rOpenSci HQ

Software 📦

CRAN: GitHub:

New Versions

  • A new version (v1.1.2) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started. dbparser dbparser
  • A new version (v1.0.4) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the docs to get started. fingertipsR fingertipsR
  • A new version (v0.3.9) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started. jstor jstor
  • A new version (v7.12.2) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. drake drake
  • A new version (v1.3.8) of skynet is on CRAN - Bureau of Transport Statistics Data client. See the release notes for changes. Checkout the docs to get started. skynet skynet
  • A new version (v0.4) of europepmc is on CRAN - Interface to the Europe PubMed Central RESTful web service. See the release notes for changes. Checkout the docs to get started. europepmc europepmc
  • A new version (v0.7.4) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the docs to get started. robotstxt robotstxt
  • A new version (v2.3) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. rgbif rgbif
  • A new version (v1.0.0) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started. webchem webchem
  • A new version (v2.2) of jsonld is on CRAN - JSON for linking data. See the release notes for changes. Checkout the README to get started. jsonld jsonld
  • A new version (v0.9.1) of hddtools is on CRAN - Hydrological Data Discovery Tools. See the release notes for changes. Checkout the docs to get started. hddtools hddtools
  • A new version (v2.3.1) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started. pdftools pdftools
  • A new version (v3.1.3) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started. qualtRics qualtRics
  • A new version (v0.9.96) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. taxize taxize
  • A new version (v0.3.0) of geoops is on CRAN - GeoJSON topology calculations and operations. See the release notes for changes. Checkout the docs to get started. geoops geoops
  • A new version (v1.4.2) of xslt is on CRAN - extensible style-sheet language transformations. See the release notes for changes. Checkout the README to get started. xslt xslt
  • A new version (v1.0.0) of natserv is on CRAN - NatureServe R Interface. See the release notes for changes. Checkout the docs to get started. natserv natserv
  • A new version (v0.1.5) of textreuse is on CRAN - detect text reuse and document similarity. See the release notes for changes. Checkout the docs to get started. textreuse textreuse
  • A new version (v0.2.4) of tidync is on CRAN - a tidy approach to NetCDF data exploration and extraction. See the release notes for changes. Checkout the docs to get started. tidync tidync
  • A new version (v2.0-15) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the release notes for changes. Checkout the docs to get started. CoordinateCleaner CoordinateCleaner



Software Review ✔


Software review is now accepting submissions again.

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 two packages were recently submitted:



On the blog

Technical notes

Jeroen Ooms wrote about a new version of the rsvg package: Superior svg graphics rendering in R, and why it matters.



Use Cases

The following 26 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.


Many new use cases were shared in the forum over the past month since our last newsletter:



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 nine recent examples of maintainer transitions within rOpenSci:

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

  • rflybase: 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. Perez‐Lamarque, B., Selosse, M., Öpik, M., Morlon, H., & Martos, F. (2020). Cheating in arbuscular mycorrhizal mutualism: a network and phylogenetic analysis of mycoheterotrophy. New Phytologist. https://doi.org/10.1111/nph.16474 

  2. Larson, J. E., Anacker, B. L., Wanous, S., & Funk, J. L. (2020). Ecological strategies begin at germination: Traits, plasticity and survival in the first 4 days of plant life. Functional Ecology. https://doi.org/10.1111/1365-2435.13543 

  3. Rodrigues, B. N., & Boscolo, D. (2020). Do bipartite binary antagonistic and mutualistic networks have different responses to the taxonomic resolution of nodes? Ecological Entomology. https://doi.org/10.1111/een.12844 

  4. Manel, S., Guerin, P.-E., Mouillot, D., Blanchet, S., Velez, L., Albouy, C., & Pellissier, L. (2020). Global determinants of freshwater and marine fish genetic diversity. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14409-7 

  5. Thompson, K. A. (2020). Experimental hybridization studies suggest that pleiotropic alleles commonly underlie adaptive divergence between natural populations. The American Naturalist. https://doi.org/10.1086/708722 

  6. Gent, D. H., Claassen, B. J., Gadoury, D. M., Grünwald, N. J., Knaus, B. J., Radišek, S., … Wolfenbarger, S. N. (2020). Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations. Phytopathology, PHYTO–12–19–044. https://doi.org/10.1094/phyto-12-19-0448-r 

  7. Bagheri, H. 2019. Domain-specific language and infrastructure for genomics. Graduate Theses and Dissertations. 17641. https://lib.dr.iastate.edu/etd/17641 

  8. Heisel, S. E. (2019). Ecological, Genomic, and Social Factors Impacting Wildlife Conservation (Doctoral dissertation, University of Georgia). https://search.proquest.com/docview/2357432037 

  9. Hannah, L., Roehrdanz, P. R., Marquet, P. A., Enquist, B. J., Midgley, G., Foden, W., … Svenning, J. (2020). 30% land conservation and climate action reduces tropical extinction risk by more than 50%. Ecography. https://doi.org/10.1111/ecog.05166 

