R package (including shiny app) to query The Plant List v1.1
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DESCRIPTION
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README.md

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Since tpl depends on tpldata, which is very large, it is likely that tpl will not be published on CRAN.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