Aug 6, 2018

rOpenSci HQ

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

• Aug 6-10, New Orleans, LA, USA, Carl Boettiger and Dan Sholler, Ecological Society of America annual meeting
• Aug 15-16, Cambridge, MA, USA, Stefanie Butland, R/Pharma meeting
• Aug 27-30, Dunedin, New Zealand, Scott Chamberlain, Biodiversity Information Standards Meeting (TDWG)

Software 📦

CRAN: GitHub:

New packages

• The first version (v1.0.5) of helminthR is on CRAN - access the London Natural History Museum Host-Helminth record database. It’s been on GitHub for a while, but this is the first version on CRAN. Check out the vignette to get started.
• The first version (v1.0.0) of phylotaR is on CRAN - Automated Phylogenetic Sequence Cluster Identification from GenBank. Check out the docs to get started. The package recently completed our software review process and is now in the rOpenSci family - welcome Dom!
• The first version (v0.1.0) of nodbi is now on CRAN - it’s like DBI, bu for NoSQL databases, supporting create/get/delete/update operations for many NoSQL databases. Check out the README to get started. The project was started a few years back at an rOpenSci Unconference, but is just now getting to CRAN.

New versions

• A new version (v0.4.0) of nomisr is on CRAN - access UK official statistics from the Nomis database. See the NEWS for changes. Checkout the nomisr docs to get started.

  docs fixes, new citation to JOSS paper

• A new version (v0.4.1) of epubr is on CRAN - read EPUB File Metadata and Text. See the NEWS for changes. Checkout the epubr docs to get started.

  many fixes, better error handling

• A new version (v3.2-0) of clifro is on CRAN - easily download and visualise climate data from CliFlo. See the release notes for changes. Checkout the clifro vignettes to get started.

  many bug fixes, XML -> xml2

• A new version (v0.9.4) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.

  new fxns to help with API keys; 11 bug fixes!

• A new version (v0.2.2) of auk is on CRAN - eBird data extraction and processing with AWK. See the NEWS for changes. Checkout the auk docs to get started.

  updated to work with EDB ver. 1.9, bug fixes

• A new version (v0.2.4) of wdman is on CRAN - Webdriver/Selenium binary manager. See the NEWS for changes. Checkout the wdman vignette to get started.

  back on CRAN!

• A new version (v4.8.0) of plotly is on CRAN. See the NEWS for changes. Checkout the plotly book to get started.

  too many to list …

• A new version (v0.8.2) of rplos is on CRAN - Public Library of Science client. See the release notes for changes. Checkout the rplos vignettes to get started.

  bug fixes; now test caching with vcr

• A new version (v0.5.0) of rredlist is on CRAN - IUCN Red List client. See the release notes for changes. Checkout the rredlist README to get started.

  new function to help setup API key; new fxns for comp groups

• A new version (v0.2-6) of dbhydroR is on CRAN - DBHYDRO hydrologic and water quality data. See the release notes for changes. Checkout the dbhydroR docs to get started.

  get_hydro() bug fix

• A new version (v0.2.2) of bomrang is on CRAN - Australian Government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the bomrang docs to get started.

  fix corrupted zip file download in get_historical(); update pkg citation

• A new version (v5.3.0) 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.

  lots of improvements, check out the release notes

• A new version (v0.6.2) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the robotstxt vignette to get started.

  pkg dep. future compatability; small fix

• A new version (v0.1.1) of binman is on CRAN - a binary download manager. See the NEWS for changes. Checkout the binman vignette to get started.

  back on CRAN!

• The package qualtRics was archived on CRAN recently - hopefully it will be back up soon.

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

• arkdb > Archive and Unarchive Databases Using Flat Files
  • Author: Carl Boettiger
  • Issue: ropensci/onboarding#224
  • Reviewers:
    • Rich FitzJohn
    • Verena Haunschmid
• MODIStsp > A Tool for Automating Download and Preprocessing of MODIS Land Products Data
  • Author: Lorenzo Busetto
  • Issue: ropensci/onboarding#184
  • Reviewers:
    • Leah Wasser
    • Jeff Hanson

The following three packages were recently submitted:

• spatsoc > Group Animal Relocation Data by Spatial and Temporal Relationship
  • Author: Alec Robitaille
  • Issue: ropensci/onboarding#237
  • Reviewers:
    • Priscilla Minotti
    • Filipe Teixeira
• rdhs > API Client and Dataset Management for the Demographic and Health Survey (DHS) Data
  • Author: OJ Watson
  • Issue: ropensci/onboarding#238
  • Reviewers: not assigned yet
• treestartr > Generate Starting Trees For Combined Molecular, Morphological and Stratigraphic Data
  • Author: April Wright
  • Issue: ropensci/onboarding#239
  • Reviewers:
    • David Bapst
    • 2nd reviewer not assigned yet

On the blog

rOpenSci Unconference

We’ve got a number of blog posts from our series of posts from teams at our recent rOpenSci Unconference:

The pkginspector team (Sam Albers, Leonardo Collado-Torres, Mauro Lepore, Joyce Robbins, Omayma Said, and Noam Ross) wrote about their pkginspector project: What’s inside? pkginspector provides helpful tools for inspecting package contents

In a series of three blog posts the rOpenSci Educators Collaborative team (Laura Ación, Mara Averick, Leonardo Collado Torres, Auriel Fournier, Alison Hill, Sean Kross, Lincoln Mullen) wrote about:

• What Are The Challenges When Teaching Science With R?
• What Educational Resources Work Well and Why?
• How Can We Develop a Community of Innovative R Educators?

