Awesome
tpl
This R package includes functions to query the latest version of The Plant List database alongside with a shiny web application as an alternative front end.
Developer
Data
All data from The Plant List are included in tpldata. Please cite The Plant List accordingly. The data included in the package come from csv files they make available on their website. There are ~1.2 million entries in the dataset.
Installation
Install devtools and shiny
install.packages("devtools")
install.packages("shiny")
library("devtools")
Install tpldata (this is a 50 Mb download)
install_github("gustavobio/tpldata")
Install tpl
Since tpl depends on tpldata, which is very large, it is likely that tpl will not be published on CRAN.
install_github("gustavobio/tpl")
Usage
The main function is tpl.get, which will fix misspelled names, replace synonyms for accepted taxa, and return a data frame with taxonomic information:
library(tpl)
# First calls are a bit slow, but the following ones are substantially faster.
tpl.get(c("Miconia albicans", "Myrcia lingua", "Cofea arabica"))
id family genus species infraspecific.rank infraspecific.epithet authorship taxonomic.status.in.tpl confidence.level source
1 tro-20300135 Melastomataceae Miconia albicans (Sw.) Steud. Accepted M TRO
2 kew-131274 Myrtaceae Myrcia guianensis (Aubl.) DC. Accepted H WCSP
3 kew-45400 Rubiaceae Coffea arabica L. Accepted H WCSP
accepted.id name note original.search
1 Miconia albicans Miconia albicans
2 Myrcia guianensis replaced synonym Myrcia lingua
3 Coffea arabica was misspelled Cofea arabica
There are a few arguments to tpl.get, including replace.synonyms, suggest.names, and drop:
tpl.get(c("Miconia albicans", "Myrcia lingua", "Cofea arabica"), replace.synonyms = F, suggest.names = F)
id family genus species infraspecific.rank infraspecific.epithet authorship taxonomic.status.in.tpl confidence.level source accepted.id name
1 tro-20300135 Melastomataceae Miconia albicans (Sw.) Steud. Accepted M TRO Miconia albicans
2 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
3 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
note original.search
1 Miconia albicans
2 check +1 entries Myrcia lingua
3 not found Cofea arabica
Other functions include noauthors, to remove authors from names, suggest.names, to get name suggestions, and trim and fixCase to fix casing and duplicate whitespaces.
sp <- trim("Miconia albicans (Sw.) Steud.")
sp
[1] "Miconia albicans (Sw.) Steud."
noauthors(sp)
[1] "Miconia albicans"
Web application
There is a local web application included where one can simply paste names into a textbox and get taxonomic information, links to the original data source, search within the results and export to a csv file.
web.tpl()
Click on the screenshot for an expanded view
