The Plant List has a web API with an accompanying R package:
Taxonstand. We will use the API to check a list of plant
names for accuracy and synonomy.
First, get necessary packages:
install.packages('Taxonstand')
library(Taxonstand)
library(tidyverse)
library(RMariaDB)
We will use the specimens table from the Bee Lab dataset:
# make your connection to local or remote db as 'con'
specimens <- dbReadTable(con, "specimens")
### Small Table so we can disconnect
##
dbDisconnect(con)
Creating a “genus-species” column helps with merging
specimens$gs <- paste(specimens$plant.genus, specimens$plant.species)
Now we get unique values for plant names in this dataset. What are some potential problems that you see here?
plants<-unique(specimens[c("plant.genus", "plant.species")])
plants
Now we can get data from The Plant List. The ‘TPL’ function does this. Note that it can take awhile with a lot of names…
sp.out <- as.data.frame(TPL(genus=plants$plant.genus, species=plants$plant.species))
sp.out
first let’s find things that do not match
out1<-filter(sp.out, Plant.Name.Index==FALSE) %>% select(Taxon, New.Genus, New.Species)
out1
We can update plant names.
out1$New.Genus <- ifelse(out1$New.Genus == "common", "Helianthus","null")
out1$New.Species <- ifelse(out1$New.Species == "sunflower", "annuus","null")
Now we have a data frame with Taxon (old name) and upated new names We want to keep this old name for joining with our data set at the end.
We can also look for typos
out2<-filter(sp.out, Typo==TRUE)%>% select(Taxon, New.Genus, New.Species)
out2
Find any synonyms returned from the Plant List for the specimen names.
Join the original specimens table to the Plant List taxonomy.
How many bees were observed on Compositae flowers?