rOpenSci HQ


Software 📦

CRAN: GitHub:

New packages

  • The first version (v0.4.1) of cde is on CRAN - download data from the Catchment Data Explorer. Checkout the docs to get started. cde cde
  • The first version (v0.1.0) of citecorp is on CRAN - client for the Open Citations Corpus. Checkout the docs to get started. citecorp citecorp
  • The first version (v0.1.1) of PostcodesioR is on CRAN - API wrapper for Postcodes.io. Checkout the docs to get started. PostcodesioR PostcodesioR

New Versions

  • A new version (v0.6) of roadoi is on CRAN - find free versions of scholarly publications via Unpaywall. See the release notes for changes. Checkout the vignette to get started. roadoi roadoi

    new data fields in Unpaywall data; minor fixes

  • A new version (v7.6.1 & v7.6.2) 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

    docs now at https://docs.ropensci.org/drake/; many bug fixes

  • A new version (v0.8.0 & v0.8.2) of pangaear is on CRAN - Client for the Pangaea database. See the release notes for changes. Checkout the vignette to get started. pangaear pangaear

    new object pg_cache to manage file caching; pg_data() now includes parsed metadata; bug fixes for pg_data()

  • A new version (v0.1.5) of gutenbergr is on CRAN - Download and process public domain works from Project Gutenberg. See the release notes for changes. Checkout the vignette to get started. gutenbergr gutenbergr

    replace data_frame() w/ tibble()

  • A new version (v0.2.8) 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. fingertipsR fingertipsR

    better failure behavior: throw informative message when no API response

  • A new version (v1.1.2) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. nasapower nasapower

    correct citation; suppress APSIM::createMetFile() console output

  • A new version (v0.3.0) of oai is on CRAN - general purpose OAI-PMH services client. See the release notes for changes. Checkout the docs to get started. oai oai

    id() gains as param; update_providers() fix; small changes

  • A new version (v1.2.6) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. UCSCXenaTools UCSCXenaTools

    update pkg citation

  • A new version (v0.3.7) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started. jstor jstor

    tidyr compatability; remove defunct fxns

  • A new version (v2.0.0) 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. GSODR GSODR

    get_GSOD() now using https rather than FTP; objects now returned as data.table objects; minor changes

  • A new version (v0.2.0) of jaod is on CRAN - Directory of Open Access Journals client. See the release notes for changes. Checkout the docs to get started. jaod jaod

    new vignette; docs changes

  • A new version (v0.3.1) of getCRUCLdata is on CRAN - use and explore CRU CL v. 2.0 climatology elements. See the release notes for changes. Checkout the docs to get started. getCRUCLdata getCRUCLdata

    fix documentation bug in an example

  • A new version (v0.2.3) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. tradestatistics tradestatistics

    fixes for testthat

  • A new version (v1.0.14) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started. lingtypology lingtypology

    some dependencies moved to Suggests; new fxns uralex.feature() and ggmap.feature()

  • A new version (v2.2) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started. magick magick

    new fxns image_read_video(), image_separate(), image_combine(); improve RStudio auto preview

  • A new version (v2.0.3) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. ijtiff ijtiff

    add libjpeg needs to SystemRequirements

  • A new version (v0.3) of av is on CRAN - working with audio and video. See the release notes for changes. Checkout the docs to get started. av av

    major refactor; new fxns av_video_convert(), av_audio_convert(), av_video_images()

  • A new version (v0.7.2) of DataSpaceR is on CRAN - interface to the CAVD DataSpace. See the release notes for changes. Checkout the docs to get started. DataSpaceR DataSpaceR

    fix broken and invalid URLs

  • A new version (v0.3.0) of vcr 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. vcr vcr

    re-recording cassettes now works, see docs about setting a re-record interval; fixes to request body matching

  • A new version (v0.2.0) of handlr is on CRAN - Convert among citation formats. See the release notes for changes. Checkout the README to get started. handlr handlr

    new fxn handl_to_df() (and associated method $as_df() on HandlClient) to convert a handl object to a data.frame

