2020-09-01

rOpenSci HQ

Contributing Guide Release 🚀

https://contributing.ropensci.org/

The purpose of the guide is to welcome you to rOpenSci and help you recognize yourself as a potential contributor. It will help you figure out what you might gain by giving your time, expertise, and experience; match your needs with things that will help rOpenSci’s mission; and connect you with resources to help you along the way. Is there something you might like to contribute that isn’t addressed there? Open an issue in the GitHub repository for the Guide.

Software 📦

CRAN: GitHub:

New Versions

A new version (v3.2-3) of clifro is on CRAN - easily download and visualise climate data from CliFlo. See the release notes for changes. Checkout the docs to get started.
A new version (v2.0-17) 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.
A new version (v0.4.0) of rsnps is on CRAN - fetch SNP (Single-Nucleotide Polymorphism) data from the web. See the release notes for changes. Checkout the docs to get started.
A new version (v0.7.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.
A new version (v0.5.0) of traits is on CRAN - species trait data from around the web. See the release notes for changes. Checkout the docs to get started.
A new version (v0.3.0) of ccafs is on CRAN - client for Climate Change, Agriculture, & Food Security (CCAFS) General Circulation Models. See the release notes for changes. Checkout the docs to get started.
A new version (v0.7.4) of DataSpaceR is on CRAN - interface to the CAVD DataSpace. See the release notes for changes. Checkout the docs to get started.
A new version (v1.2.0) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started.
A new version (v7.12.5) 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.
A new version (v0.2.2) of taxizedb is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started.
A new version (v1.3.1) of writexl is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the docs to get started.

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.

No new submissions or approved submissions.

On the blog

It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, February 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)

Software Review:

Jonathan Keane wrote about their recently rOpenSci reviewed package dittodb: Developing dittodb. Jonathan discusses the motivation behind the package, some of the technical challenges, and the story behind the name of the package.

Tech notes

Scott Chamberlain wrote a post on Scientific Name Parsing: rgnparser and namext, covering the rgnparser and namext packages.

Citations

The following 18 works use/cite rOpenSci software:

Ordynets et al. used treeio in their paper Morphologically similar but not closely related: the long-spored species of Subulicystidium (Trechisporales, Basidiomycota ¹
Ye used lingtypology in their paper Independent and dependent possessive person forms ²
Monaco et al. used taxize and rfishbase in their paper Dietary generalism accelerates arrival and persistence of coral‐reef fishes in their novel ranges under climate change ³
Tennant et al. used tesseract in their paper Climate drivers of plague epidemiology in British India, 1898–1949 ⁴
Runge et al. used rnaturalearth in their paper Pan-Arctic analysis of cultural ecosystem services using social media and automated content analysis ⁵
Swetnam et al. used rnaturalearth in their paper Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018 ⁶
Walker et al. used rdhs in their paper The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries ⁷
McDonald used weathercan in their paper Applying Geographic Information Systems to the Study of Honey Bee Diseases and Pests ⁸
Ficcadenti et al. used hunspell in their paper Words ranking and Hirsch index for identifying the core of the hapaxes in political texts ⁹
Hierink et al. used rcites and citesdb in their paper Forty-four years of global trade in CITES-listed snakes: Trends and implications for conservation and public health ¹⁰
Pal Negi et al. used taxize in their paper Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs ¹¹
Puerta et al. used rtweet in their paper Co-occurrence networks of Twitter content after manual or automatic processing. A case-study on “gluten-free ¹²
Anton et al. used MODIStsp in their paper Gray wolf habitat use in response to visitor activity along roadways in Yellowstone National Park ¹³
Loewen et al. used taxize in their paper Climate warming moderates the impacts of introduced sportfish on multiple dimensions of prey biodiversity ¹⁴
Siregar & Prawisudatama used RSelenium in their paper Improving data literacy using liteRate: an R Shiny Apps for visualizing and exploring data published on BPS-Statistics Indonesia’s Website ¹⁵
Bisbee & Honig used RSelenium in their paper Flight to Safety: 2020 Democratic Primary Election Results and COVID-19 ¹⁶
Hobert et al. used rcrossref in their paper Open Access Uptake in Germany 2010-18: Adoption in a diverse research landscape ¹⁷
Webb et al. used worrms in their paper Occupancy‐derived thermal affinities reflect known physiological thermal limits of marine species ¹⁸

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 new use case was shared in the forum over the past two weeks since our last newsletter:

Georgios Karamanis shared: Bar chart portraits; the use case employed the magick package, an rOpenSci package maintained by Jeroen Ooms

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. Check out our guidance for taking over maintenance of a package.

