rOpenSci HQ


Software 📦

CRAN: GitHub:

New packages

  • The first version (v1.7) of tidypmc is on CRAN - parse full text XML documents from PubMed Central. Checkout the vignettes to get started.
  • The first version (v1.2.5) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. Checkout the docs to get started.

New Versions

  • A new version (v0.8.4) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started.

    (Windows users please do upgrade: no longer set cainfo curl option); improve parse method in HttpResponse class

  • A new version (v1.22) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started.

    update Tika to 1.22

  • A new version (v0.3.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

    new fxns: od_to_odmatrix(), odmatrix_to_od(), od_oneway(), and many new od_id*() fxns; new vignette

  • A new version (v0.1.3) of gitignore is on CRAN - create useful .gitignore files for your project. See the release notes for changes. Checkout the docs to get started.

    fix cran check problems

  • A new version (v1.0.0) of stats19 is on CRAN - Work with Open Road Traffic Casualty Data from Great Britain. See the release notes for changes. Checkout the docs to get started.

    now much easier to download STATS19 data w/ dl_stats19()

  • A new version (v0.5.0) of brranching is on CRAN - Fetch Phylogenies from Many Sources. See the release notes for changes. Checkout the vignette to get started.

    now using pkg conditionz to make messages less frequent when user does not have an API key for NCBI

  • A new version (v0.1.2) of geoparser is on CRAN - interface to the Geoparser.io API. See the release notes for changes. Checkout the docs to get started.

    fix error caused by namespace issue; geoparser_key() fails better when no key avail.

  • A new version (v0.0.3) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started.
  • A new version (v2.1) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started.

    new docs site; many fixes

  • A new version (v4.1) of tesseract is on CRAN - bindings to Tesseract, an OCR engine https://opensource.google.com/projects/tesseract. See the release notes for changes. Checkout the vignette to get started.

    fix memory leak in ocr_data; update to libtesseract 4.1.0

  • A new version (v0.1.4) of phylocomr is on CRAN - Interface to Phylocom for analysis of phylogenetic community structure and character evolution. See the release notes for changes. Checkout the vignette to get started.

    fix some non-working examples; fixes to internal type checking; fix C lib error

  • A new version (v0.3.0) of ckanr is on CRAN - R client for the CKAN API. See the release notes for changes. Checkout the docs to get started.

    big release, first in 4 years: new pkg maintainer; many new fxns; many fxns w/ changed params; fxn name changes



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.

The following five packages were recently submitted:

The following package recently went through our software-review process and has been approved:



Use Cases

The following 15 works use/cite rOpenSci software:



In The News

Dan Quintana gives a short video demonstration of using europepmc, a package maintained by Najko Jahn



Call For Contributors

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:

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


Footnotes

  1. Wright, R. J., Gibson, M. I., & Christie-Oleza, J. A. (2019). Understanding microbial community dynamics to improve optimal microbiome selection. Microbiome, 7(1). https://doi.org/10.1186/s40168-019-0702-x 

  2. Meisner, J., Clifford, W. R., Wohrle, R. D., Kangiser, D., & Rabinowitz, P. (2019). Soil and climactic predictors of canine coccidioidomycosis seroprevalence in Washington State: an ecological cross‐sectional study. Transboundary and Emerging Diseases. https://doi.org/10.1111/tbed.13265 

  3. Tetzlaff, S. J., Sperry, J. H., & DeGregorio, B. A. (2019). Effects of antipredator training, environmental enrichment, and soft release on wildlife translocations: A review and meta-analysis. Biological Conservation, 236, 324–331. https://doi.org/10.1016/j.biocon.2019.05.054 

  4. Alhajeri, B. H., & Fourcade, Y. (2019). High correlation between species‐level environmental data estimates extracted from IUCN expert range maps and from GBIF occurrence data. Journal of Biogeography. https://doi.org/10.1111/jbi.13619 

  5. Boggs, Scheible, Machado, & Meiklejohn. (2019). Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation? Genes, 10(6), 431. https://doi.org/10.3390/genes10060431 

  6. Ros-Candeira, A., Pérez-Luque, A. J., Suárez-Muñoz, M., Bonet-García, F. J., Hódar, J. A., Giménez de Azcárate, F., & Ortega-Díaz, E. (2019). Dataset of occurrence and incidence of pine processionary moth in Andalusia, south Spain. ZooKeys, 852, 125–136. https://doi.org/10.3897/zookeys.852.28567 

  7. Van Denderen, D., Gislason, H., & Andersen, K. H. (2019). Little difference in average fish growth and maximum size across temperatures. EcoEvoRxiv. https://doi.org/10.32942/osf.io/8cu4y 

  8. Bailey, L. D., Ens, B. J., Both, C., Heg, D., Oosterbeek, K., & van de Pol, M. (2019). Habitat selection can reduce effects of extreme climatic events in a long‐lived shorebird. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13041 

  9. Palacios-Abrantes, J., Cisneros-Montemayor, A. M., Cisneros-Mata, M. A., Rodríguez, L., Arreguín-Sánchez, F., Aguilar, V., … Cheung, W. W. L. (2019). A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico. PLOS ONE, 14(6), e0216723. https://doi.org/10.1371/journal.pone.0216723 

  10. McTavish, E. J. (2019). Linking Biodiversity Data Using Evolutionary History. Biodiversity Information Science and Standards, 3. https://doi.org/10.3897/biss.3.36207 

  11. Nyboer, E. A., Liang, C., & Chapman, L. J. (2019). Assessing the vulnerability of Africa’s freshwater fishes to climate change: A continent-wide trait-based analysis. Biological Conservation, 236, 505–520. https://doi.org/10.1016/j.biocon.2019.05.003 

  12. Krah, F.-S., & Heibl, C. (2019). rGUIDANCE – alignment confidence score computation in R. Journal of Open Source Software, 4(36), 1350. https://doi.org/10.21105/joss.01350 

  13. Morelle, K., Jezek, M., Licoppe, A., & Podgorski, T. (2019). Deathbed choice by ASF‐infected wild boar can help find carcasses. Transboundary and Emerging Diseases. https://doi.org/10.1111/tbed.13267 

  14. Grattarola, F., Botto, G., da Rosa, I., Gobel, N., González, E., González, J., … Pincheira-Donoso, D. (2019). Biodiversidata: An Open-Access Biodiversity Database for Uruguay. Biodiversity Data Journal, 7. https://doi.org/10.3897/bdj.7.e36226 

  15. Kravchuk, O. I., Lyupina, Y. V., Erokhov, P. A., Finoshin, A. D., Adameyko, K. I., Mishyna, M. Y., … Mikhailov, V. S. (2019). Characterization of the 20S proteasome of the lepidopteran, Spodoptera frugiperda. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. https://doi.org/10.1016/j.bbapap.2019.06.010