Aug 17, 2015

Software

• A new package (version 0.1.0) fulltext is on CRAN. This package makes it easier to search for articles, download articles in full text if available, convert pdf format to plain text, and extract text chunks for vizualization/analysis. We are planning to add bits for analysis in future versions. See the blog post for an introduction to the package. Repository on GitHub.
• A new version (0.5.2) of rplos is on CRAN. This was a fairly minor version bump with bug fixes. See the release notes for changes.
• A new version (0.6.2) of taxize is on CRAN. This version includes numerous bug fixes; fixes to comply with changes in httr v1; general cleanup of gni_*() functions; and fixes to support COL’s change from numeric taxonomic identifiers to alphanumeric identifiers. See the release notes for changes.
• A new version (0.1.4) of geojsonio is on CRAN. This version includes bug fixes, and adds a new function map_leaf() to make maps with the leaflet package, and geojson_read allows you to optionally get back a spatial class object instead of geojson. See the release notes for changes.
• A new version (0.11) of git2r is on CRAN. See the NEWS file for changes.
• A new version (2.0.1) of rfishbase is on CRAN.
• A new version (0.0.2) of webchem is on CRAN.

Use cases

A bunch of papers appeared recently using/citing rOpenSci software:

• Boeger et al. have a paper in Zoologica Scripta titled Tracking the history of an invasion: the freshwater croakers (Teleostei: Sciaenidae) in South America that uses and cites our rfishbase package.
• Bone et al. have a paper in New Phytologist titled A macro-ecological perspective on crassulacean acid metabolism (CAM) photosynthesis evolution in Afro-Madagascan drylands: Eulophiinae orchids as a case study that uses and cites our rgbif package.
• Collins et al. have a paper in Journal of Zoological Systematics and Evolutionary Research titled Phylogenetic systematics of leaffishes (Teleostei: Polycentridae, Nandidae) that uses and cites our rfishbase package.
• Dodd et al. have a paper in Diversity and Distributions titled The changing patterns of plant naturalization in Australia that uses and cites our taxize package.
• Price et al. have a paper in Coral Reefs titled Phylogenetic insights into the history and diversification of fishes on reefs that uses and cites our rfishbase package.
• Werner et al. have a paper in PNAS titled Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism that uses and cites our rgbif package.