rOpenSci | rOpenSci News Digest, May 2021

May 21, 2021 From rOpenSci (https://deploy-preview-488--ropensci.netlify.app/blog/2021/05/21/ropensci-news-digest-may-2021/). Except where otherwise noted, content on this site is licensed under the CC-BY license.

rOpenSci News Digest, May 2021

By The rOpenSci Team

Dear rOpenSci friends, it’s time for our monthly news roundup!

You can read this post on our blog. Now let’s dive into the activity at and around rOpenSci!

🔗 rOpenSci HQ

We have no less than three categories of (online 😉) events coming up: social co-working events, a community call, a conference with contributions from four rOpenSci staff members. ✨

🔗 Community Calls

  • Our next community call is about rOpenSci’s R-universe Project and will take place on Tuesday, 25 May 2021 17:00 UTC. The R-universe platform is a new umbrella project under which rOpenSci experiments with new ideas for improving publication and discovery of research software packages in R. In this 1-hour community call, Jeroen Ooms will explain the basic steps of setting up your own universe, and getting started with publishing packages (including experimental software, development versions, research compendia) and articles on your personal subdomain. We are interested in hearing your thoughts and ideas on how this infrastructure can improve how researchers publish and discover R packages and related content.

  • Video and resources from our past community call Set Up Your Package to Foster a Community were posted. rOpenSci puts ongoing effort into exploring and communicating how developers can best attract attention to their package (e.g. usage, citations, or feedback), or how to set up their repository to encourage the types of contributions they want. In this 1-hour community call, Maëlle Salmon, Hugo Gruson, and Steffi LaZerte shared tips and examples on how to do this! Sina Rüeger summarized the call with help from Mark Padgham.

🔗 Social Co-Working

We held our first two Social Co-Working and Label-athon events on April 29th and May 13th. These were truly international events with 14 participants from Canada, Germany, Switzerland, USA, the UK, France, Singapore, and Mexico. We had a blast socializing (scavenger hunts!) and co-working on our personal R projects including repository organization, creating/labelling issues, preliminary research, personal GitHub README files, and those packages you can never find time for. We had quiet and noisy rooms to work in, so everyone was able to find an environment that worked best for them. Sound like fun? We have two more coming up!

🔗 rOpenSci at useR! 2021

Registration for the useR! 2021 conference has begun, with Early Bird Deadline until May 28th. useR! conferences are non-profit conferences organized by community volunteers for the community, supported by the R Foundation. useR! 2021 will take place online.

Get excited for four contributions by rOpenSci staff members:

  • Jeroen Ooms, rOpenSci Lead Infrastructure Engineer, will give a keynote talk about building a modern and scalable package build infrastructure, such as R-universe.

  • Maëlle Salmon, Research Software Engineer with rOpenSci, will give a tutorial, GET better at testing your R package! on Wednesday, July the 7th at 9-12AM GMT+2. This tutorial is about advanced testing of R packages, with HTTP testing as a case study.

  • Stefanie Butland, rOpenSci community manager, will present on rOpenSci’s Model for Managing a Federated Open Source Software Community.

  • Mark Padgham, rOpenSci Software Research Scientist, will also give a regular talk, about his original autotest package for automatic testing of packages.

Find out about more events.

🔗 Software review in Spanish

Another great piece of news: censo2017 was the first package to pass rOpenSci software peer-review in Spanish! 🎉 The censo2017 package by Pachá (aka Mauricio Vargas Sepúlveda) provides access to the 2017 Chilean Census. Editor Melina Vidoni was in charge of this review, the reviewers were Frans van Dunné and María Paula Caldas. Frans van Dunné most kindly translated our review template to Spanish!

Thank you to people in the Latin American R community for discussion and encouragement that helped make this happen.

🔗 Software 📦

🔗 New packages

The following two packages recently became a part of our software suite:

  • censo2017, developed by Mauricio Vargas: Provee un acceso conveniente a mas de 17 millones de registros de la base de datos del Censo 2017. Los datos fueron importados desde el DVD oficial del INE usando el Convertidor REDATAM creado por Pablo De Grande. Esta paquete esta documentado intencionalmente en castellano asciificado para que funcione sin problema en diferentes plataformas. (Provides convenient access to more than 17 million records from the Chilean Census 2017 database. The datasets were imported from the official DVD provided by the Chilean National Bureau of Statistics by using the REDATAM converter created by Pablo De Grande and in addition it includes the maps accompanying these datasets.). It is available on CRAN. It has been reviewed by Frans van Dunné, Maria Paula Caldas.

