2020-09-14

rOpenSci HQ

Our own community manager Stefanie Butland, and one of our software review editors Brooke Anderson, are remotely speaking at an R-Ladies East Lansing meetup on Thursday, October 22nd: rOpenSci - open tools for open science. If you’d like to attend, see “Who could join?” on the R-Ladies East Lansing page.

Software 📦

CRAN: GitHub:

New Packages

The first version (v0.2.0) of rbace is on CRAN - a client for interacting with the Bielefeld Academic Search Engine API. See the docs to get started.

New Versions

A new version (v3.3.0) 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.
A new version (v0.3.0) of pubchunks is on CRAN - Fetch Sections of XML Scholarly Articles. See the release notes for changes. Checkout the README to get started.
A new version (v0.7.2) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.
A new version (v0.7.13) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the docs to get started.
A new version (v2.0.2) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started.
A new version (v0.4.0) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started.
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 (v0.1.5) of virtuoso is on CRAN - interface to Virtuoso using ODBC. 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.

Citations

The following 19 works use/cite rOpenSci software:

Li et al. used taxize in their paper Changes in taxonomic and phylogenetic diversity in the Anthropocene ¹
James et al. used textreuse in their paper The internationalization of European financial networks: a quantitative text analysis of EU consultation responses ²
Drost used biomartr in their paper LTRpred: de novo annotation of intact retrotransposons ³
Granados et al. used finch in their paper Long-term monitoring of the Iberian ibex population in the Sierra Nevada of the southeast Iberian Peninsula ⁴
Brazeau used rdhs and rnaturalearth in their paper The Molecular, Spatial, and Genetic Epidemiology of Malaria in the Democratic Republic of the Congo ⁵
Pacifico et al. used CoordinateCleaner in their paper Areas of endemism on Brazilian mountaintops revealed by taxonomically verified records of Microlicieae (Melastomataceae ⁶
Hanes et al. used weathercan in their paper Preceding Fall Drought Conditions and Overwinter Precipitation Effects on Spring Wildland Fire Activity in Canada ⁷
Burda et al. used rotl in their paper Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum ⁸
Corput used osfr in their paper Locked in Syndrome Machine Learning Classification using Sentence Comprehension EEG Data ⁹
Stephens used rtweet in their paper A geospatial infodemic: Mapping Twitter conspiracy theories of COVID-19 ¹⁰
Green et al. used rtweet in their paper Elusive consensus: Polarization in elite communication on the COVID-19 pandemic ¹¹
Jayawardhana & Chathurange used MODIStsp in their paper Investigate the sensitivity of the satellite-based agricultural drought indices to monitor the drought condition of paddy and introduction to enhanced multi-temporal agricultural drought indices ¹²
Da Silva et al. used rnoaa in their paper Forecasting Brazilian and American COVID-19 cases based on artificial intelligence coupled with climatic exogenous variables ¹³
Sacchi et al. used magick in their paper Colour variation in signal crayfish Pacifastacus leniusculus ¹⁴
Charalampopoulos used rnoaa and rWBclimate and nasapower in their paper The R Language as a Tool for Biometeorological Research ¹⁵
Oh et al. used rentrez in their paper Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities ¹⁶
Sun et al. used rgbif in their paper Recent accelerated diversification in rosids occurred outside the tropics ¹⁷
Griffiths used rfishbase in their paper Foraging habitat determines predator–prey size relationships in marine fishes ¹⁸
Kurose et al. used rnaturalearth in their paper Chloroplast DNA analysis of the invasive weed, Himalayan balsam (Impatiens glandulifera), in the British Isles ¹⁹

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:

Zhanghe Goh shared: covidpreprints.com using europepmc and rAltmetric; the use case employed the europepmc package, an rOpenSci package maintained by Najko Nahn, and the rAltmetric package, maintained by Karthik Ram

The website Real Python recently had a post covering data version control with Python and DVC. The tool DVC, written in Python, is a command line tool for “machine learning projects”, somewhat similar to git - DVC reminds me of the Dat project. On the DVC website, there’s an article on using dvc with R.

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

Mailing list: Sign up with an email address to get this newsletter sent to your inbox -> ropensci.org/#subscribe
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The rOpenSci blog at ropensci.org/blog - you can subscribe in any RSS aggregator, or manually via https://ropensci.org/feed.xml. We also announce new blog posts on our Twitter account.

