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flora

R package to query the Brazilian Flora 2020 dataset.

Developer

• Gustavo Carvalho

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"