Our next Community Call, on March 27th, aims to help people learn about using rOpenSci’s R packages to access and analyze taxonomy and biodiversity data, and to recognize the breadth and depth of their applications. We also aim to learn from the discussion how we might improve these tools.

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.

Programmatic access to biodiversity data is revolutionising large-scale, reproducible biodiversity research. In the marine realm, the largest global database of species occurrence records is the Ocean Biogeographic Information System, OBIS. As of January 2017, OBIS contains 47.78 million occurrences of 117,345 species, all openly available and accessible via the OBIS API.

finch has just been released to CRAN (binaries should be up soon). finch is a package to parse Darwin Core files. Darwin Core (DwC) is: GBIF (Global Biodiversity Information Facility) is the biggest holder of biodiversity data.

Taylor Noble As the ecology community expands, it is now adopting new ways of making sense of the plethora of data produced from diverse approaches, including ocean research, eco-genomics, limnology, and macrosystems ecology, through more integrative means – improving our understanding of biology in a broader sense.

Despite the well deserved scepticism about dashboards voiced by Shannon Mattern @shannonmattern (see Mission Control: A History of the Urban Dashboard, I discovered this by reading Ignore the Bat Caves and Marketplaces: lets talk about Zoning by Leigh Dodds @ldodds) I'm intrigued by the idea a dashboard for biodiversity. We could have several different kinds of information, displayed in a single place.

The great responsibility Every discipline of science is unique.  Ecology is no exception.  We work in diverse, complex, context-dependent systems. Global change and anthropogenic influences are very real issues for the health of the planet that ecologists often examine.  As a discipline, we have moved from context-dependent, local studies to much larger, integrated studies.

The iNaturalist project is a really cool way to both engage people in citizen science and collect species occurrence data. The premise is pretty simple, users download an app for their smartphone, and then can easily geo reference any specimen they see, uploading it to the iNaturalist website. It let’s users turn casual observations into meaningful crowdsourced species occurrence data.

UPDATE: mapping functions are in a separate package now (mapr). Examples that do mapping below have been updated. The rOpenSci projects aims to provide programmatic access to scientific data repositories on the web. A vast majority of the packages in our current suite retrieve some form of biodiversity or taxonomic data.

Data on more than 10,000 species of ants recorded worldwide are available through from California Academy of Sciences’ AntWeb, a repository that boasts a wealth of natural history data, digital images, and specimen records on ant species from a large community of museum curators.