rOpenSci Community Calls

  • We’re planning a Community Call on Research Applications of rOpenSci Taxonomy and Biodiversity Tools and we want your input! What types of questions do you try to address with these tools? How do you use the tools to address your questions? Please tell us about your examples using the template in our discussion forum UseCases category.


Software 📦

CRAN: GitHub:

New packages

  • The first version (v1.0) of qpdf is on CRAN - Split, combine and compress PDF files. Checkout the README to get started. qpdf qpdf
  • The first version (v0.1.0) of handlr is on CRAN - convert among citation formats. Checkout the README and rOpenSci blog post to get started. handlr handlr
  • The first version (v0.4.1) of Rpolyhedra is on CRAN - polyhedra database from various sources as R6 objects and visualizing capabilities. (previous versions have been on CRAN, but this is the first version as an rOpenSci package). Checkout the vignette to get started. Rpolyhedra Rpolyhedra

New Versions

  • A new version (v3.0.1) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started. rfishbase rfishbase
  • A new version (v2.2.1) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the vignettes to get started. beautier beautier
  • A new version (v0.9.6) of rzmq is on CRAN - R Bindings for ZeroMQ, a lightweight messaging kernel. See the release notes for changes. Checkout the README to get started. rzmq rzmq

    allow sending of long vectors; fix some rchk warnings

  • A new version (v2.0.1) of tracerer is on CRAN - parse and analyze BEAST2 input files programmatically. See the release notes for changes. Checkout the vignettes to get started. tracerer tracerer
  • A new version (v0.6.2) of rdhs is on CRAN - Client for Demographic and Health Survey (DHS) Data. See the release notes for changes. Checkout the docs to get started. rdhs rdhs

    duplicate labels fixed; extraction() fix; geospatial covariate data sets now supported correctly

  • A new version (v0.4.2) of NLMR is on CRAN - Simulating neutral landscape models. See the release notes for changes. Checkout the docs to get started. NLMR NLMR
  • A new version (v1.20) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started. rtika rtika

    updated Tika to 1.2; includes config files for OCR; workaround for normalizePath on Windows

  • A new version (v0.6.0) of paleobioDB is on CRAN - download and process data from the Paleobiology database. See the release notes for changes. Checkout the README to get started. paleobioDB paleobioDB

    improve error reportign in pbdb_temp_range(); fix error in pbdb_occurrences()

  • A new version (v1.2.0) 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

    elevation() fxn now uses Geonames; occ_data/occ_search column ordering changes; more WKT documentation; bug fixes

  • A new version (v0.5.0) of landscapetools is on CRAN - Landscape Utility Toolbox. See the release notes for changes. Checkout the docs to get started. landscapetools landscapetools

    new interface for util_classify; removed util_import_roboto/util_plot_grey; new function util_writeESRI

  • A new version (v1.0.5) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. skimr skimr

    fix mulitbyte characters issue; fix problem where purrr cannot find mean.default

  • A new version (v0.9.6) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. taxize taxize

    new data source Kew POW; user agent string with all requests; get_colid now paginates autom.; most get_* now try direct match; new vignette; …

  • A new version (v0.999) of geonames is on CRAN - interface to the Geonames spatial query web service. See the release notes for changes. Checkout the tests to get started. geonames geonames

    base URL changed; set hostname on load instead of attach

  • A new version (v0.4) of ssh is on CRAN - Secure shell (SSH) client for R. See the release notes for changes. Checkout the vignette to get started. ssh ssh

    fix for security problem; Windows/Mac: update libssh 0.8.6; use askpass pkg



Software Review ✔

We accept community contributed packages via our onboarding 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 recently went through our onboarding process and have been approved:

The following two packagess were recently submitted:



On the blog

Software Review

Layik Hama and Robin Lovelace wrote a summary of their recently onboarded package stats19: stats19: a package for road safety research. In it, they describe the motivation for the package and go through a detailed run through of using the package.

Tech notes

Jeroen Ooms wrote about a Bugfix release for the ssh package in his recent rOpenSci tech note. The ssh package is a secure shell (SSH) client for R.


Scott Chamberlain wrote about a handlr: convert among citation formats in his recent rOpenSci tech note. The handlr package is a new package providing conversions among many different citation formats.



Use Cases

The following 14 works use/cite rOpenSci software:



In The News

Maëlle Salmon wrote a blog post on How did Axios rectangle Trump’s PDF schedule? A try with R - using our packages pdftools and magick (maintained by Jeroen Ooms) to extract text out of PDFs.