  • exoplanets, developed by Tyler Littlefield: The goal of exoplanets is to provide access to NASA’s Exoplanet Archive TAP Service. For more information regarding the API please read the documentation https://exoplanetarchive.ipac.caltech.edu/index.html. It is available on CRAN. It has been reviewed by Maëlle Salmon, Nichole Monhait.

Discover more packages, read more about Software Peer Review.

🔗 New versions

The following forty packages have had an update since the latest newsletter: gert (v1.3.0), babette (v2.3), BaseSet (v0.0.16), beastier (v2.3.1), beautier (v2.5), bold (v1.2.0), brranching (v0.7.0), c14bazAAR (2.3.0), circle (v0.7.1), codemetar (v0.3.0), drake (7.13.2), exoplanets (v0.2.1), fingertipsR (v1.0.6), ijtiff (v2.2.6), jqr (v1.2.1), lingtypology (v1.1.5), magick (v2.7.2), mauricer (v2.4), mcbette (v1.14), MtreeRing (v1.4.5), oai (v0.3.2), opencv (v0.2.1), pangaear (v1.1.0), pathviewr (v1.0.1), rbhl (v0.9.2), rdhs (0.7.2), rglobi (v0.2.24), rnoaa (v1.3.4), rzmq (v0.9.8), solrium (v1.2.0), ssh (v0.8.0), stantargets (0.0.2), tarchetypes (0.2.0), targets (0.4.2), terrainr (v0.4.0), tidyhydat (0.5.3), tracerer (v2.2), UCSCXenaTools (v1.4.4), workloopR (v1.1.4), writexl (v1.4.0).

🔗 Software Peer Review

There are sixteen recently closed and active submissions and 4 submissions on hold. Issues are at different stages:

Find out more about Software Peer Review and how to get involved.

🔗 On the blog

🔗 Software Review

A 3D rendering of the summit of Mt. Washington, including watershed boundaries and river lines.

🔗 Other topics

🔗 Citations

Below are the citations recently added to our database of 1295 articles, that you can explore on our citations page. We found use of…

  • biomartr in Böttcher, A., Büttner, M., Tritschler, S., Sterr, M., Aliluev, A., Oppenländer, L., … Lickert, H. (2021). Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates. Nature Cell Biology, 23(1), 23–31. https://doi.org/10.1038/s41556-020-00617-2

  • bold, rentrez in Batovska, J., Piper, A., Valenzuela, I., Cunningham, J., & Blacket, M. (2020). Developing a Non-destructive Metabarcoding Protocol for Detection of Pest Insects in Bulk Trap Catches. https://doi.org/10.21203/rs.3.rs-125070/v1

  • comtradr in Chini, C. M., & Peer, R. A. M. (2021). The traded water footprint of global energy from 2010 to 2018. Scientific Data, 8(1). https://doi.org/10.1038/s41597-020-00795-6

  • CoordinateCleaner in Esquivel, D. A., Aya-Cuero, C., Penagos, A. P., Chacón-Pacheco, J., Agámez-López, C. J., Ochoa, A. V., … Bennett, D. (2020). Updating the distribution of Vampyrum spectrum (Chiroptera, Phyllostomidae) in Colombia: new localities, potential distribution and notes on its conservation. Neotropical Biology and Conservation, 15(4), 689–709. https://doi.org/10.3897/neotropical.15.e58383

  • CoordinateCleaner in Suissa, J. S., & Sundue, M. A. (2020). Diversity Patterns of Neotropical Ferns: Revisiting Tryon’s Centers of Richness and Endemism. American Fern Journal, 110(4). https://doi.org/10.1640/0002-8444-110.4.211

  • CoordinateCleaner, taxize in Tamme, R., Pärtel, M., Kõljalg, U., Laanisto, L., Liira, J., Mander, Ü., … Zobel, M. (2020). Global macroecology of nitrogen‐fixing plants. Global Ecology and Biogeography, 30(2), 514–526. https://doi.org/10.1111/geb.13236

  • FedData in Porter, W. T., Barrand, Z. A., Wachara, J., DaVall, K., Mihaljevic, J. R., Pearson, T., … Nieto, N. C. (2021). Predicting the current and future distribution of the western black-legged tick, Ixodes pacificus, across the Western US using citizen science collections. PLOS ONE, 16(1), e0244754. https://doi.org/10.1371/journal.pone.0244754

