freziera Freziera
## 44 Freziera ciliata Freziera Freziera
## 49 Grewia mansouriana Grewia Grewia
## 50 Grewia milleri Grewia Grewia
## 53 Hopea quisumbingiana Hopea Hopea
## 56 Lindera oxyphylla Lindera Lindera
## 58 Machilus coriacea Machilus Machilus
## 60 Mangifera lambii Mangifera Mangifera
## 72 Piliocalyx ignambiensis Piliocalyx Syzygium
## 75 Prunus klokovii Prunus Prunus
## 78 Quercus centenaria Quercus Quercus
## 81 Ruagea beckii Ruagea Ruagea
## 82 Ruagea obovata Ruagea Ruagea
## 83 Ruagea parvifructa Ruagea Ruagea
## 93 Sterculia scortechinii Sterculia Sterculia
## 94 Symplocos juiyenensis Symplocos guianensis Symplocos guianensis
## 97 Trichilia deminuta Trichilia Trichilia
## 98 Trilepisium gymnandrum Trilepisium Trilepisium
## 99 Vachellia ormocarpoides Vachellia Vachellia
## 101 Volkameria emirnensis Volkameria Volkameria
## 102 Volkameria grevei Volkameria Volkameria
## Fuzzy.dist
## 5 10
## 6 8
## 7 10
## 8 12
## 10 7
## 15 9
## 19 11
## 21 7
## 23 16
## 24 11
## 25 10
## 26 13
## 32 11
## 33 8
## 36 8
## 37 9
## 38 3
## 42 3
## 43 11
## 44 8
## 49 12
## 50 8
## 53 15
## 56 10
## 58 9
## 60 7
## 72 13
## 75 9
## 78 11
## 81 7
## 82 8
## 83 12
## 93 13
## 94 3
## 97 9
## 98 11
## 99 14
## 101 11
## 102 7sessionInfo()## R version 4.0.2 (2020-06-22)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United Kingdom.1252
## [2] LC_CTYPE=English_United Kingdom.1252
## [3] LC_MONETARY=English_United Kingdom.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United Kingdom.1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] dplyr_1.0.2 data.table_1.12.8 WorldFlora_1.9
##
## loaded via a namespace (and not attached):
## [1] crayon_1.3.4 digest_0.6.25 R6_2.4.1 lifecycle_0.2.0
## [5] magrittr_1.5 evaluate_0.14 pillar_1.4.4 rlang_0.4.8
## [9] stringi_1.4.6 ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.4
## [13] rmarkdown_2.3 tools_4.0.2 stringr_1.4.0 glue_1.4.1
## [17] purrr_0.3.4 xfun_0.15 yaml_2.2.1 compiler_4.0.2
## [21] pkgconfig_2.0.3 htmltools_0.5.1.1 tidyselect_1.1.0 knitr_1.28
## [25] tibble_3.0.1