Daniel Nüst wrote about How to increase reproducibility and transparency in your research using our package suppdata maintained by Will Pearse.


lopierra made a Shiny app using our package tabulizer


Sam Tyner wrote a blog post on Reconstructing a plot from the National Weather Service - in which she used our package rnoaa to get NOAA climate data.



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. We’ve had three recent examples of maintainer transitions within rOpenSci:

We’ve got three packages in need of new maintainers:

  • webchem: The current maintainer of webchem, Eduard Szöcs, is looking for a new maintainer. See issue #155. Do ping Eduard in that issue and/or email us at info@ropensci.org
  • rsnps: The current maintainer would like to hand it over to someone with more expertise in the domain. Please get in touch with Scott if you’re interested.
  • rdpla: The current maintainer would like to hand it over to someone with more expertise in the domain. Please get in touch with Scott if you’re interested.






Keep up with rOpenSci


Footnotes

  1. Joish, V. N., Shah, S., Tierce, J. C., Patel, D., McKee, C., Lapuerta, P., & Zacks, J. (2019). Serotonin levels and 1-year mortality in patients with neuroendocrine tumors: a systematic review and meta-analysis. Future Oncology https://doi.org/10.2217/fon-2018-0960 

  2. Wheeler, D. L., Scott, J., Dung, J. K. S., & Johnson, D. A. (2019). Evidence of a trans-kingdom plant disease complex between a fungus and plant-parasitic nematodes. PLOS ONE, 14(2), e0211508. https://doi.org/10.1371/journal.pone.0211508 

  3. Liu, Crocker H., Nowak, Adam, and Smith, Patrick S. 2018. Does the Asset Pricing Premium Reflect Asymmetric or IncompleteInformation?. Economics Faculty Working Papers Series. 5. https://researchrepository.wvu.edu/econ_working-papers/5 

  4. Maljkovic, D. (2019). Modelling Influential Factors of Consumption in Buildings Connected to District Heating Systems. Energies, 12(4), 586. https://doi.org/10.3390/en12040586 

  5. Särkiö, I. (2019). Topic modelling of Finnish Internet discussion forums as a tool for trend. M.Sc. Thesis. http://sal.aalto.fi/publications/pdf-files/tsar19_public.pdf 

  6. Mittermeier, T. et al. 2019. A season for all things: Phenological imprints in Wikipedia usage and their relevance toconservation. PLoS Biology https://research.birmingham.ac.uk/portal/files/58082037/pbio.3000146_1.pdf 

  7. Webber, Q. M. R., & Vander Wal, E. (2019). Trends and perspectives on the use of animal social network analysis in behavioural ecology: a bibliometric approach. Animal Behaviour, 149, 77–87. https://doi.org/10.1016/j.anbehav.2019.01.010 

  8. Daru, B. H., le Roux, P. C., Gopalraj, J., Park, D. S., Holt, B. G., & Greve, M. (2019). Spatial overlaps between the global protected areas network and terrestrial hotspots of evolutionary diversity. Global Ecology and Biogeography. https://doi.org/10.1111/geb.12888 

  9. Aiello, M., Terenzi, D., Furlanis, G., Catalan, M., Manganotti, P., Eleopra, R., … Rumiati, R. I. (2019). Deep brain stimulation of the subthalamic nucleus and the temporal discounting of primary and secondary rewards. Journal of Neurology. https://doi.org/10.1007/s00415-019-09240-0 

  10. Ohmer, M. E. B., Cramp, R. L., White, C. R., Harlow, P. S., McFadden, M. S., Merino-Viteri, A., … Franklin, C. E. (2019). Phylogenetic investigation of skin sloughing rates in frogs: relationships with skin characteristics and disease-driven declines. Proceedings of the Royal Society B: Biological Sciences, 286(1896), 20182378. https://doi.org/10.1098/rspb.2018.2378 

  11. Srivastava, S., Avvaru, A. K., Sowpati, D. T., & Mishra, R. K. (2019). Patterns of microsatellite distribution across eukaryotic genomes. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-019-5516-5 

  12. Dillen, M., Groom, Q., Chagnoux, S., Güntsch, A., Hardisty, A., Haston, E., … Phillips, S. (2019). A benchmark dataset of herbarium specimen images with label data. Biodiversity Data Journal, 7. https://10.3897/bdj.7.e31817 

  13. Thomsen, P. F., & Sigsgaard, E. E. (2019). Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods. Ecology and Evolution. https://doi.org/10.1002/ece3.4809 

  14. Fitzpatrick, M. C., & Dunn, R. R. (2019). Contemporary climatic analogs for 540 North American urban areas in the late 21st century. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-08540-3