Oct 15, 2018

rOpenSci HQ

• The rOpenSci team at upcoming events:
  • Nov 15, Seoul, Korea, Nick Tierney, R User Conference in Korea
• We’re having a community call tomorrow. 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?.

Software 📦

CRAN: GitHub:

New versions

• A new version (v0.2.0) of crminer is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started.

  can now set full cache path more easily

• A new version (v0.5.0) of hoardr is on CRAN - Manage cached files. See the release notes for changes. Checkout the vignette to get started.

  can now set full cache path more easily

• A new version (v1.2.3) of GSODR is on CRAN - Global surface summary of the day (GSOD) weather data client. See the release notes for changes. Checkout the docs to get started.

  bug fixes and many minor changes

• A new version (v0.2.8) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the NEWS for changes. Checkout the docs to get started.

  minor fixes

• A new version (v1.2) of antiword is on CRAN - Extract text from Microsoft Word documents. See the release notes for changes. Checkout the README is get started.

  fix gcc8 warning

• A new version (v0.3) of ssh is on CRAN - Secure shell (SSH) client for R. See the release notes for changes. Checkout the vignette is get started.

  fix gcc8 warnings; update libssh to v0.8.3

• A new version (v1.4.2) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started.

  Solaris fixes

• A new version (v0.0.8) of piggyback is on CRAN - Managing larger data on a GitHub repository. See the NEWS for changes. Checkout the docs to get started.

  update docs; remove dependency on utils::askYesNo

• A new version (v2.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette is get started.

  split manual page because examples take too long

• A new version (v0.2.2) of comtradr is on CRAN - Interface with the United Nations Comtrade API. See the release notes for changes. Checkout the vignette to get started.

  remove unused dependency methods from Imports

• A new version (v1.1.19) of rtika is on CRAN - R Interface to Apache Tika. See the NEWS for changes. Checkout the docs to get started.

  new java() function to help usability

• A new version (v0.3.0) of auk is on CRAN - eBird data extraction and processing. See the NEWS for changes. Checkout the docs to get started.

  new functions and many fixes and improvements

• A new version (v0.3.2) of NLMR is on CRAN - Simulating neutral landscape models. See the NEWS for changes. Checkout the docs to get started.

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!

• colocr > Conduct Co-localization Analysis of Fluorescence Microscopy Images
  • Author: Mahmoud Ahmed
  • Issue: ropensci/onboarding#243
  • Reviewers:
    • Hao Zhu
    • Sean Hughes
• CoordinateCleaner > Automated Cleaning of Occurrence Records from Biological Collections
  • Author: Alexander Zizka
  • Issue: ropensci/onboarding#199
  • Reviewers:
    • Irene Steves
    • Francisco Rodriguez-Sanchez

The following packages were recently submitted:

• wateRinfo > Download Time Series Data from Waterinfo.be
  • Author: Stijn Van Hoey
  • Issue: ropensci/onboarding#255
  • Reviewers: not assigned yet
• refnet > Thomson Reuters Web of Knowledge/Science and ISI Reference Data Tools
  • Author: Auriel Fournier
  • Issue: ropensci/onboarding#256
  • Reviewers: not assigned yet
• nbaR > R Package Client for the Netherlands Biodiversity API
  • Author: Hannes Hettling
  • Issue: ropensci/onboarding#257
  • Reviewers: not assigned yet

On the blog

Software Review / Onboarding

Rafael Pilliard Hellwig wrote about his recently rOpenSci reviewed package outcomerate: outcomerate: Transparent Communication of Quality in Social Surveys. The review: ropensci/onboarding#213

Thomas Klebel wrote about his recently rOpenSci reviewed package jstor: Parsing Metadata with R - A Package Story. It includes some great lessons learned about package development. The review: ropensci/onboarding#189

Technotes

Our own Jeroen Ooms wrote about a new package av: The av Package: Production Quality Video in R. Check out the package at ropensci/av

Our own Maëlle Salmon wrote about how to Distinguish yourself in CRAN person() with ORCID.

rOpenSci HQ

Stefanie Butland writes about our upcoming community call (tomorrow!). Community Call - Code Review in the Lab, or … How do you review code that accompanies a research project?. Please join us for our next community call; this is going to be a good one.

Use cases

The following 15 works use/cite rOpenSci software:

• Gye-Soo used tokenizers in their paper Text Mining and Big Data Analysis in the Relational Database with R ¹
• Merkling et al. used our package rotl in their paper Maternal Testosterone and Offspring Sex-Ratio in Birds and Mammals: A Meta-Analysis ²
• Pfeffer et al. used spocc in their paper malariaAtlas: an R interface to global malariometric data hosted by the Malaria Atlas Project ³
• Gadelha et al. used rgbif in their preprint A Survey of e-Biodiversity: Concepts, Practices, and Challenges ⁴
• Kimmelman, V., Klezovich, A., & Moroz, G. used lingtypology in their paper IPSL: A Database of Iconicity Patterns in Sign Languages ⁵
• Sánchez et al. used rotl in their paper On the relationship between body condition and parasite infection in wildlife: a review and meta‐analysis ⁶
• Denecker & Lelandais used plotly in their paper Empowering the detection of ChIP-seq “basic peaks” (bPeaks) in small eukaryotic genomes with a web user-interactive interface ⁷
• Wylie et al. used plotly in their paper Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy ⁸
• Davydov used plotly in their white paper Forecasting Retirements: The Case of the New York City Government Workforce ⁹
• Johnson et al. used plotly in their paper Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease ¹⁰
• Haddaway & Westgate used plotly in their paper Predicting the time needed for environmental systematic reviews and systematic maps ¹¹
• Schmidt cited textreuse in his paper Stable random projection: lightweight, general-purpose dimensionality reduction for digitized libraries ¹²
• Becker et al. used rotl in their paper Handling stress and sample storage are associated with weaker complement-mediated bactericidal ability in birds but not bats ¹³
• Roettger & Gordon used lingtypology in their paper Methodological issues in the study of word stress correlates ¹⁴
• Kollar et al. used plotly in their paper Increased levels of circulating MMP3 correlate with severe rejection in face transplantation ¹⁵

In the news

Ryo Nakagawara used riem, by our own Maëlle Salmon, in a blog post about weather in Japan

new #rstats blog post 📝: Visualizing the Weather ☀️🌧️in #Japan 🇯🇵!
Link: https://t.co/Dk0tGGAois

Special thanks to:@ma_salmon for the riem 📦and @u_ribo for the jmastats 📦#ggplot2 #dataviz #weather #天気 #気象庁 pic.twitter.com/hs9S2JJ20s

— ⚽️Ryo Nakagawara📊 (@R_by_Ryo) October 4, 2018

Angela Li gave a workshop at the Center for Spatial Data Science (CSDS) at Univrersity of Chicago for State of the Map 2018 event. In the materials for her GitHub repository https://github.com/angela-li/sotmus-r she uses our package osmdata

In a package from the company dreamRs (Victor Perrier and Fanny Meyer) they use our package geojsonio

We have updated our {topogram} htmlwidget : create interactive cartograms in D3 within R! It now accepts any #sf object thanks to #geojsonio ! Here's an example with 🍷 data and a base map from #eurostat package! #rstatshttps://t.co/PJ9GTopP55 pic.twitter.com/1bUBt8lROZ

— dreamRs (@dreamRs_fr) October 9, 2018

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Footnotes