The Taxonomic and Biodiversity Software Stack in R

Scott Chamberlain (@sckottie/@ropensci)

UC Berkeley - rOpenSci

R intro

• growing in popularity

• very widespread with biologists

• similar to e.g., Ruby, Python, Julia

• > 10K packages

a pitch for R

making biodiveristy and taxonomy software in R:

• R has all parts of digital research workflow

• R software means targeting users

• meets scientists/etc. where they are, which:

• facilitates reproducible science

• facilitates open science

rOpenSci?

• non-profit

• make open-source software for R

• large community developers/users

• target science use cases

• we often play role of communicating btw. scientists/data provders

the R taxonomy landscape

R packages

* not rOpenSci

• ritis - ITIS API client

• taxa - taxonomic classes

• taxize - one stop shop for data

• taxizedb - work w/ database dumps

• wikitaxa - Wikipedia taxonomy

• worrms - WoRMS API client

• pegax - parse taxonomic names

• Taxonstand - Plant List access (*)

R taxonomy task view:  

taxize

• access to more than 20 data sources

• consistent interfaces for tasks:

  • search
  • taxonomic ids
  • hierarchy
  • up/down-stream
  • children
  • synonyms
  • name resolution

taxize citations

with > 50 citations, some e.g.'s

• Retrieving taxa names from large biodiversity data collections using a flexible matching workflow
• Comparative genomics in the Asteraceae reveals little evidence for parallel evolutionary change in invasive taxa
• Are all species necessary to reveal ecologically important patterns?
• Long-lasting effects of land use history on soil fungal communities in second-growth tropical rain forests
• Taxonomic similarity, more than contact opportunity, explains novel plant-pathogen associations between native and alien taxa
• Diversity of ecosystems: Variation in network structure among food webs.
• camtrapR: an R package for efficient camera trap data management
• Genome size variation and species diversity in salamander families

representative taxize use case

"retrieve classification hierarchy from the Integrated Taxonomic Information System"

taxa

• taxonomic classes for R: taxon IDs, names, ranks, data sources

• taxonomic classes w/ & w/o data

• manipulate taxonomic classes: grow, prune, combine, calculate, etc.

• manipulate taxonomic classes while maintaining link to data

taxa as foundation software

idea is to integrate taxa in other software, e.g.:

• in development ver. taxize (see taxa-ids branch)

Thoughts on taxa?

Would love to know what people think?

PEG - Parsing Expression Grammar

• define rules (e.g., capture any digit)

• combine rules to form a grammar

• apply grammar to strings (e.g., taxonomic names)

gnparser exists

tdwg17 talk

thanks dmitry

but ...

R and Java don't play nice

R and C++ do play nice

I'm learning from gnparser to implement R/C++ parser

pegax status

not done yet, but

can instead and into the future use Globalnames Resolver as a web service via taxize

taxize::gnr_resolve

the R biodiversity landscape

R packages

* not rOpenSci

• rgbif - GBIF

• finch - parse GBIF bulk data

• EML - read and create EML

• rbison - USGS's BISON

• rvertnet - VertNet

• rebird - eBird (see also auk)

• rinat - iNaturalist

• ridigbio - iDigBio (*)

• ALA4R - Atlas of Living Australia (*)

• robis - OBIS (*)

• spocc - one stop shop (of all above)

R packages

* not rOpenSci

• scrubr - occ. data cleaning

• speciesgeocodeR - occ. data cleaning

• ...

• dismo - lots of biodiv. analysis pkgs

GBIF

pre-print in PeerJ: 10.7287/peerj.preprints.3304v1

R: rgbif

Python: pygbif

Ruby: gbifrb

R/Python more for researchers,
Python/Ruby more for web dev

rgbif

> 35 citations, some e.g.'s

• Niche dynamics of alien species do not differ among sexual and apomictic flowering plants

• Climatological correlates of seed size in Amazonian forest trees

• Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism

• Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

• Final Report of the Task Group on GBIF Data Fitness for Use in Agrobiodiversity

• Plant Distribution Data Show Broader Climatic Limits than Expert-Based Climatic Tolerance Estimates

representative rgbif use case

"... species occurrence data were gathered for major marine phyla ... from geo-referenced specimen data on [GBIF] ... using a polygon search area in ... rgbif"

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