Nov 27, 2018

rOpenSci HQ

• We just had a community call on Working with images in R. Check out the notes and video at https://github.com/ropensci/commcalls#past-calls
• We need a new maintainer for the chromer package! It is a package for interacting with the chromosome counts database (CCDB) http://ccdb.tau.ac.il. It is in working order, though there are a number of issues outstanding to address, and other possible issues once you dive in. The package has had two citations (that we know of) so far: Sessa & Der 2017 and Zenil-Ferguson et al. 2017.

Software 📦

CRAN: GitHub:

New packages

• The first version (v1.0.0) of restez is on CRAN - create and query a local copy of GenBank. Checkout the docs to get started. You can find the software review at ropensci/onboarding#232
• The first version (v1.0.0) of rcites is on CRAN - access the CITES Speciesplus database. See the release notes for changes. Checkout the docs to get started. You can find the software review at ropensci/onboarding#244

New versions

• Two new versions (v0.2.0/v0.2.1) of rdflib are on CRAN - High level wrapper around the redland rdf package. See the release notes for changes. Checkout the docs to get started.

  rdf() now supports all major storage backends; new fxn length()

• A new version (v0.3.5) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.

  readr compatibility fix; column names in jst_get_refernces have been renamed to avoid ambiguity when matching with output from jst_get_article

• A new version (v1.3.0) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started.

  use future_apply in processing files after downloading

• A new version (v0.2.1) of tiler is on CRAN - Generate geographic and non-geographic map tiles from R. See the release notes for changes. Checkout the docs to get started.

  improved help for Windows users; added leaflet examples; bug fix for Windows users

• A new version (v0.4) of NLMR is on CRAN - Simulating neutral landscape models. See the release notes for changes. Checkout the docs to get started.

  nlm_neigh, nlm_mpd, nlm_randomrectangularcluster now implemented in Rcpp

• A new version (v0.9.0) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started.

  AntWeb data source removed; fixes to eBird internals; occ() now collects HTTP request error info & gains throw_warnings param to control warnings

• A new version (v1.19.1) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started.

  updated Tika version

• A new version (v0.2.0) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started.

  fix for select_indicators(); speed ups for indicators() fxn

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 recently went through our onboarding process and have been approved!

• tiler > Create Geographic and Non-Geographic Map Tiles
  • Author: Matthew Leonawicz
  • Issue: ropensci/onboarding#226
  • Reviewers:
    • Jasmine Daly
    • Paula Moraga
• spatsoc > Group Animal Relocation Data by Spatial and Temporal Relationship
  • Author: Alec Robitaille
  • Issue: ropensci/onboarding#237
  • Reviewers:
    • Priscilla Minotti
    • Filipe Teixeira
• restez > Create and Query a Local Copy of GenBank in R
  • Author: Dom Bennett
  • Issue: ropensci/onboarding#232
  • Reviewers:
    • Naupaka Zimmerman
    • Evan Eskew
• treeStartR > Generate Starting Trees For Combined Molecular, Morphological and Stratigraphic Data
  • Author: April Wright
  • Issue: ropensci/onboarding#239
  • Reviewers:
    • Rachel Warnock
    • David Bapst
• rcites > R Interface to the Species+ Database
  • Author: Jonas Geschke
  • Issue: ropensci/onboarding#244
  • Reviewers:
    • Margaret Siple
    • Noam Ross

The following package was recently submitted:

• git2rdata > Store and Retrieve Data.frames in a Git Repository
  • Author: Thierry Onkelinx
  • Issue: ropensci/onboarding#263
  • Reviewers: not assigned yet

On the blog

Ben Raymond and Michael Sumner wrote about The Antarctic/Southern Ocean rOpenSci community. Do check it out to see what’s going on in this flourishing community within rOpenSci of folks interested in Antarctic/Southern Ocean data and software.

Peter Desmet, Damiano Oldoni, and Lien Reyserhove wrote about Checklist Recipe - How we created a template to standardize species data. Their work won the recent GBIF Ebbe Nielsen Challenge. It’s a great example of leveraging R to create reproducible workflows!

Use cases

The following 16 works use/cite rOpenSci software:

• Tickler et al. use seaaroundus in their paper Modern slavery and the race to fish ¹
• Lynd et al. use plotly in their paper Insecticide resistance in Anopheles gambiae from the northern Democratic Republic of Congo, with extreme knockdown resistance (kdr) mutation frequencies revealed by a new diagnostic assay ²
• Robitaille et al. use spatsoc in their paper Conducting social network analysis with animal telemetry data: applications and methods using spatsoc ³
• Moura et al. use MODIStsp in their paper Relation of El Niño and La Niña phenomena to precipitation, evapotranspiration and temperature in the Amazon basin ⁴
• Bartomeus et al. use taxize and rgbif in their paper Historical collections as a tool for assessing the global pollination crisis ⁵
• Jarić et al. use rfishbase in their paper Susceptibility of European freshwater fish to climate change: species profiling based on life-history and environmental characteristics ⁶
• Weishäupl et al. use magick in their paper Physiological and pathophysiological characteristics of ataxin-3 isoforms ⁷
• Perez et al. use spocc in their paper Botanic gardens are an untapped resource for studying the functional ecology of tropical plants ⁸
• Albrecht et al. use cld2 in their paper Description of Cardiological Apps From the German App Store: Semiautomated Retrospective App Store Analysis ⁹
• Patel used tokenizers in their paper Sentiment Analysis of Harry Potter Book Series using R ¹⁰
• Varela used MODIStsp in their dissertation Applications of remote sensing in agriculture via unmanned aerial systems and satellites ¹¹
• Garmendia et al. used writexl in their paper Insect repellent and chemical agronomic treatments to reduce seed number in “Afourer” mandarin. Effect on yield and fruit diameter ¹²
• Watts & Miksis-Olds used rentrez in their white paper The Ocean as a Living Sensor: Environmental DNA and Acoustics for Detecting Marine Life ¹³
• Hurtado et al. used MODIStsp in their paper Population Dynamics of Anopheles albimanus (Diptera: Culicidae) at Ipetí-Guna, a Village in a Region Targeted for Malaria Elimination in Panamá ¹⁴
• Pietrosemoli & Dobay used rentrez in their book chapter Optimized Protein–Protein Interaction Network Usage with Context Filtering ¹⁵
• Boettiger wrote about his new package piggyback in a JOSS paper Managing Larger Data on a GitHub Repository ¹⁶

In the news

Dean Marchiori used our package bomrang (from maintainer Adam Sparks) to create an automated surf conditions email Surf Check - Automating Weather Forecast Emails in R

My latest post uses the bomrang #rstats 📦 to create an automated email each morning w my local surf conditions 🤙🌊 @rOpenSci @adamhsparks https://t.co/fqMYLgyYsi

— Dean Marchiori (@deanmarchiori) November 13, 2018

Simon Coulombe used our package weathercan (from maintainer Steffi LaZerte) in his blog post about Buying a heat pump the data scientist way

Does buying a heat pump for my 🏠 in cold 🇨🇦 makes sense, the data scientist way. I use local weather data provided by the weathercan package, my hourly electricity consumption and some tech sheets. (thanks @steffilazerte !) @rOpenSci @Rbloggers #rstats https://t.co/kP5K5XZotm pic.twitter.com/qOEEwAQzja

— Simon Coulombe (@CoulSim) November 22, 2018

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Footnotes