rgbif was seven years old yesterday!
What is rgbif?
rgbif gives you access to data from the Global Biodiversity Information Facility (GBIF) via their API.
A samping of use cases covered in rgbif:
Search for datasets
Get metrics on usage of datasets
Get metadata about organizations providing data to GBIF
Search taxonomic names
Get quick taxonomic name suggestions
Search occurrences by taxonomic name/country/collector/etc.
Download occurrences by taxonomic name/country/collector/etc.
Fetch raster maps to quickly visualize large scale biodiversity
History
Our first commit on rgbif was on 2011-08-26, uneventfully adding an empty README:
We�ve come a long way since Aug 2011. We�ve added a lot of new functionality and many new contributors.
Commit history
Get git commits for rgbif using a few packages as well as git2r, our R package for working with git repositories:
library(git2r)
library(ggplot2)
library(dplyr)
repo %
ungroup()
ggplot(df, aes(x = as.Date(date), y = cumsum)) +
geom_line(size = 2) +
theme_grey(base_size = 16) +
scale_x_date(labels = scales::date_format(&quot;%Y/%m&quot;)) +
labs(x = 'August 2011 to August 2018', y = 'Cumulative Git Commits')
Contributors
A graph of new contributors through time
date_name %
filter(rank(date, ties.method = &quot;first&quot;) == 1) %__%
ungroup() %__%
mutate(count = 1) %__%
arrange(date) %__%
mutate(cumsum = cumsum(count))
## plot
ggplot(firstdates, aes(as.Date(date), cumsum)) +
geom_line(size = 2) +
theme_grey(base_size = 18) +
scale_x_date(labels = scales::date_format(&quot;%Y/%m&quot;)) +
labs(x = 'August 2011 to August 2018', y = 'Cumulative New Contributors')
rgbif contributors, including those that have opened issues (click to go to their GitHub profile):
adamdsmith - AgustinCamacho - AlexPeap - andzandz11 - AugustT - benmarwick - cathynewman - cboettig - coyotree - damianooldoni - dandaman - djokester - dlebauer - dmcglinn - dnoesgaard - DupontCai - EDiLD - elgabbas - emhart - fxi - gkburada - hadley - ibartomeus - JanLauGe - jarioksa - jhpoelen - jkmccarthy - johnbaums - jwhalennds - karthik - kgturner - Kim1801 - ljuliusson - luisDVA - martinpfannkuchen - MattBlissett - MattOates - maxhenschell - Pakillo - peterdesmet - PhillRob - poldham - qgroom - raymondben - rossmounce - sacrevert - sckott - scottsfarley93 - SriramRamesh - steven2249 - stevenpbachman - stevensotelo - TomaszSuchan - Uzma-165 - vandit15 - vervis - vijaybarve - willgearty - zixuan75
rgbif usage
Carl Boettiger and I wrote a preprint paper describing rgbif in 2017, in PeerJ Preprints.
Chamberlain SA, Boettiger C. (2017) R Python, and Ruby clients for GBIF species occurrence data. PeerJ Preprints 5:e3304v1 https://doi.org/10.7287/peerj.preprints.3304v1
In that paper we also discuss Python (pygbif) and Ruby (gbifrb) GBIF clients. Check those out if you also sling Python or Ruby.
The paper above and/or the package have been cited 56 times over the past 7 years.
The way rgbif is used in research is most often in download occurrence data for a set of study species.
One example comes from the paper
Carvajal-Endara, S., Hendry, A. P., Emery, N. C., &amp; Davies, T. J. (2017). Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Galápagos archipelago. Ecology Letters, 20(4), 495–504. https://doi.org/10.1111/ele.12753
In another example (note the mention of removing certain records based on GBIF flags, check out rgbif::occ_issues to learn more)
Werner, G. D. A., Cornwell, W. K., Cornelissen, J. H. C., &amp; Kiers, E. T. (2015). Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism. Proc Natl Acad Sci USA, 112(33), 10262–10269. https://doi.org/10.1073/pnas.1424030112
Some features coming down the road
Fully automated pagination across the package. Some functions have automated pagination (occ_search/occ_data/all name_ functions). So users don�t have to do manual pagination.
Improved map_fetch() function. We just released this function in the last version, but it�s still early days and needs to improve a lot based on your feedback
Improved occurrence downloading queue: we rolled this out recently but just like map_fetch it�s in its early days and definitely has many rough edges. Please let us know what you think!
Thanks!
We all owe a large debt of gratitude to GBIF for making an awesome resource for all those using their data, and to all the organizations/people that contribute data to GBIF.
A huge thanks goes to all rgbif users and contributors! It�s great to see how useful rgbif has been through the years, and we look forward to making it even better moving forward.