Software 📦

CRAN: GitHub:

New Versions

  • A new version (v1.1.1) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.4.0) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.4.4) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.1.1) of colocr is on CRAN - conduct co-localization analysis of fluorescence microscopy images. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.3.2) of cRegulome is on CRAN - access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.3.6) of eia 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 (v2.3.6) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.1) of tracerer is on CRAN - parse and analyze BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.3) of writexl is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the README to get started.
  • A new version (v0.27.1) of git2r is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the README to get started.
  • A new version (v0.6.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.0.0) of bold is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.3.4) of taxa is on CRAN - taxonomic classes for groupings of taxonomic names without data, and those with data. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.9.95) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book 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 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

Maëlle Salmon has two blog posts in the past two weeks:



Use Cases

The following 23 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:



In The News

  • testing: Why You Should Document Your Tests
    • Should you document your tests? I for one, only sometimes include comments in my tests, but perhaps they should be documented better? Do you comment or document your tests? This blog post is about Python, but the ideas apply to any language.



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’ve got one package in need of a new maintainer:

  • rinat: The current maintainer is looking for a new maintainer. Email Scott if you’re interested.



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. Adil, S. H., Ebrahim, M., Ali, S. S. A., & Raza, K. 2019. Identifying Trends in Data Science Articles using Text Mining. In 2019 4th International Conference on Emerging Trends in Engineering, Sciences and Technology (ICEEST) (pp. 1-7). IEEE. https://ieeexplore.ieee.org/document/8981702 

  2. Finoshin, A. D., Adameyko, K. I., Mikhailov, K. V., Kravchuk, O. I., Georgiev, A. A., Gornostaev, N. G., … Lyupina, Y. V. (2020). Iron metabolic pathways in the processes of sponge plasticity. PLOS ONE, 15(2), e0228722. https://doi.org/10.1371/journal.pone.0228722 

  3. Pimiento, C., & Benton, M. J. (2020). The impact of the Pull of the Recent on extant elasmobranchs. Palaeontology. https://doi.org/10.1111/pala.12478 

  4. Benhadi‐Marín, J., Santos, S. A. P., Baptista, P., & Pereira, J. A. (2020). Distribution of Bactrocera oleae (Rossi, 1790) throughout the Iberian Peninsula based on a maximum entropy modeling approach. Annals of Applied Biology. https://doi.org/10.1111/aab.12584 

  5. Ahrenfeldt, J., Waisi, M., Loft, I. C., Clausen, P. T. L. C., Allesøe, R., Szarvas, J., … Lund, O. (2020). Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-59292-w 

  6. Cinelli, M. (2019). Generalized rich-club ordering in networks. Journal of Complex Networks, 7(5), 702–719. https://doi.org/10.1093/comnet/cnz002 

  7. Alfaro-Ramírez, F. U., Ramírez-Albores, J. E., Vargas-Hernández, J. J., Franco-Maass, S., & Pérez-Suárez, M. (2020). Potential reduction of Hartweg´s Pine (Pinus hartwegii Lindl.) geographic distribution. PLOS ONE, 15(2), e0229178. https://doi.org/10.1371/journal.pone.0229178 

  8. Martinez-Feria, R. A., & Basso, B. (2020). Unstable crop yields reveal opportunities for site-specific adaptations to climate variability. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-59494-2 

  9. Rego, A., Sousa, A. G. G., Santos, J. P., Pascoal, F., Canário, J., Leão, P. N., & Magalhães, C. (2020). Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica. Microorganisms, 8(2), 279. https://doi.org/10.3390/microorganisms8020279 

  10. Cederwall, J., Black, T. A., Blais, J. M., Hanson, M. L., Hollebone, B. P., Palace, V. P., … Orihel, D. M. (2020). Life under an oil slick: response of a freshwater food web to simulated spills of diluted bitumen in field mesocosms. Canadian Journal of Fisheries and Aquatic Sciences, 77(5), 779–788. https://doi.org/10.1139/cjfas-2019-0224 

  11. Mossion, V., Dauphin, B., Grant, J., Zemp, N., & Croll, D. (2020). A reference transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure. https://doi.org/10.1101/2020.02.17.952283 

  12. Funk, B., Sadeh-Sharvit, S., Fitzsimmons-Craft, E. E., Trockel, M. T., Monterubio, G. E., Goel, N. J., … Taylor, C. B. (2020). A Framework for Applying Natural Language Processing in Digital Health Interventions. Journal of Medical Internet Research, 22(2), e13855. https://doi.org/10.2196/13855 

  13. Correia, C. N., McLoughlin, K. E., Nalpas, N. C., Magee, D. A., Browne, J. A., Rue-Albrecht, K., … MacHugh, D. E. (2018). RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus). Frontiers in Genetics, 9. https://doi.org/10.3389/fgene.2018.00278 

  14. Verde Arregoitia, L. D., Teta, P., & D’Elía, G. (2020). Patterns in research and data sharing for the study of form and function in caviomorph rodents. Journal of Mammalogy. https://doi.org/10.1093/jmammal/gyaa002 

  15. Shivambu, T. C., Shivambu, N., & Downs, C. T. (2020). Impact assessment of seven alien invasive bird species already introduced to South Africa. Biological Invasions. https://doi.org/10.1007/s10530-020-02221-9 

  16. Jhwueng, D.-C., & O’Meara, B. C. (2020). On the Matrix Condition of Phylogenetic Tree. Evolutionary Bioinformatics, 16, 117693432090172. https://doi.org/10.1177/1176934320901721 

  17. Cooke, R. S. C., Eigenbrod, F., & Bates, A. E. (2020). Ecological distinctiveness of birds and mammals at the global scale. Global Ecology and Conservation, 22, e00970. https://doi.org/10.1016/j.gecco.2020.e00970 

  18. Palanisamy, S. (2019). An analysis on hidden markov model prediction factors using California wildfire and meteorological records (Doctoral dissertation, California State University, Sacramento). https://bit.ly/2yCWk2M 

  19. Panayiotou, C. (2020). An Ontological Analysis and Natural Language Processing of Figures of Speech. International Journal of Artificial Intelligence & Applications, 11(1), 17–30. https://doi.org/10.5121/ijaia.2020.11102 

  20. Ji, Y., Baker, C. C., Li, Y., Popescu, V. D., Wang, Z., Wang, J., … Yu, D. W. (2020). Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA. https://doi.org/10.1101/2020.02.10.941336 

  21. Li, X., & Guo, B. (2020). Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies. Proceedings of the Royal Society B: Biological Sciences, 287(1920), 20193008. https://doi.org/10.1098/rspb.2019.3008 

  22. Silva, I., Crane, M., Marshall, B. M., & Strine, C. T. (2020). Revisiting reptile home ranges: moving beyond traditional estimators with dynamic Brownian Bridge Movement Models. https://doi.org/10.1101/2020.02.10.941278 

  23. Schwalb‐Willmann, J., Remelgado, R., Safi, K., & Wegmann, M. (2020). moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in R. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13374