Aug 20, 2018

rOpenSci HQ

The rOpenSci team will be at a number of upcoming events:

• Aug 27-30, Dunedin, New Zealand, Scott Chamberlain, Biodiversity Information Standards Meeting (TDWG)
• Sep 3-7, Buenos Aires, Argentina, Jenny Bryan and Maëlle Salmon (remote), LatinR meeting
• Sep 11, Radolfzell, Germany, Maëlle Salmon, AniMove meeting
• Sep 12-14, The Hauge, Netherlands, Jeroen Ooms, Use of R in Official Statistics (uRos2018)

Software 📦

CRAN: GitHub:

New packages

• The first version (v0.0.1) of arkdb is on CRAN - archive and unarchive databases as flat text files. Check out the docs to get started.
• The first version (v0.15.1) of DataPackageR is on CRAN - an R package to enable reproducible data processing, packaging and sharing. Check out the vignettes to get started.

New versions

• A new version (v1.2.2) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the GSODR docs to get started.

  bug 🐛 fixes

• A new version (v1.0.6) of helminthR is on CRAN - Access London Natural History Museum Host-Helminth Record Database. See the release notes for changes. Checkout the helminthR vignette to get started.

  bug fix

• A new version (v0.3.0) of bomrang is on CRAN - Australian Government Bureau of Meteorology (BOM) Data from R. See the release notes for changes. Checkout the bomrang docs to get started.

  new function get_coastal_forecast()

• A new version (v0.8.4) of rplos is on CRAN - Interface to the Search API for Public Library of Science journals. See the release notes for changes. Checkout the rplos vignettes to get started.

  docs updates, searchplos() bug fix, make sure to update

• A new version (v2.1.2) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the NEWS for changes. Checkout the RNeXML vignettes to get started.

  fix for failing CRAN checks

• A new version (v2.3) of tesseract is on CRAN - R bindings to the Open Tesseract Open Source OCR Engine. See the release notes for changes. Checkout the tesseract vignette to get started.

  fixed problem with setlocale()

• A new version (v0.8.2) of hddtools is on CRAN - Hydrological Data Discovery Tools. Checkout the hddtools vignette to get started.
• A new version (v2.5.5) of FedData is on CRAN - get geospatial data from several federated government data sources. See the NEWS for changes. Checkout the FedData README to get started.

  fixed issue with NLCD data processing

• A new version (v0.3.1) of taxa is on CRAN - taxonomic classes for groupings of taxonomic names without data, and those with data. See the NEWS for changes. Checkout the taxa vignette to get started.

  new fxns taxonomy_table(), print_tree() & many improvements

• A new version (v0.5.2) of roadoi is on CRAN - find free versions of scholarly publications via Unpaywall. See the NEWS for changes. Checkout the roadoi vignette to get started.

  fix example, change to email address handling

• A new version (v5.4.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the drake docs to get started.

  overhauled trigger interface; docs changes; refactor igraph attributes; enable vis_drake_graph() and sankey_drake_graph()

• A new version (v0.8.4) of rcrossref is on CRAN - R client for the Crossref API. See the release notes for changes. Checkout the rcrossref vignette to get started.

  RStudio Addin can now search by article metadata; can set custom base URL for cr_cn(); many improvements and bug fixes

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 three packages recently went through our onboarding process and have been approved!

• smapr > Acquisition and Processing of NASA Soil Moisture Active-Passive (SMAP) Data
  • Author: Maxwell Joseph
  • Issue: ropensci/onboarding#231
  • Reviewers:
    • Laura DeCicco
    • Marco Sciaini
• DataPackageR > Construct Reproducible Analytic Data Sets as R Packages
  • Author: Greg Finak
  • Issue: ropensci/onboarding#230
  • Reviewers:
    • Kara Woo
    • Will Landau
• infx > OpenBIS API access to the InfectX data repository
  • Author: Nicolas Bennett
  • Issue: ropensci/onboarding#218
  • Reviewers:
    • Philipp Ottolinger
    • Tamora James

The following two packages were recently submitted:

• colocr > Conduct Co-localization Analysis of Fluorescence Microscopy Images
  • Author: Mahmoud Ahmed
  • Issue: ropensci/onboarding#243
  • Reviewers:
    • Hao Zhu
    • Sean Hughes
• rcites > R Interface to the Species+ Database
  • Author: Jonas Geschke
  • Issue: ropensci/onboarding#244
  • Reviewers:
    • Noam Ross
    • other reviewer not assigned yet

