Dec 9, 2019
rOpenSci HQ
- We’re excited to announce a new member of our team! Introducing Mark Padgham, rOpenSci’s new Software Research Scientist
- The recording and collaborative notes are up for our latest Community Call - Last Night, Testing Saved my Life.
Software 📦
CRAN: GitHub:
New Packages
- The first version (
v0.1.4
) ofbaRcodeR
after going through rOpenSci software review is on CRAN - the package deals with label creation for tracking and collecting data from biological samples. See the release notes for changes. Checkout the docs to get started.
New Versions
- A new version (
v2.0.1
) ofEML
is on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started.improve error messages; pandoc fixes; improve docs
- A new version (
v0.2.21
) ofrglobi
is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started.tests fixes
- A new version (
v0.5.0
) ofwebmockr
is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started.now supports writing to disk mocking & mocking simple auth with httr works now
- A new version (
v0.4.0
) ofvcr
is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started.now handles writing to disk; can now turn vcr completely off with a fxn call or env var; igoring specific requests now works; many httr fixes; much better docs for R6 classes
- A new version (
v0.2.7
) oftradestatistics
is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.4.0
) ofnlrx
is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started.new vignette; new crayon and EasyABC pkg deps; pandoc added to sys reqs
- A new version (
v2.1.1
) ofbeastier
is on CRAN - Provides a way to call BEAST2 from R. See the release notes for changes. Checkout the docs to get started.gains a vignette
- A new version (
v2.0.5
) ofmauricer
is on CRAN - install BEAST2 packages. See the release notes for changes. Checkout the docs to get started.gains a vignette
- A new version (
v2.0.2
) oftracerer
is on CRAN - parse and analyze BEAST2 input files programmatically. See the release notes for changes. Checkout the vignettes to get started.gains a vignette; better error checking
- A new version (
v2.3.2
) ofbeautier
is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the vignettes to get started. - A new version (
v7.8.0
) ofdrake
is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.dynamic branching implemented; new fxns subtargets, get_trace/read_trace, id_chr; bug fixes and many improvements
- A new version (
v0.5.0
) oftidyhydat
is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the vignettes to get started.bug fixes; allow downloading HYDAT to altnerative location; better docs
- A new version (
v0.6.1
) ofepubr
is on CRAN - read EPUB File Metadata and Text. See the release notes for changes. Checkout the docs to get started.fix warnings from a package dependency
- A new version (
v0.3.4
) ofeia
is on CRAN - API wrapper for US Energy Information Administration open data. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.2
) ofwritexl
is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the README to get started.update bundled libxlswriter to v0.8.8; xl_formula and xl_hyperlink now correctly support NA
- A new version (
v2.0.2
) ofskimr
is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. - A new version (
v0.2.4
) oftiler
is on CRAN - generate geographic and non-geographic map tiles from R. See the release notes for changes. Checkout the docs to get started.now precompiling vignettes; update gdal2tiles to v2.4; updated docs
Software Review ✔
We accept community contributed packages via our software review 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.
No new submissions or approved submissions.
On the blog
Jeroen Ooms wrote about How to precompute package vignettes or pkgdown articles.
Use Cases
The following 11 works use/cite rOpenSci software:
- Paudyal et al. used treeio in their paper Characterization of Salmonella Dublin isolated from bovine and human hosts 1
- Bohner & Diez used brranching in their paper Extensive mismatches between species distributions and performance and their relationship to functional traits 2
- Defolie et al. used rotl in their paper Patterns and variation in the mammal parasite–glucorticoid relationship 3
- Blischak et al. used git2r in their paper Creating and sharing reproducible research code the workflowr way 4
- Millard et al. used taxize in their paper Text‐analysis reveals taxonomic and geographic disparities in animal pollination literature 5
- Hung et al. used taxize in their paper A pilot study of the performance of captive‐reared delta smelt Hypomesus transpacificus in a semi‐natural environment 6
- Chalmandrier et al. used taxize in their paper Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales 7
- Mishra & Narayan Tripathi used rplos, rcrossref, and fulltext in their paper Characterization of two‐dimensional materials from Raman spectral data 8
- Christensen & Kenett used hunspell in their paper Semantic Network Analysis (SemNA): A Tutorial on Preprocessing, Estimating, and Analyzing Semantic Networks 9
- Zhong et al. used rnoaa in their paper Assessment of Winter Barley in Minnesota: Relationships among Cultivar, Fall Seeding Date, Winter Survival, and Grain Yield 10
- Tada et al. used webchem in their paper Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics 11
Related News
- Robin Lovelace, who maintains stats19 (work w/ open road traffic casualty data from Great Britain), put out a call for contributors: check out the beginners tutorial and open issues.
