Awesome
WARNING: The package is no long supported on CRAN. Both the database and the code are now outdated in their repository and should not be used. The only way to get the most recent version is from GitHub. Please follow the instructions below. There is a 5Mb limit to packages uploaded to CRAN. With recent inclusions, the database distributed within the package grew larger than that and CRAN administrators are not accepting my submissions.
flora
R package to query the Brazilian Flora 2020 dataset.
Developer
Data
The dataset included in the package was kindly made available by the Brazilian Flora 2020, which is a joint effort by hundreds of taxonomists to provide an improved checklist of plants and fungi that occur in Brazil.
Installation
Install devtools
install.packages("devtools")
Install flora
install_github("gustavobio/flora")
Usage
The main function is get.taxa, which will fix misspelled names, replace synonyms, and get taxonomic information for a vector of names.
library(flora)
get.taxa(c("Miconia albicans", "Myrcia lingua", "Cofea arabica"))
id scientific.name accepted.name family taxon.rank taxon.status
1 9668 Miconia albicans (Sw.) Triana <NA> Melastomataceae species accepted
2 10699 Myrcia guianensis (Aubl.) DC. <NA> Myrtaceae species accepted
3 24410 Coffea arabica L. <NA> Rubiaceae species accepted
search.str threat.status notes original.search
1 Miconia albicans <NA> Miconia albicans
2 Myrcia guianensis LC replaced synonym Myrcia lingua
3 Coffea arabica <NA> Coffea arabica
There are several arguments to get.taxa. For instance, you can get the domains in Brazil where the taxa occur:
get.taxa(c("Miconia albicans", "Myrcia lingua", "Cofea arabica"), domain = TRUE)
get.taxa(c("Miconia albicans", "Myrcia lingua", "Cofea arabica"), domain = TRUE)
id scientific.name accepted.name family taxon.rank taxon.status search.str threat.status
1 9668 Miconia albicans (Sw.) Triana <NA> Melastomataceae species accepted Miconia albicans <NA>
2 10699 Myrcia guianensis (Aubl.) DC. <NA> Myrtaceae species accepted Myrcia guianensis LC
3 24410 Coffea arabica L. <NA> Rubiaceae species accepted Coffea arabica <NA>
notes original.search domain
1 Miconia albicans Amazônia|Caatinga|Cerrado|Mata Atlântica
2 replaced synonym Myrcia lingua Amazônia|Caatinga|Cerrado|Mata Atlântica
3 was misspelled Cofea arabica Amazônia|Caatinga|Cerrado|Mata Atlântica
Other arguments include life.form, habitat, vernacular, states, and establishment.
get.taxa can automatically fix misspelled names when possible (when suggest.names = TRUE), but you can also use suggest.names for that:
suggest.names("Cofea arabyca")
[1] "Coffea arabica"
If you have names with authors, you can try to remove them with remove.authors
remove.authors("Symplocos phaeoclados var. acuminata Gontsch.")
[1] "Symplocos phaeoclados var. acuminata"
The function lower.taxa gets all names, accepted or not, which descends from a family or genus:
lower.taxa("Rapanea")
[1] "Rapanea" "Rapanea ferruginea" "Rapanea gardneriana" "Rapanea guianensis"
[5] "Rapanea leuconeura" "Rapanea parvifolia" "Rapanea umbellata" "Rapanea venosa"
[9] "Rapanea intermedia" "Rapanea oblonga" "Rapanea perforata" "Rapanea schwackeana"
[13] "Rapanea congesta" "Rapanea hermogenesii" "Rapanea lineata" "Rapanea lancifolia"
[17] "Rapanea loefgrenii" "Rapanea quaternata" "Rapanea matensis" "Rapanea villicaulis"
[21] "Rapanea villosissima" "Rapanea acuminata" "Rapanea megapotamica" "Rapanea lorentziana"
[25] "Rapanea laetevirens" "Rapanea balansae" "Rapanea emarginella" "Rapanea glazioviana"
[29] "Rapanea parvula" "Rapanea squarrosa" "Rapanea glaucorubens" "Rapanea ovalifolia"
[33] "Rapanea umbrosa" "Rapanea glomeriflora" "Rapanea oblongifolia" "Rapanea lauriformis"
[37] "Rapanea depauperata" "Rapanea paulensis" "Rapanea wettsteinii"
The function get.synonyms returns all synonyms of a given name:
get.synonyms("Myrcia guianensis")
[1] "Myrcia pallens" "Myrcia torta" "Myrcia obtecta" "Myrcia amethystina"
[5] "Myrcia corumbensis" "Myrcia cymosa" "Myrcia daphnoides" "Myrcia decrescens"
[9] "Myrcia elaeodendra" "Myrcia hepatica" "Myrcia hiemalis" "Myrcia intermedia"
[13] "Myrcia lingua" "Myrcia microcarpa" "Myrcia nigropunctata" "Myrcia obtusa"
[17] "Myrcia rhabdoides" "Myrcia rorida" "Myrcia rubella" "Myrcia suaveolens"
[21] "Myrcia angustifolia" "Myrcia camapuana" "Myrcia campestris" "Myrcia collina"
[25] "Myrcia dermatophylla" "Myrcia dictyophylla" "Myrcia didrichseniana" "Myrcia leucadendron"
[29] "Myrcia mansoi" "Myrcia myoporina" "Myrcia parnahibensis" "Myrcia scrobiculata"
[33] "Myrcia vacciniifolia" "Myrcia velhensis" "Myrcianthes cymosa" "Aguava guianensis"
...
[137] "Myrcia plumbea" "Myrcia poeppigiana" "Myrcia pusilla" "Myrcia vattimoi"
You can also return the relationships between names using get.synonyms:
get.synonyms("Myrcia guianensis", relationship = T)
spp synonym relationship
1 Myrcia guianensis Myrcia pallens Tem como sinônimo HETEROTIPICO
2 Myrcia guianensis Myrcia torta Tem como sinônimo HETEROTIPICO
3 Myrcia guianensis Myrcia obtecta Tem como sinônimo HETEROTIPICO
4 Myrcia guianensis Myrcia amethystina Tem como sinônimo HETEROTIPICO
5 Myrcia guianensis Myrcia corumbensis Tem como sinônimo HETEROTIPICO
6 Myrcia guianensis Myrcia cymosa Tem como sinônimo HETEROTIPICO
...
139 Myrcia guianensis Myrcia pusilla Tem como sinônimo HETEROTIPICO
140 Myrcia guianensis Myrcia vattimoi Tem como sinônimo HETEROTIPICO
You may also search for a species using vernacular names:
vernacular("Pimenta", exact = T)
id search.str family vernacular.name locality
1 7697 Erythroxylum daphnites Erythroxylaceae pimenta Minas Gerais
2 110560 Xylopia brasiliensis Annonaceae Pimenta <NA>
3 110583 Xylopia sericea Annonaceae Pimenta <NA>
Smaller things like casing and missplaced whitespaces are also automatically fixed in get.taxa, but there are specific functions for those as well:
fixCase("myrcia lingua")
[1] "Myrcia lingua"
trim("Myrcia lingua ")
[1] "Myrcia lingua"
standardize.names("Myrcia sp01")
[1] "Myrcia sp.1"
standardize.names("Myrcia sp2")
[1] "Myrcia sp.2"
standardize.names("Myrcia sp.3")
[1] "Myrcia sp.3"