Aug 17, 2020
Software đŠ
CRAN:
GitHub:
New Versions
- A new version (
v0.2.0
) oftaxizedb
is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.1.4
) ofbabette
is on CRAN - control BEAST2 from R. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.4.0
) offinch
is on CRAN - parse Darwin Core files. See the release notes for changes. Checkout the README to get started. - A new version (
v2.1
) ofmauricer
is on CRAN - install BEAST2 packages. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.1.3
) ofbeastier
is on CRAN - Provides a way to call BEAST2 from R. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.3.7
) ofbeautier
is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.2.0
) 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 (
v1.3.3
) ofUCSCXenaTools
is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.1-3
) ofsuppdata
is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started.
Software Review â
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. Weâll 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 weâll ping you when thereâs a submission that fits in your area of expertise.
No new submissions or approved submissions.
Citations
The following 22 works use/cite rOpenSci software:
- Connors et al. used rnaturalearth in their paper Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean 1
- Hesselbarth used NLMR in their paper Analysing and modelling spatial patterns to infer the influence of environmental heterogeneity using point pattern analysis, individual-based simulation modelling and landscape metrics 2
- Geller et al. used hunspell in their paper Sans forgetica is not desirable for learning 3
- BiberâFreudenberger et al. used magick in their paper Bioeconomy futures: Expectation patterns of scientists and practitioners on the sustainability of bioâbased transformation 4
- Siqueira et al. used rfishbase in their paper Trophic innovations fuel reef fish diversification 5
- DâOrazio et al. used nlrx in their paper Sustainable and resilient strategies for touristic cities against COVID-19 6
- Stringham et al. used RSelenium and taxize in their paper A guide to using the Internet to monitor and quantify the wildlife trade 7
- Morselli et al. used hunspell in their paper Sos Venezuela: an analysis of the anti-Maduro protest movements using Twitter 8
- Vogler & SchĂ€fer used textreuse in their paper Growing Influence of University PR on Science News Coverage? A Longitudinal Automated Content Analysis of University Media Releases and Newspaper Coverage in Switzerland, 2003â2017 9
- Szöcs et al. used taxize in their paper webchem: An R Package to Retrieve Chemical Information from the Web 10
- Manning et al. used rdryad in their paper An experimental test of the capacity for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage 11
- Greco & La Rocca used rtweet in their paper The Topics-scape of the Pandemic Crisis: The Italian Sentiment on Political Leaders 12
- Fernåndez-Ruiz & Estrada-Peña used MODIStsp in their paper Could climate trends disrupt the contact rates between Ixodes ricinus (Acari, Ixodidae) and the reservoirs of Borrelia burgdorferi s.l.? 13
- Santana et al. used brranching in their paper Climate, and not fire, drives the phylogenetic clustering of species with hard-coated seeds in Mediterranean Basin communities 14
- Sales et al. used spocc in their paper Climate niche mismatch and the collapse of primate seed dispersal services in the Amazon 15
- BarriosâOâNeill used rtweet in their paper Focus and social contagion of environmental organization advocacy on Twitter 16
- Gaynor et al. used spocc and CoordinateCleaner in their paper Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis 17
- Liu et al. used MODIStsp in their paper Optimal MODIS data processing for accurate multi-year paddy rice area mapping in China 18
- Estrada-Peña et al. used rotl in their paper A community approach to the Neotropical ticks-hosts interactions 19
- Trinka et al. used MODISTools in their paper Multivariate Functional Singular Spectrum Analysis Over Different Dimensional Domains 20
- McKnelly et al. used skimr in their paper Extraction on Paper Activity: An Active Learning Technique to Facilitate Student Understanding of LiquidâLiquid Extraction 21
- Davis used rnaturalearth in their paper Leaf the kids outdoors: approaches and enquiries in quantifying natural environments for health 22
From the Forum
We have a discussion forum (using Discourse) for the rOpenSci community. Itâs a really nice way to have conversations on the internet. From time to time weâll highlight recent discussions of interest.
A new use case was shared in the forum over the past two weeks since our last newsletter:
- Kenneth Tay shared: Basic manipulation of GIF frames with magick; 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.