  • neotoma in Byun, E., Sato, H., Cowling, S. A., & Finkelstein, S. A. (2020). Extensive wetland development in mid-latitude North America during the Bølling–Allerød. Nature Geoscience, 14(1), 30–35. https://doi.org/10.1038/s41561-020-00670-4

  • NLMR in Thompson, P. R., Derocher, A. E., Edwards, M. A., & Lewis, M. A. (2021). Describing spatiotemporal memory patterns using animal movement modelling. arXiv preprint arXiv:2101.04183. https://arxiv.org/pdf/2101.04183

  • nlrx in Dahirel, M., Bertin, A., Haond, M., Blin, A., Lombaert, E., Calcagno, V., … Vercken, E. (2020). Shifts from pulled to pushed range expansions caused by reduction of landscape connectivity. https://doi.org/10.1101/2020.05.13.092775

  • osmdata in Moradi, M. (2020). Evaluating the quality of OSM roads and buildings in the Québec Province. https://corpus.ulaval.ca/jspui/bitstream/20.500.11794/67232/1/36576.pdf

  • osmdata in Wilkins, E.J. 2020. Using Social Media to Assess the Impact of Weather and Climate on Visitation to Outdoor Recreation Settings. https://digitalcommons.usu.edu/etd/7986

  • pdftools in Li, B., Trueman, B. F., Rahman, M. S., & Gagnon, G. A. (2021). Controlling lead release due to uniform and galvanic corrosion — An evaluation of silicate-based inhibitors. Journal of Hazardous Materials, 407, 124707. https://doi.org/10.1016/j.jhazmat.2020.124707

  • pdftools, tesseract in Hines, R. E., Grandage, A. J., & Willoughby, K. G. (2020). Staying Afloat: Planning and Managing Climate Change and Sea Level Rise Risk in Florida’s Coastal Counties. Urban Affairs Review, 107808742098052. https://doi.org/10.1177/1078087420980526

  • phylocomr, brranching in Perez, T. M., Socha, A., Tserej, O., & Feeley, K. J. (2021). Photosystem II heat tolerances characterize thermal generalists and the upper limit of carbon assimilation. Plant, Cell & Environment. https://doi.org/10.1111/pce.13990

  • rfishbase in Palacios-Abrantes, J., Reygondeau, G., Wabnitz, C. C. C., & Cheung, W. W. L. (2020). The transboundary nature of the world’s exploited marine species. Scientific Reports, 10(1). doi:10.1038/s41598-020-74644-2

  • rfishbase in Parravicini, V., Casey, J. M., Schiettekatte, N. M. D., Brandl, S. J., Pozas-Schacre, C., Carlot, J., … Stuart-Smith, R. D. (2020). Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny. PLOS Biology, 18(12), e3000702. https://doi.org/10.1371/journal.pbio.3000702

  • rgbif in Ascensão, F., D’Amico, M., Martins, R. C., Rebelo, R., Barbosa, A. M., Bencatel, J., … Capinha, C. (2021). Distribution of alien tetrapods in the Iberian Peninsula. NeoBiota, 64, 1–21. https://doi.org/10.3897/neobiota.64.55597

  • rgbif in Freimuth, J., Bossdorf, O., Scheepens, J. F., & Willems, F. M. (2021). Climate warming changes synchrony of plants and pollinators. https://doi.org/10.1101/2021.01.10.425984

  • rgbif in Liao, H., Li, D., Zhou, T., Huang, B., Zhang, H., Chen, B., & Peng, S. (2020). The role of functional strategies in global plant distribution. Ecography, 44(4), 493–503. https://doi.org/10.1111/ecog.05476

  • rgbif in Pineda-Munoz, S., Wang, Y., Lyons, S. K., Tóth, A. B., & McGuire, J. L. (2021). Mammal species occupy different climates following the expansion of human impacts. Proceedings of the National Academy of Sciences, 118(2), e1922859118. https://doi.org/10.1073/pnas.1922859118

  • rgbif in Santos, G. N. dos, Silva, A. C. da, & Higuchi, P. (2020). IMPACT OF CLIMATE CHANGE ON THE GEOGRAPHICAL DISTRIBUTION OF A CLOUD FOREST INDICATOR TREE SPECIES. Revista Árvore, 44. https://doi.org/10.1590/1806-908820200000032