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

RSelenium: now maintained by Ju Kim
chromer: now maintained by Paula Andrea
qualtRics: now maintained by Julia Silge
rsnps: now maintained by Julia Gustavsen and Sina Rüeger
webchem: now maintained by Erik Sapper
mregions: now maintained by Lennert Schepers (VLIZ)
rWBclimate: now maintained by Sergio Ibarra-Espinosa and Amanda Rehbein
rinat: now maintained by Stéphane Guillou

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

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Footnotes

Ordynets, A., Liebisch, R., Lysenko, L., Scherf, D., Volobuev, S., Saitta, A., … Langer, E. (2020). Morphologically similar but not closely related: the long-spored species of Subulicystidium (Trechisporales, Basidiomycota). Mycological Progress, 19(7), 691–703. https://doi.org/10.1007/s11557-020-01587-3 ↩
Ye, J. (2020). Independent and dependent possessive person forms. Studies in Language, 44(2), 363–406. https://doi.org/10.1075/sl.19020.ye ↩
Monaco, C. J., Bradshaw, C. J. A., Booth, D. J., Gillanders, B. M., Schoeman, D. S., & Nagelkerken, I. (2020). Dietary generalism accelerates arrival and persistence of coral‐reef fishes in their novel ranges under climate change. Global Change Biology. https://doi.org/10.1111/gcb.15221 ↩
Tennant, W. S. D., Tildesley, M. J., Spencer, S. E. F., & Keeling, M. J. (2020). Climate drivers of plague epidemiology in British India, 1898–1949. Proceedings of the Royal Society B: Biological Sciences, 287(1928), 20200538. https://doi.org/10.1098/rspb.2020.0538 ↩
Runge, C. A., Hausner, V. H., Daigle, R. M., & Monz, C. A. (2020). Pan-Arctic analysis of cultural ecosystem services using social media and automated content analysis. Environmental Research Communications, 2(7), 075001. https://doi.org/10.1088/2515-7620/ab9c33 ↩
Swetnam, D. M., Stuart, J. B., Young, K., Maharaj, P. D., Fang, Y., Garcia, S., … Coffey, L. L. (2020). Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018. PLOS Neglected Tropical Diseases, 14(6), e0008343. https://doi.org/10.1371/journal.pntd.0008343 ↩
Walker, P. G. T., Whittaker, C., Watson, O. J., Baguelin, M., Winskill, P., Hamlet, A., … Ghani, A. C. (2020). The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries. Science, eabc0035. https://doi.org/10.1126/science.abc0035 ↩
McDonald, S. (2020). Applying Geographic Information Systems to the Study of Honey Bee Diseases and Pests (Doctoral dissertation). https://bit.ly/34Ox33c ↩
Ficcadenti, V., Cerqueti, R., Ausloos, M., & Dhesi, G. (2020). Words ranking and Hirsch index for identifying the core of the hapaxes in political texts. Journal of Informetrics, 14(3), 101054. https://doi.org/10.1016/j.joi.2020.101054 ↩
Hierink, F., Bolon, I., Durso, A. M., Ruiz de Castañeda, R., Zambrana-Torrelio, C., Eskew, E. A., & Ray, N. (2020). Forty-four years of global trade in CITES-listed snakes: Trends and implications for conservation and public health. Biological Conservation, 248, 108601. https://doi.org/10.1016/j.biocon.2020.108601 ↩
Pal Negi, A., Singh, R., Sharma, A., & Negi, V. S. (2020). Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs. Computational Biology and Chemistry, 87, 107306. https://doi.org/10.1016/j.compbiolchem.2020.107306 ↩
Puerta, P., Laguna, L., Vidal, L., Ares, G., Fiszman, S., & Tárrega, A. (2020). Co-occurrence networks of Twitter content after manual or automatic processing. A case-study on “gluten-free.” Food Quality and Preference, 86, 103993. https://doi.org/10.1016/j.foodqual.2020.103993 ↩
Anton, C. B., Smith, D. W., Suraci, J. P., Stahler, D. R., Duane, T. P., & Wilmers, C. C. (2020). Gray wolf habitat use in response to visitor activity along roadways in Yellowstone National Park. Ecosphere, 11(6). https://doi.org/10.1002/ecs2.3164 ↩
Loewen, C. J. G., Strecker, A. L., Gilbert, B., & Jackson, D. A. (2020). Climate warming moderates the impacts of introduced sportfish on multiple dimensions of prey biodiversity. Global Change Biology, 26(9), 4937–4951. https://doi.org/10.1111/gcb.15225 ↩
Siregar, E., & Prawisudatama, A. Improving data literacy using liteRate: an R Shiny Apps for visualizing and exploring data published on BPS-Statistics Indonesia’s Website https://bit.ly/2ELTyuZ ↩
Bisbee, J., & Honig, D. (2020). Flight to Safety: 2020 Democratic Primary Election Results and COVID-19. Covid Economics, 3(10), 54-84. https://bit.ly/2YRiWWP ↩
Hobert, A., Jahn, N., Mayr, P., Schmidt, B., & Taubert, N. C. (2020). Open Access Uptake in Germany 2010-18: Adoption in a diverse research landscape. https://bit.ly/3bt1LjP ↩
Webb, T. J., Lines, A., & Howarth, L. M. (2020). Occupancy‐derived thermal affinities reflect known physiological thermal limits of marine species. Ecology and Evolution, 10(14), 7050–7061. https://doi.org/10.1002/ece3.6407 ↩