Footnotes

Li, D., Olden, J. D., Lockwood, J. L., Record, S., McKinney, M. L., & Baiser, B. (2020). Changes in taxonomic and phylogenetic diversity in the Anthropocene. Proceedings of the Royal Society B: Biological Sciences, 287(1929), 20200777. https://doi.org/10.1098/rspb.2020.0777 ↩
James, S., Pagliari, S., & Young, K. L. (2020). The internationalization of European financial networks: a quantitative text analysis of EU consultation responses. Review of International Political Economy, 1–28. https://doi.org/10.1080/09692290.2020.1779781 ↩
Drost, H.-G. (2020). LTRpred: de novo annotation of intact retrotransposons. Journal of Open Source Software, 5(50), 2170. https://doi.org/10.21105/joss.02170 ↩
Granados, J. E., Ros-Candeira, A., Pérez-Luque, A. J., Moreno-Llorca, R., Cano-Manuel, F. J., Fandos, P., … Zamora, R. (2020). Long-term monitoring of the Iberian ibex population in the Sierra Nevada of the southeast Iberian Peninsula. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0544-1 ↩
Brazeau, N. (2020). The Molecular, Spatial, and Genetic Epidemiology of Malaria in the Democratic Republic of the Congo. https://cdr.lib.unc.edu/downloads/7s75dj87g ↩
Pacifico, R., Almeda, F., Frota, A., & Fidanza, K. (2020). Areas of endemism on Brazilian mountaintops revealed by taxonomically verified records of Microlicieae (Melastomataceae). Phytotaxa, 450(2), 119–148. https://doi.org/10.11646/phytotaxa.450.2.1 ↩
Hanes, C., Wotton, M., Woolford, D. G., Martell, D. L., & Flannigan, M. (2020). Preceding Fall Drought Conditions and Overwinter Precipitation Effects on Spring Wildland Fire Activity in Canada. Fire, 3(2), 24. https://www.mdpi.com/2571-6255/3/2/24/pdf ↩
Burda, P.-C., Crosskey, T., Lauk, K., Zurborg, A., Söhnchen, C., Liffner, B., … Gilberger, T.-W. (2020). Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum. Cell Reports, 31(12), 107817. https://doi.org/10.1016/j.celrep.2020.107817 ↩
Corput, D. V. D. (2020). Locked in Syndrome Machine Learning Classification using Sentence Comprehension EEG Data. arXiv preprint arXiv:2006.12336 https://arxiv.org/pdf/2006.12336.pdf ↩
Stephens, M. (2020). A geospatial infodemic: Mapping Twitter conspiracy theories of COVID-19. Dialogues in Human Geography, 10(2), 276–281. https://doi.org/10.1177/2043820620935683 ↩
Green, J., Edgerton, J., Naftel, D., Shoub, K., & Cranmer, S. J. (2020). Elusive consensus: Polarization in elite communication on the COVID-19 pandemic. Science Advances, 6(28), eabc2717. https://doi.org/10.1126/sciadv.abc2717 ↩
Jayawardhana, W. G. N. N., & Chathurange, V. M. I. (2020). Investigate the sensitivity of the satellite-based agricultural drought indices to monitor the drought condition of paddy and introduction to enhanced multi-temporal agricultural drought indices. J Remote Sens GIS, 9, 271. https://bit.ly/2RoRprZ ↩
Da Silva, R. G., Ribeiro, M. H. D. M., Mariani, V. C., & Coelho, L. dos S. (2020). Forecasting Brazilian and American COVID-19 cases based on artificial intelligence coupled with climatic exogenous variables. Chaos, Solitons & Fractals, 139, 110027. https://doi.org/10.1016/j.chaos.2020.110027 ↩
Sacchi, R., Cancian, S., Ghia, D., Fea, G., & Coladonato, A. (2020). Colour variation in signal crayfish Pacifastacus leniusculus. Current Zoology. https://academic.oup.com/cz/advance-article/doi/10.1093/cz/zoaa031/5865267 ↩
Charalampopoulos, I. (2020). The R Language as a Tool for Biometeorological Research. Atmosphere, 11(7), 682. https://doi.org/10.3390/atmos11070682 ↩
Oh, S., Yeom, J., Cho, H. J., Kim, J.-H., Yoon, S.-J., Kim, H., … Kim, H. S. (2020). Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17139-y ↩
Sun, M., Folk, R. A., Gitzendanner, M. A., Soltis, P. S., Chen, Z., Soltis, D. E., & Guralnick, R. P. (2020). Recent accelerated diversification in rosids occurred outside the tropics. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17116-5 ↩
Griffiths, D. (2020). Foraging habitat determines predator–prey size relationships in marine fishes. Journal of Fish Biology. https://doi.org/10.1111/jfb.14451 ↩
Kurose, D., Pollard, K. M., & Ellison, C. A. (2020). Chloroplast DNA analysis of the invasive weed, Himalayan balsam (Impatiens glandulifera), in the British Isles. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-67871-0 ↩