  • rnaturalearth in Ionela-Andreea, P., & Marian, N. (2020). Cluster Analysis of Regional Research and Development Disparities in Europe. Studies in Business and Economics, 15(3), 303–312. https://doi.org/10.2478/sbe-2020-0060

  • rnaturalearth in Mari, A., Roloff, T.-C., Stange, M., Soegaard, K. K., Asllanaj, E., Tauriello, G., … Egli, A. (2021). Global surveillance of potential antiviral drug resistance in SARS-CoV-2: proof of concept focussing on the RNA-dependent RNA polymerase. https://doi.org/10.1101/2020.12.28.20248663

  • rnaturalearth in Pogorevc, N., Simčič, M., Khayatzadeh, N., Soelkner, J., Berger, B., Bojkovski, D., … Horvat, S. (2020). Post-Genotyping Optimization of Dataset Formation Could Affect Genetic Diversity Parameters: An Example of Analyses with Alpine Goat Breeds. https://doi.org/10.21203/rs.3.rs-133590/v1

  • rnaturalearth in Shaw, E. C., Fowler, R., Ohadi, S., Bayly, M. J., Barrett, R. A., Tibbits, J., … Cousens, R. D. (2020). Explaining the worldwide distributions of two highly mobile species: Cakile edentula and Cakile maritima. Journal of Biogeography, 48(3), 603–615. https://doi.org/10.1111/jbi.14024

  • rotl in Sandoval-Herrera, N. I., Mastromonaco, G. F., Becker, D. J., Simmons, N. B., & Welch, K. C. (2021). Inter- and intra-specific variation in hair cortisol concentrations of Neotropical bats. https://doi.org/10.1101/2021.01.10.426004

  • rredlist, rfishbase in Murgier, J., McLean, M., Maire, A., Mouillot, D., Loiseau, N., Munoz, F., … Auber, A. (2021). Rebound in functional distinctiveness following warming and reduced fishing in the North Sea. Proceedings of the Royal Society B: Biological Sciences, 288(1942), 20201600. https://doi.org/10.1098/rspb.2020.1600

  • rtweet in Boehm, F. J., & Hanlon, B. M. (2021). What Is Happening on Twitter? A Framework for Student Research Projects With Tweets. Journal of Statistics and Data Science Education, 29(sup1), S95–S102. https://doi.org/10.1080/10691898.2020.1848486

  • rtweet in Gutiérrez García-Pardo, I., Guevara Gil, J. A., Gómez González, D., Castro Cantalejo, J., & Espínola Vílchez, R. (2021). Community Detection Problem Based on Polarization Measures. An application to Twitter: the COVID-19 case in Spain. https://doi.org/10.20944/preprints202101.0080.v1

  • rtweet in Lucas, B., & Landman, T. (2020). Social listening, modern slavery, and COVID-19. Journal of Risk Research, 1–21. https://doi.org/10.1080/13669877.2020.1864009

  • skimr in Behrendt, I., Fasshauer, M., & Eichner, G. (2020). Gluten Intake and All-Cause and Cause-Specific Mortality: Prospective Findings from the UK Biobank. The Journal of Nutrition, 151(3), 591–597. https://doi.org/10.1093/jn/nxaa387

  • taxize in Albery, G. F., Carlson, C. J., Cohen, L. E., Eskew, E. A., Gibb, R., Ryan, S. J., … Becker, D. J. (2021). Urban-adapted mammal species have more known pathogens. https://doi.org/10.1101/2021.01.02.425084

  • taxize in Janssen, J., & Gomez, L. (2021). An examination of the import of live reptiles from Indonesia by the United States from 2000 to 2015. Journal for Nature Conservation, 59, 125949. https://doi.org/10.1016/j.jnc.2020.125949

  • taxize in Meireles, J. E., Cavender‐Bares, J., Townsend, P. A., Ustin, S., Gamon, J. A., Schweiger, A. K., … O’Meara, B. C. (2020). Leaf reflectance spectra capture the evolutionary history of seed plants. New Phytologist, 228(2), 485–493. https://doi.org/10.1111/nph.16771

