taxize allows users to search over many taxonomic data sources for species names (scientific and common) and download taxonomic hierarchical information.

In brief, taxize is a R package developed to clean and manage taxonomic information.

Install taxize with

install.packages("taxize") #or
devtools::install_github("ropensci/taxize")

Tutorial available at ROpenSci website

If your meta-analyses involve working on organisms with several collaborators:

Two situations could easily happen…

Situation 1 - Mispelled by collaborators

plants <- c("Poa annua", "Poa anua", " Poa annua")

Situation 2 - Inconsistent taxonomy within papers: species taxonomy changed over the time…

Monterey cypress has been Callitropsis macrocarpa, Cupressus macrocarpa, Cupressus hartwegii, Neocupressus macrocarpa, then back to Callitropsis macrocarpa…

Taking advantage of the existant taxonomic backbones…

• Encylopedia of Life
• Taxonomic Name Resolution Service
• Integrated Taxonomic Information Service
• Global Names Resolver
• IUCN Red List
  
• CANADENSYS Vascan name search API
• etc.

Total: 21 sources implemented

For this case, we use Global Names Resolver service:

temp <- taxize::gnr_resolve(names = c("Poa annua", "Poa anua", "  Poa annua"),
                            data_source_ids=c(3))
head(temp)

R>>    user_supplied_name submitted_name matched_name data_source_title score
R>>  1          Poa annua      Poa annua Poa annua L.              ITIS 0.988
R>>  2           Poa anua       Poa anua       Poa L.              ITIS 0.750
R>>  3          Poa annua      poa annua Poa annua L.              ITIS 0.988

Fuzzy matches could be done with several taxonomy providers:

taxize::gnr_datasources()

If we go back, to our Monterey cypress example with a scenario:

• Find one publication with Cupressus macrocarpa in 1987
• And another with Callitropsis macrocarpa in 1990

I want to harmonize them with the newest species name for Monterey cypress.

I'll use ITIS to perform this task.

• First step: Get the taxonomic serial number (TSN) for each species name.
• Second step: Check if this these TSN are valid and if not get the valid one with the accepted names.

• First step: Get the taxonomic serial number (TSN) for each species names.

mysps <- c("Callitropsis macrocarpa", "Cupressus macrocarpa")
(tsn <- taxize::get_tsn(mysps, accepted = FALSE, verbose=FALSE))

R>>  [1] "822598" "183480"
R>>  attr(,"match")
R>>  [1] "found" "found"
R>>  attr(,"multiple_matches")
R>>  [1] FALSE FALSE
R>>  attr(,"pattern_match")
R>>  [1] FALSE FALSE
R>>  attr(,"uri")
R>>  [1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=822598"
R>>  [2] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=183480"
R>>  attr(,"class")
R>>  [1] "tsn"

• Second step: Check if this these TSN are valid and if not get the valid one with the accepted names.

library(taxize)
(accept_tsn <- lapply(tsn, itis_acceptname))

R>>  [[1]]
R>>    submittedtsn acceptedname acceptedtsn author
R>>  1       822598           NA      822598     NA
R>>  
R>>  [[2]]
R>>    submittedtsn            acceptedname acceptedtsn               author
R>>  1       183480 Callitropsis macrocarpa      822598 (Hartw.) D.P. Little

Retrieve the English common name from valid scientific name

sci2comm('Cupressus macrocarpa', db = 'itis')

R>>  
R>>  Retrieving data for taxon 'Cupressus macrocarpa'

R>>  $`Cupressus macrocarpa`
R>>  [1] "ciprés Monterrey" "Monterey cypress"

Retrieve higher taxonomic information

classification(822598, db = 'itis')

R>>  $`822598`
R>>                        name          rank     id
R>>  1                  Plantae       kingdom 202422
R>>  2            Viridiplantae    subkingdom 954898
R>>  3             Streptophyta  infrakingdom 846494
R>>  4              Embryophyta superdivision 954900
R>>  5             Tracheophyta      division 846496
R>>  6          Spermatophytina   subdivision 846504
R>>  7                Pinopsida         class 500009
R>>  8                  Pinidae      subclass 954916
R>>  9                  Pinales         order 500028
R>>  10            Cupressaceae        family  18042
R>>  11            Callitropsis         genus 822533
R>>  12 Callitropsis macrocarpa       species 822598
R>>  
R>>  attr(,"class")
R>>  [1] "classification"
R>>  attr(,"db")
R>>  [1] "itis"

1. Some species might be absent from databases.
2. Some taxonomic groups are under-represented (e.g. nonvascular plants, some insects families etc.)

If you want to learn more about the features of this package:

1. ROpenSci tutorial
2. Package Documentation

Have a look at the ROpenSci initiative:

sp <- c("your_favorite_sp1","your_favorite_sp1","..")

1. Using the taxize package, clean up this vector using the gnr_resolve() function and ITIS as taxonomic provider.
2. Find the TSN of your favorite species
3. Change the provider (data_source_ids argument) in favor to Tropica and see what happen.
4. Try getting higher taxonomic information for your own species list.