Latest rOpenSci News Digest

Dear rOpenSci friends, it’s time for our monthly news roundup! Some housekeeping first: We’ve been changing the infrastructure of our newsletter a bit so please update your RSS and JSON feeds to https://ropensci.org/tags/newsletter/index.xml and https://ropensci.org/tags/newsletter/index.json, respectively. You can read this post on our blog. Now let’s dive into the activity at and around rOpenSci!

🔗 rOpenSci HQ

Our R-universe project now has its own page on our website! ???? The R-universe platform is a new umbrella project under which we experiment with various new ideas for improving publication and discovery of research software in R.

Regarding another exciting project of ours… We’ve run the first comm call of our series on the statistical software review project! rOpenSci Statistical Software Testing and Peer Review took place on March 2nd. The video recording (including closed captions) and resources as well as a summary have been posted.

Find out about more events.

🔗 Software ????

🔗 New packages

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

• pathviewr, developed by Vikram B. Baliga together with Melissa S. Armstrong, Eric R. Press: Tools to import, clean, and visualize movement data, particularly from motion capture systems such as Optitracks Motive, the Straw Labs Flydra, or from other sources. We provide functions to remove artifacts, standardize tunnel position and tunnel axes, select a region of interest, isolate specific trajectories, fill gaps in trajectory data, and calculate 3D and per-axis velocity. For experiments of visual guidance, we also provide functions that use subject position to estimate perception of visual stimuli. It has been reviewed by Anne-Sophie Bonnet-Lebrun, Marco Sciaini.

• terrainr, developed by Michael Mahoney: Functions for the retrieval, manipulation, and visualization of geospatial data, with an aim towards producing 3D landscape visualizations in the Unity 3D rendering engine. Functions are also provided for retrieving elevation data and base map tiles from the USGS National Map (https://apps.nationalmap.gov/services/). It is available on CRAN. It has been reviewed by Mike Johnson, Sydney Foks.

Discover more packages, read more about Software Peer Review.

🔗 New versions

The following twenty-one packages have had an update since the latest newsletter: chlorpromazineR (v0.2.0), crul (v1.1.0), eia (v0.3.7), epubr (v0.6.2), essurvey (v1.0.7), fulltext (v1.7.0), magick (v2.7.0), opencage (v0.2.2), osmextract (v0.2.1), parzer (v0.4.0), pathviewr (v1.0.0), phonfieldwork (v0.0.11), rerddap (v0.7.4), rinat (v0.1.8), rnoaa (v1.3.2), rplos (v1.0.0), tarchetypes (0.1.0), targets (0.2.0), terrainr (v0.3.1), tiler (v0.2.5), webmockr (v0.8.0).

🔗 Software Peer Review

There are eighteen recently closed and active submissions and 2 submissions on hold. Issues are at different stages:

• Five at ‘6/approved’:

  • terrainr, Retrieve Data from the USGS National Map and Transform it for 3D Landscape Visualizations. Submitted by Michael Mahoney.

  • pathviewR, Wrangle, Analyze, and Visualize Animal Movement Data. Submitted by Vikram Baliga.

  • pixelclasser, A Package for Classifying Pixels by Colour. Submitted by Carlos Real Rodríguez.

  • coder, Deterministic Categorization of Items Based on External Code Data. Submitted by Erik Bülow.

  • SymbiotaR2, Downloading data from Symbiota2 portals into R. Submitted by Austin Koontz.

• One at ‘5/awaiting-reviewer(s)-response’:

  • censo2017, Base de Datos de Facil Acceso del Censo 2017 de Chile. Submitted by Pachamaltese.

• Three at ‘4/review(s)-in-awaiting-changes’:

  • dataaimsr, AIMS Data Platform API Client. Submitted by Diego Barneche.

  • healthdatacsv, Access data in the healthdata.gov catalog. Submitted by iecastro.

  • circle, R Client Package for Circle CI. Submitted by Patrick Schratz.

• Four at ‘3/reviewer(s)-assigned’:

  • stantargets, Targets for Stan Workflows. Submitted by Will Landau.

  • dataspice, Create Lightweight Schema.org Descriptions of Data. Submitted by Bryce Mecum.

  • chemspiderapi, R Wrapper for ChemSpider’s API Services. Submitted by Raoul Wolf.

  • exoplanets, Provides access to NASA’s Exoplanet Archive, see https://exoplanetarchive.ipac.caltech.edu/index.html. Submitted by Tyler Littlefield.

