Software 📦

CRAN: GitHub:

New Versions

  • A new version (v1.1.3) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.24.1) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.3.0) of googleLanguageR is on CRAN - Google’s Natural Language, Cloud Translation, Cloud Speech, and Cloud Text-to-Speech APIs. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.1.0) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.4.0) of natserv is on CRAN - NatureServe R Interface. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.9.0) of ritis is on CRAN - an R client for ITIS (Integrated Taxonomic Information Service). See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.3.4) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.3.0) of citecorp is on CRAN - client for the Open Citations Corpus. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.0.3) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started.
  • A new version (v2.1.1) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started.
  • A new version (v1.4.1) of xslt is on CRAN - extensible style-sheet language transformations. See the release notes for changes. Checkout the README to get started.
  • A new version (v0.2.1.0) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.5.0) of fauxpas is on CRAN - HTTP error classes. See the release notes for changes. Checkout the vignette to get started.



Software Review ✔

In the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review. Please check back at our software review repository after 17 April for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent. Other rOpenSci community activities continue. We express our continued great appreciation for the work of our authors and reviewers.



On the blog

There’s a new version of the rOpenSci Dev Guide. The software review editors wrote a post describing the accumulated changes since v0.3: rOpenSci Dev Guide 0.4.0: Updates. Some highlights:

It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, April 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)

Software Review

Matthew Lau wrote a post on their package (Rclean) that recently went through rOpenSci software review: Automatic Code Cleaning in R with Rclean

Technical notes

Matthew Strimas-Mackey wrote a blog post on Extracting eBird Data from a Polygon using the auk package.

Maëlle Salmon has a nice blog post about R Markdown and Hugo learnings! Miscellaneous Wisdom about R Markdown & Hugo Gained from Work on our Website



Use Cases

The following 20 works use/cite rOpenSci software:



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.


A few new use cases were shared in the forum recently:



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 eight recent examples of maintainer transitions within rOpenSci:

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.



Get involved with rOpenSci

We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.






Keep up with rOpenSci


Footnotes

  1. Benito, B. M., & Birks, H. J. B. (2020). distantia: an open‐source toolset to quantify dissimilarity between multivariate ecological time‐series. Ecography. https://doi.org/10.1111/ecog.04895 

  2. Ceschin, D. G., Pires, N. S., Mardirosian, M. N., Lascano, C. I., & Venturino, A. (2020). The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-57961-4 

  3. von Schmidt, A., Cyganski, R., & Heinrichs, M. 2019. Web-based Visualization of Daily Mobility Patterns in R. International Journal on Advances in Internet Technology, vol 12 (3 & 4). https://elib.dlr.de/133599/1/inttech_v12_n34_2019_2.pdf 

  4. Oliphant, K., Cochrane, K., Schroeter, K., Daigneault, M. C., Yen, S., Verdu, E. F., & Allen-Vercoe, E. (2020). Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria In Vitro. mSystems, 5(1). https://doi.org/10.1128/msystems.00404-19 

  5. Lourenço, A. F. P. (2019). Eco-evolutionary implications underlying the emergence of a derived reproductive mode in fire salamanders. https://repositorio-aberto.up.pt/bitstream/10216/125665/2/378408.pdf 

  6. Lope, D. J., & Dolgun, A. (2020). Measuring the inequality of accessible trams in Melbourne. Journal of Transport Geography, 83, 102657. https://doi.org/10.1016/j.jtrangeo.2020.102657 

  7. Tetzlaff, S. J. (2019). Thinking outside the box: Effects of environmental enrichment and rearing duration on head-starting success of box turtles (Doctoral dissertation, University of Illinois at Urbana-Champaign) https://bit.ly/3eZwZA7 

  8. Wiscovitch-Russo, R., Rivera-Perez, J., Narganes-Storde, Y. M., García-Roldán, E., Bunkley-Williams, L., Cano, R., & Toranzos, G. A. (2020). Pre-Columbian zoonotic enteric parasites: An insight into Puerto Rican indigenous culture diets and life styles. PLOS ONE, 15(1), e0227810. https://doi.org/10.1371/journal.pone.0227810 

  9. Nüst, D., Eddelbuettel, D., Bennett, D., Cannoodt, R., Clark, D., Daroczi, G., … & Marwick, B. (2020). The Rockerverse: Packages and Applications for Containerization with R. arXiv preprint arXiv:2001.10641 https://arxiv.org/pdf/2001.10641.pdf 

  10. Pérez-Goya, U., Montesino-SanMartin, M., Militino, A. F., & Ugarte, M. D. (2020). RGISTools: Downloading, Customizing, and Processing Time Series of Remote Sensing Data in R. arXiv preprint arXiv:2002.01859 https://arxiv.org/pdf/2002.01859.pdf 

  11. Senior, S. (2020, February 4). Does Sure Start spending improve school readiness? An ecological longitudinal study. https://doi.org/10.31235/osf.io/rbcz5 

  12. Mooney, A., Conde, D. A., Healy, K., & Buckley, Y. M. (2020). A system wide approach to managing zoo collections for visitor attendance and in situ conservation. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14303-2 

  13. Gagné, T. O., Reygondeau, G., Jenkins, C. N., Sexton, J. O., Bograd, S. J., Hazen, E. L., & Van Houtan, K. S. (2020). Towards a global understanding of the drivers of marine and terrestrial biodiversity. PLOS ONE, 15(2), e0228065. https://doi.org/10.1371/journal.pone.0228065 

  14. Gomez Isaza, D. F., Cramp, R. L., & Franklin, C. E. (2020). Living in polluted waters: A meta-analysis of the effects of nitrate and interactions with other environmental stressors on freshwater taxa. Environmental Pollution, 114091. https://doi.org/10.1016/j.envpol.2020.114091 

  15. Vílchez-Román, C., Huamán-Delgado, F., & Alhuay-Quispe, J. (2020). Social dimension activates the usage and academic impact of Open Access publications in Andean countries: a structural modeling-based approach. Information Development, 026666692090184. https://doi.org/10.1177/0266666920901849 

  16. Caseys, C., Gongjun Shi, Nicole Soltis, Raoni Gwinner, Jason Corwin, Susanna Atwell, Daniel Kliebenstein. 2020. Quantitative interactions drive Botrytis cinerea disease outcome across the plant kingdom. bioRxiv preprint 507491; doi: https://doi.org/10.1101/507491 

  17. Van Zonneveld, M., Rakha, M., Tan, S. yee, Chou, Y.-Y., Chang, C.-H., Yen, J.-Y., … Solberg, S. Ø. (2020). Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-58646-8 

  18. Kim, J., Yoon, S., & Nam, D. (2020). netGO: R-Shiny package for network-integrated pathway enrichment analysis. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa077 

  19. Callanan, J., Stockdale, S. R., Shkoporov, A., Draper, L. A., Ross, R. P., & Hill, C. (2020). Expansion of known ssRNA phage genomes: From tens to over a thousand. Science Advances, 6(6), eaay5981. https://doi.org/10.1126/sciadv.aay5981 

  20. Mattatia, I. 2020. An empirical assessment of the extent to which the realized niche of bird species is truncated. Masters Thesis. University of Lausanne. https://bit.ly/2W0Nu6o