Apr 13, 2020
Software 📦
CRAN:
GitHub:
New Versions
- A new version (
v0.9.0
) ofrplos
is on CRAN - Interface to the Search API for Public Library of Science journals. See the release notes for changes. Checkout the vignettes to get started. - A new version (
v0.3.2
) ofcrminer
is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started. - A new version (
v0.9.2
) ofgeojsonio
is on CRAN - Convert Data from and to GeoJSON or TopoJSON. See the release notes for changes. Checkout the vignettes to get started. - A new version (
v0.9.6
) ofrnoaa
is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started. - A new version (
v0.3.2
) ofscrubr
is on CRAN - clean biological occurrence records. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.0.5
) ofijtiff
is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.3.8
) ofrdefra
is on CRAN - get data from DEFRA’s UK-AIR website https://uk-air.defra.gov.uk/. See the release notes for changes. Checkout the rdefra vignette to get started. - A new version (
v0.5.2
) ofstplanr
is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. - A new version (
v4.9.2.1
) ofplotly
is on CRAN - Create Interactive Web Graphics via plotly.js. See the release notes for changes. Checkout the plotly book to get started. - A new version (
v0.4.1
) ofauk
is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.3.8
) ofjstor
is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.0
) oftradestatistics
is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.4
) ofxslt
is on CRAN - extensible style-sheet language transformations. See the release notes for changes. Checkout the README to get started. - A new version (
v1.1
) oflightr
is on CRAN - read spectrometric data and metadata. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.9.94
) oftaxize
is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. - A new version (
v0.5.4
) ofvcr
is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started.
Software Review ✔
In the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review. Please check back at our software review repository after 17 April for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent. Other rOpenSci community activities continue. We express our continued great appreciation for the work of our authors and reviewers.
On the blog
Stefanie Butland and Maëlle Salmon wrote a post on lessons learned from creating the new blog guide: 10 Things We Learned in Creating the Blog Guide with bookdown
Use Cases
The following 21 works use/cite rOpenSci software:
- Cirtwill et al. used taxize in their paper Related plants tend to share pollinators and herbivores, but strength of phylogenetic signal varies among plant families 1
- Léveillé-Bourret et al. used rgbif and CoordinateCleaner in their paper RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae 2
- Moudrý & Devillers used CoordinateCleaner in their paper Quality and usability challenges of global marine biodiversity databases: An example for marine mammal data 3
- Deng et al. used hunspell in their paper Sentiment analysis of real-world migraine tweets for population research 4
- Shan et al. used rotl in their paper Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems 5
- Horne et al. used rotl in their paper Selection for increased male size predicts variation in sexual size dimorphism among fish species 6
- Akpınar et al. used taxize in their paper Pathogenicity of human mtDNA variants is revealed by combining a novel phylogenetic analysis with machine learning 7
- Milla et al. used rgbif and CoordinateCleaner in their paper Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food 8
- Scherer et al. used NLMR and landscapetools in their paper Moving infections: individual movement decisions drive disease persistence in spatially structured landscapes 9
- Burns & Bloom used rfishbase in their paper Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes 10
- Santos used rentrez in their paper Phylogenetic Analyses of Chemokine Receptors from Sequence Retrieval to Phylogenetic Trees 11
- Walczyńska et al. used rotl in their paper Should I shrink or should I flow? – body size adjustment to thermo-oxygenic niche 12
- Mathes used rnoaa in their paper The Dynamics of Residential Sorting and Health: Implications of Climate Change in the US 13
- Théroux-Rancourt et al. used brranching in their paper Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size 14
- M. et al. used rgbif in their paper Creating Maps 15
- Wraith et al. used rgbif in their paper Orchid conservation and research: An analysis of gaps and priorities for globally Red Listed species 16
- Vincent & Bowler used rglobi in their paper Diatoms Are Selective Segregators in Global Ocean Planktonic Communities 17
- Sawa et al. used phylogram in their paper Molecular epidemiology of clinically high‐risk Pseudomonas aeruginosa strains: Practical overview 18
- Yuan et al. used MODISTools in their paper Habitat use, interspecific competition and phylogenetic history shape the evolution of claw and toepad morphology in Lesser Antillean anoles 19
- Gilbertson et al. used spatsoc in their paper Trade‐offs with telemetry‐derived contact networks for infectious disease studies in wildlife 20
- Bachman et al. used taxize and wicket and rgbif in their paper Rapid Least Concern: towards automating Red List assessments 21
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 reported in the forum recently:
- Emmanuel Ọlámíjùwọ́n shared a use case for our pacakge magick: {magick}ally Visualize Historical Google Maps Traffic Data. magick is a package for advanced graphics and image-processing in 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. Checkout our Contributing Guide for why and how to contribute to rOpenSci.
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
- rdpla: now maintained by Alyssa Columbus
- webchem: now maintained by Erik Sapper
- mregions: in process of moving to maintenance by VLIZ
- rWBclimate: now maintained by Sergio Ibarra-Espinosa and Amanda Rehbein
We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.
