Oct 29, 2018

rOpenSci HQ

• OzUnconf https://ozunconf18.ropensci.org/ is running for the third year. The unconference is 22-23 November in Melbourne, Australia. OzUnconf is based on our main unconference in the US (http://unconf18.ropensci.org/) but more accessible to folks in Australia/Asia.
• We just had a community call. See a recent blog post for all the details: Community Call - Code Review in the Lab, or … How do you review code that accompanies a research project?. And here’s links to other resources from the call, including recording: http://communitycalls.ropensci.org/#past-calls
• We’re having another community call coming up soon. See a recent blog post for all the details. Community Call - Working with images in R.

Software 📦

CRAN: GitHub:

New packages

• A new version (v1.0.1) of nasapower is on CRAN - NASA POWER API client. Checkout the docs to get started.

New versions

• A new version (v0.8.0) of bold is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the vignette to get started.

  bold_identify_parents() improvements, and bold_specimens() bug fix

• A new version (v6.1.0) of drake is on CRAN - pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.

  new fxns map_plan()/plan_to_code()/drake_debug(); many improvements and bug fixes

• A new version (v0.7.0) of rbison is on CRAN - interface to the USGS BISON API. See the release notes for changes. Checkout the vignette to get started.

  bison() now paginates internally and loses what parameter; bisonmap() fix

• A new version (v0.4.0) of microdemic is on CRAN - Microsoft Academic API client. See the release notes for changes. Checkout the README to get started.

  tests now use vcr; ma_abstract() now a data.frame

• A new version (v0.15.4) of DataPackageR is on CRAN - construct reproducible analytic data sets as R packages. Checkout the vignette to get started.
• A new version (v2.0-3) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the NEWS for changes. Checkout the docs to get started.
• A new version (v0.3.0) of isdparser is on CRAN - parse NOAA Integrated Surface data files. See the release notes for changes. Checkout the vignette to get started.

  small bug fix; working on incorporating metadata

• A new version (v1.1.0) of jqr is on CRAN - a client for JQ, the JSON processor. See the release notes for changes. Checkout the vignette to get started.

  jq() now supports connections (file paths, urls) and json objects; new build_ fxns

• A new version (v0.0.8) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started.

  bug fixes in trim_osmdata and opq

• A new version (v0.2.2) of bikedata is on CRAN - download and aggregate data from public hire bicycle systems. See the release notes for changes. Checkout the docs to get started.

  minor bug fixes

• A new version (v0.5.0) of epubr is on CRAN - read EPUB file metadata and text. See the release notes for changes. Checkout the vignette to get started.

  new fxn epub_cat(); epub() gains encoding param

• A new version (v0.2.6) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

  new fxn route_local(); line2route() gains time_sleep param

• A new version (v1.1.0) of fulltext is on CRAN - full text of scholarly articles across many data sources. See the release notes for changes. Checkout the fulltext book to get started.

  new fxns cache_file_info() & as.ft_data(); better error info in ft_get(); many, many, many bug fixes and improvements

• A new version (v1.1.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started.

  now using vcr for tests; name issues metadata added; map_fetch() changes

• A new version (v0.2.8) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started.

  gains support for httr!

• A new version (v0.2.0) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started.

  gains support for httr!

• A new version (v0.3.0) of wikitaxa is on CRAN - taxonomic information from Wikipedia. See the release notes for changes. Checkout the docs to get started.

  now using vcr for tests; wt_wikipedia() bug fix

• A new version (v0.3.0) of charlatan is on CRAN - make fake data. See the release notes for changes. Checkout the vignette to get started.

  ch_job()/JobsProvider gain da_DK locale support; many fixes for JobsProvider/PersonProvider

• A new version (v0.3.4) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.

  parse references if available

Software Review ✔

We accept community contributed packages via our onboarding system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system), and the authors of the packages!

If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.

The following packages were recently submitted:

• DataSpaceR > An R Interface to the CAVD DataSpace
  • Author: Ju Yeong Kim
  • Issue: ropensci/onboarding#261
  • Reviewers: not assigned yet
• nlrx > Setup, run and analyze NetLogo model simulations from R via XML
  • Author: Jan Salecker
  • Issue: ropensci/onboarding#262
  • Reviewers: not assigned yet

On the blog

Technotes

Scott Chamberlain wrote about a new package pubchunks: pubchunks: extract parts of scholarly XML articles. Check out the package at ropensci/pubchunks.

rOpenSci HQ

Stefanie Butland writes about our next upcoming community call. Community Call - Working with images in R. Please join us for our next community call!

Use cases

The following 12 works use/cite rOpenSci software:

• Baquero & Machado used tabulizer in their paper Spatiotemporal dynamics and risk factors for human Leptospirosis in Brazil ¹
• Rahman et al. used plotly in their paper KinaMetrix: a web resource to investigate kinase conformations and inhibitor space ²
• Vieilledent et al. used taxize in their paper New formula and conversion factor to compute basic wood density of tree species using a global wood technology database ³
• McAfee et al. used FedData in their paper Changing station coverage impacts temperature trends in the Upper Colorado River Basin ⁴
• Shema et al. used rAltmetric in their conference paper Retractions from altmetric and bibliometric perspectives ⁵
• Borer used pdftools in their dissertation Creating a Water Quality Geodatabase for the West Hawai ‘i Island Region ⁶
• Testo et al. used rgbif in their paper The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae) ⁷
• Horvatić et al. used plotly in their paper Integrated dataset on acute phase protein response in chicken challenged with Escherichia coli lipopolysaccharide endotoxin ⁸
• Milla et al. used taxize in their paper Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food ⁹
• Hagerman et al. used riem in their paper Temporal and geographic distribution of weather conditions favorable to airborne spread of foot-and-mouth disease in the coterminous United States ¹⁰
• Yu, G. et al. used treeio in their paper Two methods for mapping and visualizing associated data on phylogeny using ggtree ¹¹
• Degen & Faulwetter used rfishbase in their paper The Arctic Traits Database – A repository of arctic benthic invertebrate trait ¹²

In the news

Two people played with one of our newest packages (av) and shared their experience:

Average daily temperature in Bratislava (2016 - ~ Now). Thx @rOpenSci for av package, @thomasp85 for gganimate, and @JustTheSpring for sample code! There is lot of to improve... #ggplot2 #rstats #DataScience #Weather #gganimate #dataviz #datavideo pic.twitter.com/sMwg0z0M7d

— Peter Laurinec (@petolauri) October 16, 2018

In a blog post Animated Prison someone used av to help visualize the rate of incarceration over time in the US.

In a recent presentation rnoaa was cited: Improving pollution source resolution for real time low cost sensors using widely available data resources

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Footnotes