The umapr team (Sean Hughes, Angela Li, Ju Kim, Malisa Smith, and Ted Laderas) wrote about their pkginspector project: A package for dimensionality reduction of large data

Technotes

Jeroen Ooms wrote about a new package: Gifski on CRAN: the fastest GIF encoder in the universe. This is not only a fun package, but also demonstrates usage of the programming language Rust inside an R package!

Use cases

The following seven works use/cite rOpenSci software:

• Rodriguez & cited pdftools in their conference paper Uncovering the digital “x” phenomena in the IS field: A text analysis approach ¹
• Longbottom et al. used our package spocc in their paper Vulnerability to snakebite envenoming: a global mapping of hotspots ²
• Araujo & Alves used our package rAltmetric in their preprint The altmetric performance of publications authored by Brazilian researchers: analysis of CNPq productivity scholarship holders ³
• Ruiz et al. used iheatmapr in their paper Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum ⁴
• Paseka & Grunberg used rotl in their paper Allometric and trait-based patterns in parasite stoichiometry ⁵
• Finak et al. wrote a paper about their package DataPackageR: DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis ⁶
• Rojas-Garcia et al. used crminer in their paper Semi-automatic extraction of processes affecting beaches from a specialized corpus ⁷

The following seven papers cited our plotly package:

• Brechtmann, F., Matuseviciute, A., Mertes, C., Yepez, V. A., Avsec, Z., Herzog, M., … Gagneur, J. (2018). OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data. https://doi.org/10.1101/322149 ⁸
• Václav Brázda, Jiri Lysek, Martin Bartas, and Miroslav Fojta. 2018. Complex analyses of short inverted repeats in all sequenced chloroplast DNAs. BioMed Research International. https://www.hindawi.com/journals/bmri/aip/1097018/ ⁹
• Fontaine, A., Lequime, S., Moltini-Conclois, I., Jiolle, D., Leparc-Goffart, I., Reiner, R. C., & Lambrechts, L. (2018). Epidemiological significance of dengue virus genetic variation in mosquito infection dynamics. PLOS Pathogens, 14(7), e1007187. https://doi.org/10.1371/journal.ppat.1007187 ¹⁰
• Lawrence, T. N., & Bhalla, R. S. (2018). Spatially explicit action research for coastal fisheries management. PLOS ONE, 13(7), e0199841. https://doi.org/10.1371/journal.pone.0199841 ¹¹
• Glanz, H., & Pileggi, S. 2018. Improving statistical communication in statistical computing courses. In M. A. Sorto, A. White, & L. Guyot (Eds.), Looking back, looking forward. Proceedings of the Tenth International Conference on Teaching Statistics (ICOTS10, July, 2018), Kyoto, Japan. Voorburg, The Netherlands: International Statistical Institute. https://iase-web.org/icots/10/proceedings/pdfs/ICOTS10_3F1.pdf ¹²
• Zhang, Y., Oates, L. G., Serate, J., Xie, D., Pohlmann, E., Bukhman, Y. V., … Ong, R. G. (2018). Diverse lignocellulosic feedstocks can achieve high field-scale ethanol yields while providing flexibility for the biorefinery and landscape-level environmental benefits. GCB Bioenergy. https://doi.org/10.1111/gcbb.12533 ¹³
• Wang, C., Moya, L., Clements, J. A., Nelson, C. C., & Batra, J. (2018). Mining human cancer datasets for kallikrein expression in cancer: the “KLK-CANMAP” Shiny web tool. Biological Chemistry, 0(0). https://doi.org/10.1515/hsz-2017-0322 ¹⁴

In the news

Alex Koiter used two of our packages, weathercan and tidyhydat, to explore historical precipitation and sediment load in a single creek in 1975.

Thought there was an error in the data until I combined @steffilazerte's weathercan and @big_bad_sam's tidyhydat #rstats packages. Must have been an interesting day in Riding Mtn @ParksCanada Wilsons Crk back on Sept 19, 1975! Over 20 cm of rain in one day! pic.twitter.com/w3qh5DCv6E

— Alex K (@Alex_Koiter) July 10, 2018

Serdar Balci demonstrated in a tweet how to add NCBI references into an R markdown document with our package RefManageR

How to add @ncbi_pubmed references into R #Markdown document? Here is my #rstats code: pic.twitter.com/wCt0rZcZ5T

— Serdar Balcı (@serdarbalci) July 10, 2018

Paul Oldham used our package rorcid in a “practical introduction to the rorcid package”: Introduction to ORCID Researcher Identifiers in R with rorcid. This is a great intro to rorcid - if you’ve been wanting to use it this is a great place to get started.

Mara Averick pointed out a blog post on Image Manipulation for Machine Learning in R, which used our package magick.

✨ Lessons in {magick}…
📝 “Image Manipulation for Machine Learning in R” by AMR https://t.co/T5KQPyx9Ec #rstats #machinelearning pic.twitter.com/pKE9Utop92

— Mara Averick (@dataandme) July 17, 2018

Xavier Rotllan-Puig used our package rgbif in his first R package: PreSPickR

#MyFirstRPackage is on @github. Use #PreSPickR to download species presences (occurrences) from @GBIF and from #Bioatles.https://t.co/16Wku4EOuO
Please, report bugs and suggest improvements! #Rstats

— Xavi Rotllan-Puig 🎗 (@xavi_rp) July 17, 2018

Amanda Dobbyn wrote a blog post recently Sentiment analysis of Slack reviews using R using our packages monkeylearn and robotstxt

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Footnotes