Biodiversity & Taxonomy Software Tools in R

Scott Chamberlain ( @sckottie/@ropensci)

UC Berkeley / rOpenSci

rOpenSci Does

Questions addressed using our software

Citations of rOpenSci Biodiv Software

use case 1

in the methods section:

... using the Encyclopedia of Life invasive species comprehensive list, which was accessed programmatically on August 12, 2014 using the taxize package in R .

use case 2

in the methods section:

... we used rOpenSci’s worrms package in R to standardize spellings of species names and synonyms ...

Taxonomy

• taxa - Taxonomic classes and taxonomically aware data manipulation

• taxize - Taxonomic "toolbelt" - work w/ taxonomy web APIs

• taxizedb - taxize, but with local SQL databases

• rentrez - NCBI's Entrez, including taxonomy

• worrms - WORMS web service

• ritis - USGS's ITIS web service

• ... many others

R taxonomy task view: github.com/ropensci/taxonomy

Taxonomic data from >20 sources - taxize

always try to move from:

• taxonomic name -- to

• taxonomic ID -- to

• whatever other data
  (e.g., synonyms, classifications, etc.)

Occurrence data

• rgbif - GBIF

• rbison - USGS's BISON

• rvertnet - VertNet

• rebird - eBird (see also auk)

• spocc - one stop shop (of all above)

• finch - parse GBIF bulk data

• EML - read and create EML

• ridigbio ALA4R robis *

GBIF p.s.

we also maintain GBIF clients in Python and Ruby

taxonomy tools: in the works

• taxonomic name parsing: fast & platform independent for other R tool builders & tools for R users (see pegax poster)

• package taxa: needs more user testing - feedback plz!

• package taxadc: serialize R taxonomic data to Darwin Core- in early development

• package taxizedb - hard to a) make similar interface to SQL DB's as web services & 2) simplify varied database installs

• package taxview - summarise and visualize data sets from with respect to taxonomy

occurrence tools: in the works

• taking the pain out of GBIF downloads: ropensci/rgbif#266: queuing tool for GBIF downloads - hard problem

• occurrence cleaning in R: hard problem! A few efforts:

• package scrubr

• package CoordinateCleaner

• deduplication badly needed: aggregation up the data provider ladder

occurrence tools: questions

• DOIs for GBIF search service (and other services)?

• related to above: Sharing dataset associated with paper

• Visualzing huge occurrence datasets? (GBIF map API now in dev ver of rgbif ~ rgbif::map_fetch)

scotttalks.info/bocc

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