rOpenSci & R packages for Biodiversity Analysis

Scott Chamberlain (@sckottie/@ropensci)

UC Berkeley / rOpenSci

open science

Open science as a lego set

Open science as a lego set

open science may be hard to do

but - you can work on different components

and - individual components are worth learning

Open Data

make your data open

funders/journals often requiring this anyway

future self will thank you

Versioning: code/data/text

Versioning: code/data/text

failure proofs your work

experiment freely!

Do all work programatically

Do all work programatically

Key to reproduciblity

Most important person that wants to reproduce your work is you!

Do all work programatically

you and yourself

- one week from now

- two months from now

- & so on

An example to shoot for

R language

• used widely in biology, psychology, medicine, etc.

• rapidly growing user base, companies surrounding it

• includes all tools for open science workflow

• though work to be done ...

Open science ecosytsem

rOpenSci does:

rOpenSci Staff

• 4 full time

• now including a community manager!

• leadership team

• advisory board

Community stats

• ~ 250 code contributors

• large no. bug reports/feature requests

• ~ 364 Github repositories

• ~ 30,000 commits

• ~ 123 published R packages

What data do you use in your research?

the research workflow

the research workflow

the research workflow

the research workflow

the research workflow

rOpenSci Tools

use case 1

use case 2

use case 3

Taxonomy

• taxize - Taxonomic toolbelt

• taxizesoap - Taxonomic toolbelt (SOAP)

• ritis - ITIS client (avail. in taxize)

• taxizedb - Access to SQL dumps

• wikitaxa - Taxonomy from Wiki-pedia/-species/-commons

• worrms - WORMS client (avail. in taxize)

• natserv - Natureserve client (avail. in taxize)

• taxa - Taxonomic classes to be used by other pkgs (coming soon)

Taxonomic IDs

always try to move from:

• taxonomic name -- to

• taxonomic ID -- to

• whatever other data

Species occurrence data

• spocc - One client to rule them all

• rgbif - GBIF data (avail. in spocc)

• AntWeb - AntWeb ant data (avail. in spocc)

• ecoengine - Berekeley Ecoengine client (avail. in spocc)

• rinat - iNaturalist client (avail. in spocc)

• rbison - USGS BISON client (avail. in spocc)

• rebird - eBird data (avail. in spocc)

• rvertnet - VertNet data (avail. in spocc)

• rfishbase - Fishbase.org data

• rAvis - PreyectoAvis data

Species occurrence data: other

• ALA4R - Atlas of Living Australia R client

• rseaaroundus - SeaAroundUs

Biodiveristy related data

• finch - Parse Darwin Core archives

• rredlist - IUCN Red List

• Reol - EOL client

• mregions - Marineregions.org data

• natserv - NatureServe data

• neotoma - Neotoma data

• pangaear - Pangaea www.pangaea.de

• natserv - NatureServe data

Occurrence data cleaning

• scrubr - general purpose cleaner

• rgeospatialquality - API wrapper for checking occ. data

how do you clean your data?

Geospatial

• geojson - GeoJSON classes

• geojsonio - GeoJSON/TopoJSON input/output

• geonames - Geonames API client

• wicket Well-Known Text tools

• wellknown - WKT from R objects - and convert to GeoJSON

• rnaturalearth - NaturalEarth data

• osmplotr - Open Street Maps tools

• opencage - OpenCage geocoding API

• lawn - Turf.js javascript geo client

• geojsonlint - lint GeoJSON

Geospatial: conversion between data/spatial data formats - geojsonio

• geojson_list - convert to GeoJSON as R list

• geojson_json - convert to GeoJSON as JSON

• geojson_read/geojson_write - read/write GeoJSON

from most R object types + many spatial data formats

Climate data

• rnoaa - Lots of NOAA data

• ccafs - Climate Change, Agriculture, and Food Security (CCAFS) General Circulation Models (GCM) data

• camsRad - CAMS Radiation service

• clifro - New Zealand's National Climate Database CliFlo

• GSODR - NOAA Global Summary Daily Weather Data

• riem - ASOS data via the Iowa Environment Mesonet

• ropenaq - OpenAQ API client

• rWBclimate - World Bank climate data

Phylogenies

• brranching - Phylomatic

• phylocomr - Phylocom client :)

• rotl - Open Tree of Life

• treebase - TreeBase

What's too hard?

scotttalks.info/ossps2

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