Biodiversity & Taxonomy Software Tools @
rOpenSci
Scott Chamberlain (
@sckottie)
UC Berkeley / rOpenSci
Broad areas of packages
Taxonomy
Occurrence data
Environmental data
Citations
Questions addressed w/ our software
Use cases: taxize
- classify species invasive or not
-
software uses taxize to check user names against
ITIS
-
check names against TPL, EOL, COL, IUCN, uBIO
- get name data for NCBI sequence data
- validate genus names for a food web
-
compiled dataset of tropical forest tree species
names checked w/ TNRS
-
add taxonomic classification data to
meta-analysis dataset
Use cases: rgbif
-
occurrence records to construct niche models
-
collect occurrence records for catfishes in a
Brazilian river
-
occurrence records of Acacia species in
Australia through time
-
assessing niche expansion of invasive plants
with occurrence records
-
small note in manuscript about a species being
in a study area
Use cases: rfishbase
- collect fish life history traits
-
extract fecundity data for four fish species
-
group species into trophic guilds using trophic
position
-
fetch salinity associated traits for many fish
species
-
acquire depth ranges for many species to
determine a phylogenetic signal
Use cases: rentrez
- search PubMed for mentions of phrases
-
demonstrate rentrez use to search NCBI for
articles in institutional repositories
-
fetch NCBI taxonomic information for sequence
data
- use NCBI's Gene Expression Omnibus service
-
extract citations (presumably from PubMed) using
rentrez
Use cases: spocc
-
use GBIF data to explore genome size variation
against many variables
-
use GBIF data to construct species range and
niche centroids
-
use GBIF, VertNet, BISON, Ecoengine, iNaturalist
data to construct species niche models
-
use Vertnet and iNaturalist data to identify
most vulernable populations for snakebites
-
use GBIF data via zoon in malariaAtlas R pkg
-
use GBIF and iDigBio data to construct future
species ranges
Use cases: rnoaa
-
fetch sea surface temperature (SST): check if
latitude/SST explains variation in body size
-
use many variables from ISD to predict airplane
flight time
-
use climate data to identify opportunities for
stream restoration
-
estimate interannual climatic variability in
urban areas
- government report on precipitation
future work /
hard problems