  10. Ryt-Hansen, P., Pedersen, A. G., Larsen, I., Kristensen, C. S., Krog, J. S., Wacheck, S., & Larsen, L. E. (2020). Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses. Viruses, 12(2), 248. https://doi.org/10.3390/v12020248 

  11. Armitage, D. W., & Jones, S. E. (2020). Barriers to coexistence limit the poleward range of a globally-distributed plant. https://doi.org/10.1101/2020.02.24.946574 

  12. Hamid M., Khuroo A.A., Ahmad R., Rasheed S., Malik A.H., Dar G.H. (2020) Threatened Flora of Jammu and Kashmir State. In:Dar G., Khuroo A. (eds) Biodiversity of the Himalaya:Jammu and Kashmir State. Topics in Biodiversity and Conservation, vol 18. Springer, Singapore https://doi.org/10.1007/978-981-32-9174-4_37 

  13. Kaczvinsky, C., & Hardy, N. B. (2020). Do major host shifts spark diversification in butterflies? Ecology and Evolution, 10(8), 3636–3646. https://doi.org/10.1002/ece3.6116 

  14. Zizka, A., Carvalho‐Sobrinho, J. G., Pennington, R. T., Queiroz, L. P., Alcantara, S., Baum, D. A., … Antonelli, A. (2020). Transitions between biomes are common and directional in Bombacoideae (Malvaceae). Journal of Biogeography. https://doi.org/10.1111/jbi.13815 

  15. Jung, E.-Y., Gaviria, J., Sun, S., & Engelbrecht, B. M. J. (2020). Comparative drought resistance of temperate grassland species: testing performance trade-offs and the relation to distribution. Oecologia, 192(4), 1023–1036. https://doi.org/10.1007/s00442-020-04625-9 

  16. Howard, C. C., & Cellinese, N. (2020). Tunicate bulb size variation in monocots explained by temperature and phenology. Ecology and Evolution, 10(5), 2299–2309. https://doi.org/10.1002/ece3.5996 

  17. Du, C., Chen, J., Jiang, L., & Qiao, G. (2020). High correlation of species diversity patterns between specialist herbivorous insects and their specific hosts. Journal of Biogeography. https://doi.org/10.1111/jbi.13816 

  18. Long, J. D., & Turner, D. (2020). Applied R in the Classroom. Australian Economic Review, 53(1), 139–157. https://doi.org/10.1111/1467-8462.12362 

  19. Reyes, J. A., & Lira-Noriega, A. (2020). Current and future global potential distribution of the fruit fly Drosophila suzukii (Diptera: Drosophilidae). The Canadian Entomologist, 1–13. https://doi.org/10.4039/tce.2020.3 

  20. Lara-Lizardi, F., Hoyos-Padilla, M., Hearn, A., Klimley, A. P., Galván-Magaña, F., Arauz, R., … Ketchum, J. T. (2020). Shark movements in the Revillagigedo Archipelago and connectivity with the Eastern Tropical Pacific. https://doi.org/10.1101/2020.03.02.972844 

  21. Cichosz, P. (2020). Unsupervised modeling anomaly detection in discussion forums posts using global vectors for text representation. Natural Language Engineering, 1–28. https://doi.org/10.1017/s1351324920000066 

  22. Pietzke, M., Vazquez, A. 2020. Metabolite AutoPlotter–an application to automatically process and visualise metabolite data in the web-browser. https://assets.researchsquare.com/files/6b8d169e-e621-4ebd-8c6e-ff607a788ebe/v1/Manuscript.pdf 

  23. Kusumoto, B., Costello, M. J., Kubota, Y., Shiono, T., Wei, C., Yasuhara, M., & Chao, A. (2020). Global distribution of coral diversity: Biodiversity knowledge gradients related to spatial resolution. Ecological Research, 35(2), 315–326. https://doi.org/10.1111/1440-1703.12096 

  24. Potter, R. J. (2019). Machine learning for resource economics; a review of modern computational statistics with empirical applications in fisheries management (Master’s thesis). https://openaccess.nhh.no/nhh-xmlui/bitstream/handle/11250/2644607/masterthesis.pdf?sequence=1 

  25. Marshall, D. J., Pettersen, A. K., Bode, M., & White, C. R. (2020). Developmental cost theory predicts thermal environment and vulnerability to global warming. Nature Ecology & Evolution, 4(3), 406–411. https://doi.org/10.1038/s41559-020-1114-9 

  26. Amiri Roudbar, M., Mohammadabadi, M. R., Ayatollahi Mehrgardi, A., Abdollahi-Arpanahi, R., Momen, M., Morota, G., … Rosa, G. J. M. (2020). Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls. Heredity, 124(5), 658–674. https://doi.org/10.1038/s41437-020-0301-4