  • treeio in Gates, M. W., Zhang, Y. M., & Buffington, M. L. (2020). The great greenbriers gall mystery resolved? New species of Aprostocetus Westwood (Hymenoptera, Eulophidae) gall inducer and two new parasitoids (Hymenoptera, Eurytomidae) associated with Smilax L. in southern Florida, USA. Journal of Hymenoptera Research, 80, 71–98. https://doi.org/10.3897/jhr.80.59466

  • treeio in Maruyama, H., Masago, A., Nambu, T., Mashimo, C., Takahashi, K., & Okinaga, T. (2020). Inter-site and interpersonal diversity of salivary and tongue microbiomes, and the effect of oral care tablets. F1000Research, 9, 1477. https://doi.org/10.12688/f1000research.27502.1

  • treeio in Oswald, K. N., Lee, A. T. K., & Smit, B. (2021). Seasonal metabolic adjustments in an avian evolutionary relict restricted to mountain habitat. Journal of Thermal Biology, 95, 102815. https://doi.org/10.1016/j.jtherbio.2020.102815

  • treeio in Toparslan, E., Karabag, K., & Bilge, U. (2020). A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences. PLOS ONE, 15(12), e0243927. https://doi.org/10.1371/journal.pone.0243927

  • UCSCXenaTools in Cui, Y., Hunt, A., Li, Z., Birkin, E., Lane, J., Ruge, F., & Jiang, W. G. (2021). Lead DEAD/H box helicase biomarkers with the therapeutic potential identified by integrated bioinformatic approaches in lung cancer. Computational and Structural Biotechnology Journal, 19, 261–278. https://doi.org/10.1016/j.csbj.2020.12.007

  • webchem in Hammoud, Z., & Kramer, F. (2020). Multipath: An R Package to Generate Integrated Reproducible Pathway Models. Biology, 9(12), 483. https://doi.org/10.3390/biology9120483

  • webchem in Su, Q.-Z., Vera, P., Nerín, C., Lin, Q.-B., & Zhong, H.-N. (2021). Safety concerns of recycling postconsumer polyolefins for food contact uses: Regarding (semi-)volatile migrants untargetedly screened. Resources, Conservation and Recycling, 167, 105365. https://doi.org/10.1016/j.resconrec.2020.105365

Thank you for citing our tools!

🔗 Use cases

Three use cases of our packages and resources have been reported since we sent the last newsletter.

Explore other use cases and report your own!

🔗 Call for maintainers

There’s no open call for new maintainers at this point but you can refer to our contributing guide for finding ways to get involved! As the maintainer of an rOpenSci package, feel free to contact us on Slack or email info@ropensci.org to get your call for maintainer featured in the next newsletter.

🔗 Package development corner

Some useful tips for R package developers. 👀

Sometimes you find yourself documenting internal functions with roxygen2 without really wanting everyone to get to see the docs. Do you know the difference between the @internal and @NoRd tags?

  • Keyword @internal means there will be a manual page for the function but it won’t be in the documentation index. " @keywords internal is useful because it removes the function from the documentation index; it’s useful for functions aimed primarily at other developers, not typical users of the package."
  • @NoRd means there won’t even be a manual page so the roxygen2 documentation of that function only lives in the R script. We at rOpenSci strongly encourage documentation of internal functions, and advise doing so within code itself rather than as separate manual pages – that is, using @noRd and not @internal. It is also recommended in the tidyverse style guide.

Speaking of documentation, when writing examples, do you know the difference between \dontrun{}, \donttest{} and \dontshow{}? (Is this newsletter section turning into a quizz? 😅) The roxygen2 docs feature a table explaining when different types of examples are run depending on the context (in example(), help(), R CMD check, R CMD check –as-cran) which is very useful when you wonder how to safeguard your package examples on e.g. CRAN. The same documentation section introduces the very handy @examplesIf roxygen2 tag that you can use for finer control.

Now on to code archaeology! Do you want to “pinpoint the version at which a certain argument appeared in a specific function of a package (or that its default value changed)", e.g. to figure out the minimal version required? You might like the apicheck package by David Hugh-Jones, that helps you “explore the historical API of functions in CRAN packages”; and rcheology by the same author for data on base packages. Related to this are:

🔗 Last words

Thanks for reading! If you want to get involved with rOpenSci, check out our Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or contribute in other ways like sharing use cases.

If you haven’t subscribed to our newsletter yet, you can do so via a form. Until it’s time for our next newsletter, you can keep in touch with us via our website and Twitter account.

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