  • A new version (v0.5.0) of rnassqs is on CRAN - access the NASS Quick Stats API. See the release notes for changes. Checkout the docs to get started. rnassqs rnassqs

    change how queries are specified; simplified token management; docs improved



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 three packages were recently submitted:

The following two packages recently went through our software-review process and have been approved:



On the blog

Stefanie Butland wrote the second of a semi-monthly summary of the rOpenSci Newsletter including software reviews, packages on CRAN, use cases, posts from staff and community, and events - 2 Months in 2 Minutes - rOpenSci News, August 2019


Sam Tyner wrote a post describing her free online book on forensic science in R. This work was funded by a 2018 rOpenSci Research Fellowship. Read the post here: Introducing Open Forensic Science in R


Tiffany Timbers in a recent post Using rOpenSci Software Peer Review Guidelines for Teaching wrote about the Collaborative Software Development course she teaches at University of British Columbia. In this course, they recommend students use our book rOpenSci Packages: Development, Maintenance, and Peer Review; and the students and teachers use our Review Template when submitting and reviewing assignments.


Software Review

Aldo Compagnoni wrote a post on his package that recently went through review, popler: Synthesizing population time-series data from the USA Long Term Ecological Research Network. Aldo talks about the motivation for making the package and the database behind the package.



Use Cases

The following 24 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.



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. Saxena, P., Saxena, D., Nie, X., Helmers, A., Ramachandran, N., Sakib, N., & Ahamed, S. (2019). Feature Boosting in Natural Image Classification. 2019 IEEE 43rd Annual Computer Software and Applications Conference (COMPSAC). https://doi.org/10.1109/compsac.2019.10184 

  2. Pilogallo, A., Saganeiti, L., Scorza, F., & Murgante, B. (2019). Investigating Urban Growth Dynamic – Land Surface Temperature Relationship. Lecture Notes in Computer Science, 701–710. https://doi.org/10.1007/978-3-030-24302-9_51 

  3. Sang, Zihaohan. No-analog ecological communities since the last glacial maximum inferred from fossil pollen records for North America. Diss. University of Alberta, 2019. https://sites.ualberta.ca/~ahamann/people/pdfs/Sang_2019_MSc.pdf 

  4. Xia, Liu, Zhang, & Guo. (2019). GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins. Cells, 8(7), 675. https://doi.org/10.3390/cells8070675 

  5. Burkett, Kaitlyn E. Who Is Ready To Retire: Your Average Life Expectancy And The Savings Needed To Support You. Diss. Appalachian State University, 2019. https://libres.uncg.edu/ir/asu/f/Burkett_Kaitlyn_2019_Thesis.pdf 

  6. Valdez, J. W., & Mandrekar, K. (2019). Assessing the Species in the CARES Preservation Program and the Role of Aquarium Hobbyists in Freshwater Fish Conservation. https://doi.org/10.20944/preprints201907.0030.v1 

  7. Correia, R. A., Ruete, A., Stropp, J., Malhado, A. C. M., dos Santos, J. W., Lessa, T., … Ladle, R. J. (2019). Using ignorance scores to explore biodiversity recording effort for multiple taxa in the Caatinga. Ecological Indicators, 106, 105539. https://doi.org/10.1016/j.ecolind.2019.105539 

  8. Lin, C., Lou, Y.-S., Tsai, D.-J., Lee, C.-C., Hsu, C.-J., Wu, D.-C., … Fang, W.-H. (2019). Projection Word Embedding Model With Hybrid Sampling Training for Classifying ICD-10-CM Codes: Longitudinal Observational Study. JMIR Medical Informatics, 7(3), e14499. https://doi.org/10.2196/14499 

  9. Stöver, B. C., Wiechers, S., & Müller, K. F. (2019). JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface. BMC Bioinformatics, 20(1). https://doi.org/10.1186/s12859-019-2982-3 

