Sep 26, 2017
rOpenSci HQ
Community Calls
Video is now up for our latest community call on rOpenSci Software Review and Onboarding.
https://github.com/ropensci/commcalls/issues/15
Discussion forum
Recently, on our discussion forum https://discuss.ropensci.org:
- [Best Practices] A research compendium and methylation raw data
- [Questions] How to avoid space-hogging raster tempfiles?
- [Questions] Resources for leaning C++/Rcpp?
- [Community] How do you hire data people in a fair and unbiased way?
- [Gists] traits::ncbi_byname to DNAbin objects
Software
New packages
- A new package
microdemic
(v0.1.0
) is on CRAN.microdemic
is an R client for the Microsoft Academic Knowledge API. Check out the microdemic README to get started. Repository on GitHub
Releases
- A new version (
v0.5.2
) ofbiomartr
is on CRAN. See the NEWS for details. Check out the biomartr vignettes to get started. Repository on GitHub - A new version (
v0.3.0
) oftraits
is on CRAN. This version adds new data sources and makes a suite of functions defunct (that were previsouly marked deprecated) that have moved to the [originr][] package. See the release notes for details. Check out the traits vignettes to get started. Repository on GitHub - A new version (
v0.2.10
) ofrglobi
is on CRAN. See the release notes for details. Check out the vignette to get started. Repository on GitHub - A new version (
v1.0.6
) ofGSODR
is on CRAN. See the release notes for details. Check out the vignettes to get started. Repository on GitHub - A new version (
v1.2
) ofxslt
is on CRAN. See the release notes for details. Check out Jeroen’s blog post to get started. Repository on GitHub - A new version (
v0.4.0
) oflawn
is on CRAN. This version has updated versions of most of the JS libraries bundled with the package, and other improvements. See the release notes for details. Check out the vignette to get started. Repository on GitHub - A new version (
v1.0.7
) oflingtypology
is on CRAN. See the release notes for details. Check out the vignette to get started. Repository on GitHub - A new version (
v0.8.0
) ofelastic
is on CRAN. This version brings many changes to scrolling, adds new functions, and fixes some bugs. See the release notes for details. Check out the README to get started. Repository on GitHub
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 for review:
- tidyhydat > Extract and Tidy Canadian Hydrometric Data
- Author: Sam Albers
- Issue: ropensci/onboarding#152
- Reviewers: not assigned yet
- EndoMineR > Functions to mine endoscopic and associated pathology datasets
- Author: Sebastian Zeki
- Issue: ropensci/onboarding#153
- Reviewers: not assigned yet
On the blog
We’ve had one blog post on our main blog in the past two weeks:
Use cases
The following four works use/cite rOpenSci or rOpenSci software:
- Olson et al. used taxize in their paper Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data 1
- Reznik et al. used taxize in their paper Genome-scale architecture of small molecule regulatory networks and the fundamental trade-off between regulation and enzymatic activity 2
- Cardoso et al. used rgbif in their paper Amazon plant diversity revealed by a taxonomically verified species list 3
- Jayasankar cited rfishbase and rfisheries in his paper Computational options for marine fisheries research and management 4
If you’ve used rOpenSci software in a blog post or a paper, tell us on the discussion forum and we’ll share it with our community here.
In the news
One of our own, Karthik Ram, was on the Changelog podcast: Conversations about sustaining open source
Submit news to rOpenSci
Reach out to us with your news suggestions by sending us an email info@ropensci.org or by contacting us on Twitter @ropensci
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Footnotes
-
Olson, N. D., Zook, J. M., Morrow, J. B., & Lin, N. J. (2017). Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data. PeerJ, 5, e3729. https://doi.org/10.7717/peerj.3729 ↩
-
Reznik, E., Christodoulou, D., Goldford, J. E., Briars, E., Sauer, U., Segrè, D., & Noor, E. (2017). Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. Cell Reports, 20(11), 2666–2677. https://doi.org/10.1016/j.celrep.2017.08.066 ↩
-
Cardoso, D., Särkinen, T., Alexander, S., Amorim, A. M., Bittrich, V., Celis, M., … Forzza, R. C. (2017). Amazon plant diversity revealed by a taxonomically verified species list. Proceedings of the National Academy of Sciences, 201706756. https://doi.org/10.1073/pnas.1706756114 ↩
-
Jayasankar, J. Computational options for marine fisheries research and management. Advanced Methods for Fish Stock Assessment and Fisheries Management, 136. http://eprints.cmfri.org.in/12174/1/13-Computational%20options%20for%20marine%20fisheries%20research.pdf ↩