• One at ‘2/seeking-reviewer(s)’:

  • occCite, Querying and Managing Large Biodiversity Occurrence Datasets. Submitted by Hannah Owens.

• Three at ‘1/editor-checks’:

  • slopes, Calculate Slopes of Roads, Rivers and Trajectories. Submitted by RFlx.

  • epair, Grabs data from EPA API, simplifies getting pollutant data. Submitted by Leo Orozco-Mulfinger.

  • tidytags, Simple Collection and Powerful Analysis of Twitter Data. Submitted by Bret Staudt Willet.

• One at ‘0/editorial-team-prep’:

  • ROriginStamp, Interface to OriginStamp API to Obtain Trusted Time Stamps. Submitted by Rainer M Krug.

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

🔗 On the blog

🔗 Software Review

• coder Makes Medical Coding less Messy by Erik Bülow. The coder package helps to summarize and interpret (medical) coding in R (think ICD, ATC and more).

  

• rOpenSci Dev Guide 0.6.0: Updates by Maëlle Salmon, Brooke Anderson, Laura DeCicco, Julia Gustavsen, Anna Krystalli, Mauro Lepore, Karthik Ram, Noam Ross, Melina Vidoni. Updates in version 0.6.0 of the online book ‘rOpenSci Packages: Development, Maintenance, and Peer Review rOpenSci Packages: Development, Maintenance, and Peer Review’.

  

• rOpenSci Statistical Software Testing and Peer Review – Community Call Summary by Noam Ross, Mark Padgham, Anna Krystalli, Alex Hayes, John Sakaluk, Steffi LaZerte. Summary of the Community Call on Statistical Software Testing and Peer Review.

  

🔗 Other topics

• Make Your R Package Easier to Cite by Maëlle Salmon, Scott Chamberlain, Karthik Ram. Some tips to promote scientific citations of your work.

🔗 Tech Notes

• A first look at the R-universe build infrastructure by Jeroen Ooms.

🔗 Citations

Below are the citations recently added to our database of 1254 articles, that you can explore on our citations page. We found use of…

• baRcodeR in Walker, V. K., Das, P., Li, P., Lougheed, S. C., Moniz, K., Schott, S., … Koch, I. (2020). Identification of Arctic Food Fish Species for Anthropogenic Contaminant Testing Using Geography and Genetics. Foods, 9(12), 1824. https://doi.org/10.3390/foods9121824

• CoordinateCleaner, rnaturalearth in Farooq, H., Azevedo, J. A. R., Soares, A., Antonelli, A., & Faurby, S. (2020). Mapping Africa’s Biodiversity: More of the Same Is Just Not Good Enough. Systematic Biology. https://doi.org/10.1093/sysbio/syaa090

• magick in Ball, J. (2020). Food Classification with Convolutional Neural Networks and Multi-Class Linear Discernment Analysis. arXiv preprint arXiv:2012.03170. https://arxiv.org/pdf/2012.03170

• magick in Hillary, R. F., & Marioni, R. E. (2020). MethylDetectR: a software for methylation-based health profiling. Wellcome Open Research, 5, 283. https://doi.org/10.12688/wellcomeopenres.16458.1

• magick in Liang, X., Hu, Y., Yan, C., & Xu, K. (2020). i2d: an R package for simulating data from images and the implications in biomedical research. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa991

• magick in Loser, D., Schaefer, J., Danker, T., Möller, C., Brüll, M., Suciu, I., … Kraushaar, U. (2020). Human neuronal signaling and communication assays to assess functional neurotoxicity. Archives of Toxicology, 95(1), 229–252. https://doi.org/10.1007/s00204-020-02956-3

• magick in Wang, J., Wang, X., Gao, Y., Lin, Z., Chen, J., Gigantelli, J., … Pierre, S. V. (2020). Stress Signal Regulation by Na/K-ATPase As a New Approach to Promote Physiological Revascularization in a Mouse Model of Ischemic Retinopathy. Investigative Opthalmology & Visual Science, 61(14), 9. https://doi.org/10.1167/iovs.61.14.9

• NLMR in Braziunas, K. H., Seidl, R., Rammer, W., & Turner, M. G. (2020). Can we manage a future with more fire? Effectiveness of defensible space treatment depends on housing amount and configuration. Landscape Ecology, 36(2), 309–330. https://doi.org/10.1007/s10980-020-01162-x

• osmdata in Padgham, M., Lovelace, R., Salmon, M., & Rudis, B. (2017). osmdata. The Journal of Open Source Software, 2(14), 305. https://doi.org/10.21105/joss.00305