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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Footnotes
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Cirtwill, A. R., Dalla Riva, G. V., Baker, N. J., Ohlsson, M., Norström, I., Wohlfarth, I., … Stouffer, D. B. (2020). Related plants tend to share pollinators and herbivores, but strength of phylogenetic signal varies among plant families. New Phytologist. https://doi.org/10.1111/nph.16420 ↩
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Léveillé-Bourret, É., Chen, B.-H., Garon-Labrecque, M.-È., Ford, B. A., & Starr, J. R. (2020). RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae). Molecular Phylogenetics and Evolution, 145, 106727. https://doi.org/10.1016/j.ympev.2019.106727 ↩
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Moudrý, V., & Devillers, R. (2020). Quality and usability challenges of global marine biodiversity databases: An example for marine mammal data. Ecological Informatics, 56, 101051. https://doi.org/10.1016/j.ecoinf.2020.101051 ↩
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Deng, H., Wang, Q., Turner, D. P., Sexton, K. E., Burns, S. M., Eikermann, M., … Houle, T. T. (2020). Sentiment analysis of real-world migraine tweets for population research. Cephalalgia Reports, 3, 251581631989886. https://doi.org/10.1177/2515816319898867 ↩
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Shan, S., Soltis, P. S., Soltis, D. E., & Yang, B. (2020). Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems. Applications in Plant Sciences, 8(1). https://doi.org/10.1002/aps3.11314 ↩
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Horne, C. R., Hirst, A. G., & Atkinson, D. (2020). Selection for increased male size predicts variation in sexual size dimorphism among fish species. Proceedings of the Royal Society B: Biological Sciences, 287(1918), 20192640. https://doi.org/10.1098/rspb.2019.2640 ↩
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Akpınar, B. A., Carlson, P. O., Paavilainen, V. O., & Dunn, C. D. (2020). Pathogenicity of human mtDNA variants is revealed by combining a novel phylogenetic analysis with machine learning. https://doi.org/10.1101/2020.01.10.902239 ↩
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Milla, R., Bastida, J. M., Turcotte, M. M., Jones, G., Violle, C., Osborne, C. P., … Byun, C. (2018). Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food. Nature Ecology & Evolution, 2(11), 1808–1817. https://doi.org/10.1038/s41559-018-0690-4 ↩
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Scherer, C., Radchuk, V., Franz, M., Thulke, H., Lange, M., Grimm, V., & Kramer‐Schadt, S. (2020). Moving infections: individual movement decisions drive disease persistence in spatially structured landscapes. Oikos. https://doi.org/10.1111/oik.07002 ↩
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Burns, M. D., & Bloom, D. D. (2020). Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes. Proceedings of the Royal Society B: Biological Sciences, 287(1918), 20192615. https://doi.org/10.1098/rspb.2019.2615 ↩
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Santos, J. C. (2020). Phylogenetic Analyses of Chemokine Receptors from Sequence Retrieval to Phylogenetic Trees. In Immune Mediators in Cancer (pp. 313-343). Humana, New York, NY. https://link.springer.com/protocol/10.1007/978-1-0716-0247-8_27 ↩
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Walczyńska, A., Gudowska, A., & Sobczyk, Ł. (2020). Should I shrink or should I flow? – body size adjustment to thermo-oxygenic niche. https://doi.org/10.1101/2020.01.14.905901 ↩
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Mathes, S. (2019). The Dynamics of Residential Sorting and Health: Implications of Climate Change in the US. https://sophiemathescom.files.wordpress.com/2019/11/job_market_paper_sophie_mathes-1.pdf ↩
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Théroux-Rancourt, G., Roddy, A. B., Earles, J. M., Gilbert, M. E., Zwieniecki, M. A., Boyce, C. K., … Brodersen, C. R. (2020). Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size. https://doi.org/10.1101/2020.01.16.904458 ↩
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Lakicevic M., Povak N., Reynolds K.M. (2020) Creating Maps. In: Introduction to R for Terrestrial Ecology. Springer, Cham https://link.springer.com/chapter/10.1007/978-3-030-27603-4_3 ↩
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Wraith, J., Norman, P., & Pickering, C. (2020). Orchid conservation and research: An analysis of gaps and priorities for globally Red Listed species. Ambio. https://doi.org/10.1007/s13280-019-01306-7 ↩
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Vincent, F., & Bowler, C. (2020). Diatoms Are Selective Segregators in Global Ocean Planktonic Communities. mSystems, 5(1). https://doi.org/10.1128/msystems.00444-19 ↩
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Sawa, T., Momiyama, K., Mihara, T., Kainuma, A., Kinoshita, M., & Moriyama, K. (2020). Molecular epidemiology of clinically high‐risk Pseudomonas aeruginosa strains: Practical overview. Microbiology and Immunology. https://doi.org/10.1111/1348-0421.12776 ↩
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Yuan, M. L., Jung, C., Wake, M. H., & Wang, I. J. (2020). Habitat use, interspecific competition and phylogenetic history shape the evolution of claw and toepad morphology in Lesser Antillean anoles. Biological Journal of the Linnean Society, 129(3), 630–643. https://doi.org/10.1093/biolinnean/blz203 ↩
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Gilbertson, M. L. J., White, L. A., & Craft, M. E. (2020). Trade‐offs with telemetry‐derived contact networks for infectious disease studies in wildlife. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13355 ↩
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Bachman, S., Walker, B., Barrios, S., Copeland, A., & Moat, J. (2020). Rapid Least Concern: towards automating Red List assessments. Biodiversity Data Journal, 8. https://doi.org/10.3897/bdj.8.e47018 ↩