- The Chan Zuckerberg Initiative last month awarded grants to 42 open source projects. A noteable R project that recieved funding was: Bioconductor Build System: Continuous Integration and Developer Feedback. In addition, Python’s Pandas recieved funding, as well as pip - the package installer for Python; two tools used by many readers of this newsletter.
From the Forum
We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.
- Najko Jahn filed a use case on Analyzing invoice data from Elsevier relative to hybrid open access. He used a number of rOpenSci packages: rcrossref, crminer, and tabulizer.
- Rory Spanton filed a use case on Batch image manipulation using magick. The magick package is maintained by Jeroen Ooms.
Call For Maintainers
Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
We’ve had six recent examples of maintainer transitions within rOpenSci:
- RSelenium: now maintained by Ju Kim
- chromer: now maintained by Paula Andrea
- qualtRics: now maintained by Julia Silge
- rsnps: now maintained by Julia Gustavsen and Sina Rüeger
- rdpla: now maintained by Alyssa Columbus
- webchem: now maintained by Erik Sapper
- mregions: in process of moving to maintainance by VLIZ
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
Keep up with rOpenSci
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Footnotes
-
Paudyal, N., Pan, H., Elbediwi, M., Zhou, X., Peng, X., Li, X., … Yue, M. (2019). Characterization of Salmonella Dublin isolated from bovine and human hosts. BMC Microbiology, 19(1). https://doi.org/10.1186/s12866-019-1598-0 ↩
-
Bohner, T., & Diez, J. (2019). Extensive mismatches between species distributions and performance and their relationship to functional traits. Ecology Letters. https://doi.org/10.1111/ele.13396 ↩
-
Defolie, C., Merkling, T., & Fichtel, C. (2019). Patterns and variation in the mammal parasite–glucorticoid relationship. Biological Reviews. https://doi.org/10.1111/brv.12555 ↩
-
Blischak, J. D., Carbonetto, P., & Stephens, M. (2019). Creating and sharing reproducible research code the workflowr way. F1000Research, 8, 1749. https://doi.org/10.12688/f1000research.20843.1 ↩
-
Millard, J. W., Freeman, R., & Newbold, T. (2019). Text‐analysis reveals taxonomic and geographic disparities in animal pollination literature. Ecography. https://doi.org/10.1111/ecog.04532 ↩
-
Hung, T., Rosales, M., Kurobe, T., Stevenson, T., Ellison, L., Tigan, G., … Teh, S. (2019). A pilot study of the performance of captive‐reared delta smelt Hypomesus transpacificus in a semi‐natural environment. Journal of Fish Biology. https://doi.org/10.1111/jfb.14162 ↩
-
Chalmandrier, L., Pansu, J., Zinger, L., Boyer, F., Coissac, E., Génin, A., … Thuiller, W. (2019). Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales. Ecography. https://doi.org/10.1111/ecog.04492 ↩
-
Mishra, P., & Narayan Tripathi, L. (2019). Characterization of two‐dimensional materials from Raman spectral data. Journal of Raman Spectroscopy. https://doi.org/10.1002/jrs.5744 ↩
-
Christensen, A. P., & Kenett, Y. (2019, October 22). Semantic Network Analysis (SemNA): A Tutorial on Preprocessing, Estimating, and Analyzing Semantic Networks. https://doi.org/10.31234/osf.io/eht87 ↩
-
Zhong, B. H. W., Wiersma, J. J., Sheaffer, C. C., Steffenson, B. J., & Smith, K. P. (2019). Assessment of Winter Barley in Minnesota: Relationships among Cultivar, Fall Seeding Date, Winter Survival, and Grain Yield. Cftm, 5(1), 0. https://doi.org/10.2134/cftm2019.07.0055 ↩
-
Tada, I., Tsugawa, H., Meister, I., Zhang, P., Shu, R., Katsumi, R., … Chaleckis, R. (2019). Creating a Reliable Mass Spectral–Retention Time Library for All Ion Fragmentation-Based Metabolomics. Metabolites, 9(11), 251. https://doi.org/10.3390/metabo9110251 ↩