• 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

• phylotaR in Crespo, L. C., Silva, I., Enguídanos, A., Cardoso, P., & Arnedo, M. A. (2020). Integrative taxonomic revision of the woodlouse-hunter spider genus Dysdera (Araneae: Dysderidae) in the Madeira archipelago with notes on its conservation status. Zoological Journal of the Linnean Society. https://doi.org./10.1093/zoolinnean/zlaa089

• refsplitr in Smith, T. B., Vacca, R., Krenz, T., & McCarty, C. (2021). Great minds think alike, or do they often differ? Research topic overlap and the formation of scientific teams. Journal of Informetrics, 15(1), 101104. https://doi.org/10.1016/j.joi.2020.101104

• rfishbase in Gandra, M., Assis, J., Martins, M. R., & Abecasis, D. (2020). Reduced Global Genetic Differentiation of Exploited Marine Fish Species. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msaa299

• rfishbase in Kopf, R. K., Yen, J. D. L., Nimmo, D. G., Brosse, S., & Villéger, S. (2020). Global patterns and predictors of trophic position, body size and jaw size in fishes. Global Ecology and Biogeography, 30(2), 414–428. https://doi.org/10.1111/geb.13227

• rgbif in Ludt, W. B., & Myers, C. E. (2020). Distinguishing between dispersal and vicariance: A novel approach using anti‐tropical taxa across the fish Tree of Life. Journal of Biogeography, 48(3), 577–589. https://doi.org/10.1111/jbi.14021

• rgbif in Mayani-Parás, F., Botello, F., Castañeda, S., Munguía-Carrara, M., & Sánchez-Cordero, V. (2021). Cumulative habitat loss increases conservation threats on endemic species of terrestrial vertebrates in Mexico. Biological Conservation, 253, 108864. https://doi.org/10.1016/j.biocon.2020.108864

• rgbif in Pons, J., Campión, D., Chiozzi, G., Ettwein, A., Grangé, J., Kajtoch, Ł., … Fuchs, J. (2020). Phylogeography of a widespread Palaearctic forest bird species: The White‐backed Woodpecker (Aves, Picidae). Zoologica Scripta, 50(2), 155–172. https://doi.org/10.1111/zsc.12466

• rgbif in Zonneveld, M., Kindt, R., Solberg, S. Ø., N’Danikou, S., & Dawson, I. K. (2020). Diversity and conservation of traditional African vegetables: Priorities for action. Diversity and Distributions, 27(2), 216–232. https://doi.org/10.1111/ddi.13188

• rnaturalearth in Rose Vineer, H., Morgan, E. R., Hertzberg, H., Bartley, D. J., Bosco, A., Charlier, J., … Rinaldi, L. (2020). Increasing importance of anthelmintic resistance in European livestock: creation and meta-analysis of an open database. Parasite, 27, 69. https://doi.org/10.1051/parasite/2020062

• rnaturalearthdata, rnaturalearth in Bennie, J. A., De Cocker, K., Smith, J. J., & Wiesner, G. H. (2020). The epidemiology of muscle-strengthening exercise in Europe: A 28-country comparison including 280,605 adults. PLOS ONE, 15(11), e0242220. https://doi.org/10.1371/journal.pone.0242220

• rnoaa in Dumitrescu, L., & Schiopu-Kratina, I. (2021). Asymptotic results with estimating equations for time-evolving clustered data. Journal of Statistical Planning and Inference. arXiv preprint. https://arxiv.org/pdf/2011.14017

• ropenaq in Le, V. V., Huynh, T. T., Ölçer, A., Hoang, A. T., Le, A. T., Nayak, S. K., & Pham, V. V. (2020). A remarkable review of the effect of lockdowns during COVID-19 pandemic on global PM emissions. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects, 1–16. https://doi.org/10.1080/15567036.2020.1853854

• rotl in Dániel-Ferreira, J., Bommarco, R., Wissman, J., & Öckinger, E. (2020). Linear infrastructure habitats increase landscape-scale diversity of plants but not of flower-visiting insects. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-78090-y

• rotl in Kunc, H. P., & Schmidt, R. (2020). Species sensitivities to a global pollutant: A meta‐analysis on acoustic signals in response to anthropogenic noise. Global Change Biology, 27(3), 675–688. https://doi.org/10.1111/gcb.15428