  10. Myers, E. A., Xue, A. T., Gehara, M., Cox, C., Davis Rabosky, A. R., Lemos‐Espinal, J., … Burbrink, F. T. (2019). Environmental Heterogeneity and Not Vicariant Biogeographic Barriers Generate Community Wide Population Structure in Desert Adapted Snakes. Molecular Ecology. https://doi.org/10.1111/mec.15182 

  11. Van Schaik, P., Peng, Y., Ojelabi, A., & Ling, J. (2019). Explainable statistical learning in public health for policy development: the case of real-world suicide data. BMC medical research methodology, 19(1), 152. https://bmcmedresmethodol.biomedcentral.com/articles/10.1186/s12874-019-0796-7 

  12. Hagen, O., Vaterlaus, L., Albouy, C., Brown, A., Leugger, F., Onstein, R. E., … Pellissier, L. (2019). Mountain building, climate cooling and the richness of cold‐adapted plants in the Northern Hemisphere. Journal of Biogeography. https://doi.org/10.1111/jbi.13653 

  13. Carlström, K. E., Ewing, E., Granqvist, M., Gyllenberg, A., Aeinehband, S., Enoksson, S. L., … Piehl, F. (2019). Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis associates with ROS pathway in monocytes. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-11139-3 

  14. Dag, O., Karabulut, E., & Alpar, R. (2019). GMDH2: Binary Classification via GMDH-Type Neural Network Algorithms—R Package and Web-Based Tool. International Journal of Computational Intelligence Systems, 12(2), 649. https://doi.org/10.2991/ijcis.d.190618.001 

  15. Wüest, R. O., Zimmermann, N. E., Zurell, D., Alexander, J. M., Fritz, S. A., Hof, C., … Karger, D. N. (2019). Macroecology in the age of Big Data – Where to go from here? Journal of Biogeography. https://doi.org/10.1111/jbi.13633 

  16. Saunders, K. R., Stephenson, A. G., & Karoly, D. J. (2019). A Regionalisation Approach for Rainfall based on Extremal Dependence. arXiv preprint https://arxiv.org/pdf/1907.05750.pdf 

  17. Collins, R. A., Bakker, J., Wangensteen, O. S., Soto, A. Z., Corrigan, L., Sims, D. W., … Mariani, S. (2019). Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13276 

  18. Elsner, J. B., & Schroder, Z. (2019, July 18). Tornado damage ratings estimated with cumulative logistic regression. https://doi.org/10.31223/osf.io/k9wv6 

  19. Abhilash, L., & Sheeba, V. (2019). RhythmicAlly: Your R and Shiny–Based Open-Source Ally for the Analysis of Biological Rhythms. Journal of Biological Rhythms, 074873041986247. https://doi.org/10.1177/0748730419862474 

  20. Peters, A., Delhey, K., Nakagawa, S., Aulsebrook, A., & Verhulst, S. (2019). Immunosenescence in wild animals: meta‐analysis and outlook. Ecology Letters. https://doi.org/10.1111/ele.13343 

  21. Die, J. V., Elmassry, M. M., LeBlanc, K. H., Awe, O. I., Dillman, A., & Busby, B. (2019). geneHummus: an R package to define gene families and their expression in legumes and beyond. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-019-5952-2 

  22. Saadi, M., Oudin, L., & Ribstein, P. (2019). Random Forest Ability in Regionalizing Hourly Hydrological Model Parameters. Water, 11(8), 1540. https://doi.org/10.3390/w11081540 

  23. Jaganathan, G. K., & Dalrymple, S. E. (2019). Internal Seed Structure of Alpine Plants and Extreme Cold Exposure. Data, 4(3), 107. https://doi.org/10.3390/data4030107 

  24. Alhajeri, B. H., Porto, L., & Maestri, R. (2019). Habitat productivity is a poor predictor of body size in rodents. Current Zoology. https://academic.oup.com/cz/advance-article/doi/10.1093/cz/zoz037/5539488