On the blog

Software Review / Onboarding

Matthew Strimas-Mackey wrote a post about their recently rOpenSci reviewed package auk: Extracting and Processing eBird Data. The review: ropensci/onboarding#136

Animal Movement series

We’re doing a series of posts corresponding to the material for a talk Maëlle will give at the Animal Movement Analysis summer school in Radolfzell, Germany on September the 12th, in a Max Planck Institute of Ornithology. Here’s the first:

Where to go observe birds in Radolfzell? An answer with R and open data

Technotes

Dom Bennett wrote about a new package: phylotaR: Retrieve Orthologous Sequences from GenBank.

Jeroen Ooms wrote about a new version of mongolite: Mongolite 2.0: GridFS, connection pooling, and more.

Use cases

The following 12 works use/cite rOpenSci software:

• Krah et al. used rusda in their paper Evolutionary dynamics of host specialization in wood-decay fungi ¹
• Babcock et al. used rfishbase in their paper Fish community and single-species indicators provide evidence of unsustainable practices in a multi-gear reef fishery ²
• Almeida et al. used skimr in their paper Alcohol Expectancy-Adolescent Questionnaire (AEQ-AB): Validation for portuguese college students ³
• García et al. used textreuse in their paper Locating similar names through locality sensitive hashing and graph theory ⁴
• Abolaffio et al. used rerddap in their paper Olfactory-cued navigation in shearwaters: linking movement patterns to mechanisms ⁵
• Pierson used rnoaa in their thesis Flow From Flexibility: Identifying Opportunities For Streamflow Restoration in a Transboundary Municipal Watershed Through Water Budgeting ⁶
• Locard-Paulet et al. used plotly in their paper VisioProt-MS: interactive 2D maps from intact protein mass spectrometry ⁷
• Lortie et al. used rgbif in their paper Better late than never: a synthesis of strategic land retirement and restoration in California ⁸
• Van Gemert & Andersen rfishbase in their paper Challenges to fisheries advice and management due to stock recovery ⁹
• Tsuboi et al. used taxize in their paper Breakdown of brain–body allometry and the encephalization of birds and mammals ¹⁰
• Horvatić et al. used plotly in their paper Quantitative proteomics using tandem mass tags in relation to the acute phase protein response in chicken challenged with Escherichia coli lipopolysaccharide endotoxin ¹¹
• Samy et al. used spocc in their paper Mapping the potential distributions of etiological agent, vectors, and reservoirs of Japanese Encephalitis in Asia and Australia ¹²

In the news

Jorge López shared an example of how to use ckanr to extract data from Open Data Bacelona (code shared in a gist)

Very quick example of how to use the CKAN API in R to extract data from Open Data Bcn (open data service from @bcn_ajuntament). It shows a plot with the number of visitors at the main libraries in Barcelona (2016). #rstats

Code: https://t.co/oWb9AGV3Of pic.twitter.com/cY3ZHTxgu7

— Jorge López (@jlopezper) July 25, 2018

Two packages by Dmytro Perepolkin use rOpenSci packages:

• polite uses our robotstxt package to help promote responsible web etiquette when web scraping
• hocr uses our tesseract package to do post-processing of hOCR files into tidy formats

In a blog post John Waller wrote about GBIF download trends and used rgbif to collect the data from GBIF. It includes a Shiny app you can use to explore the data interactively.

Dan Olner shared a plot showing use of our bib2df package for parsing BibTeX files to a tibbles

Fun with @0ttlngr 's bib2df package. Think I might be a geographer... #R https://t.co/dpFlcdrS9k pic.twitter.com/LFDLAYoyX4

— Dan Olner (@DanOlner) August 10, 2018

At the recent Author Carpentry meeting a workshop was run using rorcid

Props to @rOpenSci for the rorcid pkg which we used at #fsci2018 and #DataTrieste18 to autopopulate our biosketches included in our reproducible reports created w/ Rmarkdown + knitr. @AuthorCarpentry lesson online &ready for forking at https://t.co/PKASSuIBd0 #rstats @ORCID_Org

— Gail (((Clement))) (@Repositorian) August 10, 2018

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Footnotes