• rtweet in Bittermann, A., Batzdorfer, V., Müller, S. M., & Steinmetz, H. (2021). Mining Twitter to detect hotspots in psychology. Zeitschrift für Psychologie. https://www.psycharchives.org/bitstream/20.500.12034/3956/1/ESM%201_methods.pdf

• stplanr in Fitzgerald, D. B., Henderson, A. R., Maloney, K. O., Freeman, M. C., Young, J. A., Rosenberger, A. E., … Smith, D. R. (2021). A Bayesian framework for assessing extinction risk based on ordinal categories of population condition and projected landscape change. Biological Conservation, 253, 108866. https://doi.org/10.1016/j.biocon.2020.108866

• taxize in Freiberg, M., Winter, M., Gentile, A., Zizka, A., Muellner-Riehl, A. N., Weigelt, A., & Wirth, C. (2020). LCVP, The Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-00702-z

• tesseract in Candarli, D. (2020). A longitudinal study of multi-word constructions in L2 academic writing: the effects of frequency and dispersion. Reading and Writing. https://doi.org/10.1007/s11145-020-10108-3

• treeio in Chak, S. T. C., Baeza, J. A., & Barden, P. (2020). Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msaa297

• treeio in Wagner, E., Zaiser, A., Leitner, R., Quijada, N. M., Pracser, N., Pietzka, A., … Rychli, K. (2020). Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains. BMC Genomics, 21(1). https://doi.org/10.1186/s12864-020-07263-w

• UCSCXenaTools in Gvaldin, D. Y., Pushkin, A. A., Timoshkina, N. N., Rostorguev, E. E., Nalgiev, A. M., & Kit, O. I. (2020). Integrative analysis of mRNA and miRNA sequencing data for gliomas of various grades. Egyptian Journal of Medical Human Genetics, 21(1). https://doi.org/10.1186/s43042-020-00119-8

• monkeylearn in Dawson, H. A., & Allison, M. (2021). Requirements for Autonomous Underwater Vehicles (AUVs) for scientific data collection in the Laurentian Great Lakes: A questionnaire survey. Journal of Great Lakes Research, 47(1), 259–265. https://doi.org/10.1016/j.jglr.2020.11.004

Thank you for citing our tools!

🔗 Use cases

Nine use cases of our packages and resources have been reported since the 1st of January.

• Using terrainr to retrieve spatial data and make 3D landscape visualizations. Reported by Michael Mahoney.

• Using dittodb to test database queries. Reported by Gordon Shotwell.

• Mapping collaborations in Neotropical Taxonomy with refsplitr. Reported by Emilio M Bruna.

• Use gert to scan all git repos in a directory. Reported by Danielle Navarro.

• Shiny apps to search #rstudioglobal or #rstats tweets with rtweet. Reported by Sharon Machlis.

• pdftools for extracting complex (e.g. text-wrapped/multiline) tables from pdfs. Reported by Lizlaw.

• Getting and plotting weather and climate data. Reported by Alex Koiter.

• Using ghql to analyze all my 2020 GitHub commits. Reported by Frie.

• Scraping liked posts on Twitter using rtweet. Reported by Isabella Velásquez.

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. ????

Do you have some questions around licensing of your R package? The license chapter of the R packages book by Hadley Wickham and Jenny Bryan was recently updated. A less recent but interesting read is Colin Fay’s Licensing R e-book.

Encoding can also be a tricky topic for package developers. Useful resources include Kevin Ushey’s blog post “String encoding and R”, Irene Steves’ blog post “Encoding in R”, searching for encoding in “Writing R Extensions” (e.g. “If the DESCRIPTION file is not entirely in ASCII it should contain an ‘Encoding’ field specifying an encoding. This is used as the encoding of the DESCRIPTION file itself and of the R and NAMESPACE files, and as the default encoding of .Rd files."), some threads of R-package-devel.

Afraid to forget something when you submit your package to CRAN? A check list could help! You can use usethis::use_release_issue(), number one “secret” [of the tidyverse team] for avoiding multiple rounds of review with CRAN. Now, if you want to add your own specific bullet e.g. “Update my brag document” or “Consider writing a tech note for rOpenSci blog”, you can add an unexported release_bullets() function returning a character vector to your package.

release_bullets <- function() {
c(
"Update my brag document.",
"Contact rOpenSci blog editors to schedule a tech note."
)
}

For inspiration you can search the CRAN mirror maintained by R-hub. For more resources around CRAN, see Isabella Velásquez’s post “You CRAN Do It, What CRAN First-Timers Should Know”.

🔗 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.