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name: get-taxa-downstream layout: post title: Getting taxonomic names downstream date: 2012-10-16 author: Scott Chamberlain tags:

  • R
  • open access
  • data
  • taxonomy
  • ropensci
  • ritis
  • taxize

It can be a pain in the ass to get taxonomic names. For example, I sometimes need to get all the Class names for a set of species. This is a relatively easy problem using the ITIS API (example below).

The much harder problem is getting all the taxonomic names downstream. ITIS doesn't provide an API method for this - well, they do (getHirerachyDownFromTSN), but it only provides direct children (e.g., the genera within a tribe - but it won't give all the species within each genus).

So in the taxize package, we wrote a function called downstream, which allows you to get taxonomic names to any downstream point, e.g.:

  • get all Classes within Animalia,
  • get all Species within a Family
  • etc.

Install packages. You can get other packages from CRAN, but taxize is only on GitHub for now.

# install_github('ritis', 'ropensci') # uncomment if not already installed
# install_github('taxize_', 'ropensci') # uncomment if not already installed
library(ritis); library(taxize)

Get upstream taxonomic names.

# Search for a TSN by scientific name
df <- searchbyscientificname("Tardigrada")
tsn <- df[df$combinedname %in% "Tardigrada","tsn"]

# Get just one immediate higher taxonomic name
gethierarchyupfromtsn(tsn = tsn)

# Get full hierarchy upstream from TSN
getfullhierarchyfromtsn(tsn = tsn)

Get taxonomc names downstream.

# Get genera downstream fromthe Class Bangiophyceae
downstream(846509, "Genus")

# Get families downstream from __Acridoidea__
downstream(650497, "Family")

# Get species downstream from __Ursus__
downstream(180541, "Species")

Get the .Rmd file used to create this post at my github account - or .md file.

Written in Markdown, with help from knitr.