Match lists of taxa against the Brazilian Flora 2020 and The Plant List.
install.packages("devtools")
devtools::install_github("gustavobio/tpldata")
devtools::install_github("gustavobio/tpl")
devtools::install_github("gustavobio/flora")
install.packages("shiny")
install.packages("DT")
install.packages("shinydashboard")
library("shiny")
download.file("https://raw.githubusercontent.com/gustavobio/plantminer/master/app.R", paste0(tempdir(), "app.R"))
runApp(paste0(tempdir(), "app.R"), launch.browser = TRUE)Use the /flora method to GET request a taxon using the taxon querystring:
http://www.plantminer.com/flora?taxon=Coffea%20arabica The response is always a json object, even if there is no match.
#####id Taxon id in the Brazilian Flora Checklist.
#####scientific name Full name with authors
#####original search Character string supplied by the user and matched against the database.
#####search str Character string used internally to query the database. If the user entered a misspelled name and a suggestion could be made, this will not match the original search.
#####taxon status Taxonomical status. Possible values are as follows: accepted synonym
#####notes Notes about a taxon. Empty string if there is nothing to report. Otherwise, possible values are as follows:
not found, if a name was not found.
was misspelled, if a name was misspelled.
replaced synonym, if a name was a synonym and was replaced by an accepted name.
check no accepted name if a synonym is not linked to a accepted name.
check no accepted +1 synonyms if a supplied taxon matches several names listed as synonyms and none are linked to an accepted name.
check +1 accepted if a synonym is linked to two or more accepted names.
check +1 entries if a supplied taxon matches several entries in the database.
check undefined status if a name is neither accepted or a synonym according to the data.
Multiple notes are separated with a |
#####taxon rank Taxonomical rank of the user supplied taxon. Possible values are:
family
genus
species
#####family Taxon family according to the Brazilian Flora Checklist
#####threat status Taxon threat status according to CNC Flora 2013. Statuses follow the IUCN convention.
Use the /tpl method to GET request a taxon using the taxon querystring:
http://www.plantminer.com/tpl?taxon=Coffea%20arabica The response is always a json object, even if a match couldn't be made.
#####id Taxon id in The Plant List
#####family Taxon family according to The Plant List. There is an option to return APG families instead.
#####genus Taxon genus
#####species Specific epiteth
#####infraspecific rank Taxon infraspecific rank
#####infraspecific epithet Taxon infraspecific epithet
#####authorship Taxon author(s)
#####taxonomic status in tpl Taxon status according to The Plant List. Possible values are:
Accepted
Synonym
#####confidence level
Status confidence level. Possible values are:
H: high confidence
M: medium confidence
L: low confidence
#####source Source of the data. Please check their website for a list of all possible sources and how to cite them.
#####accepted id id of the accepted name of a taxon in The Plant List. Return only if the user chooses not to automatically replace synonyms.
#####name Taxon name without authors.
#####note Notes about the taxon matching. Possible values are:
not found, if a name was not found.
was misspelled, if a name was misspelled.
replaced synonym, if a name is listed as a synonym and an accepted name was found.
Multiple notes are separated with a |
#####original search The user supplied character string.