Weâve had nine 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 RĂŒeger
- 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
- 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
- Alternatively, you can subscribe to this newsletter via our XML feed at https://news.ropensci.org/feed.xml or our JSON feed at https://news.ropensci.org/feed.json
- rOpenSci on Twitter: @ropensci
- 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
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Connors, B., Malick, M. J., Ruggerone, G. T., Rand, P., Adkison, M., Irvine, J. R., ⊠Gorman, K. (2020). Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean. Canadian Journal of Fisheries and Aquatic Sciences, 77(6), 943â949. https://www.nrcresearchpress.com/doi/10.1139/cjfas-2019-0422 ↩
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Hesselbarth, M. H. 2020. Analysing and modelling spatial patterns to infer the influence of environmental heterogeneity using point pattern analysis, individual-based simulation modelling and landscape metrics. Dissertation https://bit.ly/2E0yuAx ↩
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Geller, J., Davis, S. D., & Peterson, D. (2020, May 23). Sans forgetica is not desirable for learning. https://doi.org/10.31234/osf.io/ku5bz ↩
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BiberâFreudenberger, L., Ergeneman, C., Förster, J. J., Dietz, T., & Börner, J. (2020). Bioeconomy futures: Expectation patterns of scientists and practitioners on the sustainability of bioâbased transformation. Sustainable Development. https://doi.org/10.1002/sd.2072 ↩
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Siqueira, A. C., Morais, R. A., Bellwood, D. R., & Cowman, P. F. (2020). Trophic innovations fuel reef fish diversification. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-16498-w ↩
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DâOrazio, M., Bernardini, G., & Quagliarini, E. (2020). Sustainable and resilient strategies for touristic cities against COVID-19: an agent-based approach. arXiv preprint arXiv:2005.12547. https://arxiv.org/pdf/2005.12547.pdf ↩
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Stringham, O., Toomes, A., Kanishka, A. M., Mitchell, L., Heinrich, S., Ross, J. V., & Cassey, P. (2020). A guide to using the Internet to monitor and quantify the wildlife trade. https://ecoevorxiv.org/5yzw9/download?format=pdf ↩
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Morselli, D., Passini, S., & McGarty, C. (2020). Sos Venezuela: an analysis of the anti-Maduro protest movements using Twitter. Social Movement Studies, 1â22. https://doi.org/10.1080/14742837.2020.1770072Â ↩
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Vogler, D., & SchĂ€fer, M. S. (2020). Growing Influence of University PR on Science News Coverage? A Longitudinal Automated Content Analysis of University Media Releases and Newspaper Coverage in Switzerland, 2003â2017. International Journal of Communication, 14, 22. https://ijoc.org/index.php/ijoc/article/download/13498/3113 ↩
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Szöcs, E., Stirling, T., Scott, E. R., ScharmĂŒller, A., & SchĂ€fer, R. B. (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(1), 1-17. https://www.jstatsoft.org/article/view/v093i13/v93i13.pdf ↩
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Manning, F., Curtis, P. J., Walker, I., & Pither, J. (2020, June 2). An experimental test of the capacity for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage. https://doi.org/10.32942/osf.io/h97pw ↩
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Greco, F., & La Rocca, G. (2020). The Topics-scape of the Pandemic Crisis: The Italian Sentiment on Political Leaders. Culture e Studi del Sociale, 5(1, Special), 335-346. http://www.cussoc.it/index.php/journal/article/view/134Â ↩
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FernĂĄndez-Ruiz, N., & Estrada-Peña, A. (2020). Could climate trends disrupt the contact rates between Ixodes ricinus (Acari, Ixodidae) and the reservoirs of Borrelia burgdorferi s.l.? PLOS ONE, 15(5), e0233771. https://doi.org/10.1371/journal.pone.0233771 ↩
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Santana, V. M., Alday, J. G., Adamo, I., Alloza, J. A., & Baeza, M. J. (2020). Climate, and not fire, drives the phylogenetic clustering of species with hard-coated seeds in Mediterranean Basin communities. Perspectives in Plant Ecology, Evolution and Systematics, 45, 125545. https://doi.org/10.1016/j.ppees.2020.125545Â ↩
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Sales, L., Culot, L., & Pires, M. M. (2020). Climate niche mismatch and the collapse of primate seed dispersal services in the Amazon. Biological Conservation, 247, 108628. https://doi.org/10.1016/j.biocon.2020.108628Â ↩
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BarriosâOâNeill, D. (2020). Focus and social contagion of environmental organization advocacy on Twitter. Conservation Biology. https://doi.org/10.1111/cobi.13564Â ↩
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Gaynor, M. L., Fu, C., Gao, L., Lu, L., Soltis, D. E., & Soltis, P. S. (2020). Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis. Journal of Systematics and Evolution. https://doi.org/10.1111/jse.12646Â ↩
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Liu, L., Huang, J., Xiong, Q., Zhang, H., Song, P., Huang, Y., ⊠Wang, X. (2020). Optimal MODIS data processing for accurate multi-year paddy rice area mapping in China. GIScience & Remote Sensing, 57(5), 687â703. https://doi.org/10.1080/15481603.2020.1773012 ↩
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Estrada-Peña, A., Nava, S., Tarragona, E., de la Fuente, J., & Guglielmone, A. A. (2020). A community approach to the Neotropical ticks-hosts interactions. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-66400-3 ↩
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Trinka, J., Haghbin, H., & Maadooliat, M. (2020). Multivariate Functional Singular Spectrum Analysis Over Different Dimensional Domains. arXiv preprint arXiv:2006.03933. https://arxiv.org/pdf/2006.03933Â ↩
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McKnelly, K. J., Howitz, W. J., Lam, S., & Link, R. D. (2020). Extraction on Paper Activity: An Active Learning Technique to Facilitate Student Understanding of LiquidâLiquid Extraction. Journal of Chemical Education, 97(7), 1960â1965. https://doi.org/10.1021/acs.jchemed.9b00975Â ↩
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Davis, Z. (2020). Leaf the kids outdoors: approaches and enquiries in quantifying natural environments for health (Doctoral dissertation, University of British Columbia). https://open.library.ubc.ca/collections/ubctheses/24/items/1.0391841Â ↩