2020-06-22

Software 📦

CRAN: GitHub:

New Versions

A new version (v2.4.5) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the docs to get started.
A new version (v1.1.0) of bold is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the docs to get started.
A new version (v0.1.3) of outsider.base is on CRAN - base package for outsider. See the release notes for changes. Checkout the docs to get started.
A new version (v2.1.1) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started.
A new version (v1.0.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the docs to get started.
A new version (v0.6.0) of brranching is on CRAN - Fetch Phylogenies from Many Sources. See the release notes for changes. Checkout the docs to get started.
A new version (v0.4.0) of originr is on CRAN - Fetch species origin data from the web. See the release notes for changes. Checkout the docs to get started.
A new version (v0.2.3.0) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started.
A new version (v0.9.97) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.
A new version (v1.1.2) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started.
A new version (v1.0.0) of rbison is on CRAN - interface to the USGS BISON API. See the release notes for changes. Checkout the docs to get started.

Software Review ✔

Software review is now accepting submissions again.

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.

The following package was recently submitted:

tidytags > Simple Collection and Powerful Analysis of Twitter Data
- Author: Bret Willet
- Issue: ropensci/software-review#382
- Reviewers: not yet assigned

On the blog

It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, June 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)

Use Cases

The following 27 works use/cite rOpenSci software:

Wesener et al. used nlrx in their paper Stress priming affects fungal competition – evidence from a combined experimental and modeling study ¹
Deribe et al. used opencage in their paper Predicting the Environmental Suitability and Population at Risk of Podoconiosis in Africa ²
Parravicini et al. used rfishbase in their paper Global gut content data synthesis and phylogeny delineate reef fish trophic guilds ³
Vantas et al. used hydroscoper in their paper Estimating Current and Future Rainfall Erosivity in Greece Using Regional Climate Models and Spatial Quantile Regression Forests ⁴
Ashby used roadoi and rromeo in their paper Three quarters of new criminological knowledge is hidden from policy makers ⁵
Yu used treeio in their paper Using ggtree to Visualize Data on Tree‐Like Structures ⁶
Lequime et al. used treeio in their paper nosoi: a stochastic agent-based transmission chain simulation framework in R ⁷
Wei et al. used rotl in their paper Pollinator niche partitioning and asymmetric facilitation contribute to the maintenance of diversity ⁸
Fontanelli & Mansilla used rtweet in their paper Modeling the Popularity of Twitter Hashtags with Master Equations ⁹
Young et al. used taxize and rgbif and rbison in their paper A modeling workflow that balances automation and human intervention to inform invasive plant management decisions at multiple spatial scales ¹⁰
Allen & Kim used rotl in their paper A permutation test and spatial cross-validation approach to assess models of interspecific competition between trees ¹¹
Borgoni et al. used osmdata in their paper Assessing the Risk of Car Crashes in Road Networks ¹²
Dadi used skimr in their paper Modeling malaria cases associated with environmental risk factors in Ethiopia using geographically weighted regression ¹³
Pruchnik used hunspell in their paper Identification of Trends in the Polish Media on the Example of the Quarterly Studia Medioznawcze The Use of Big Data Tools ¹⁴
Pavlovich et al. used rentrez in their paper Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells ¹⁵
Hagen et al. used rtweet in their paper Rise of the Machines? Examining the Influence of Social Bots on a Political Discussion Network ¹⁶
Chakraborty used MODISTools in their paper Multi-scale assessment of drought-induced forest dieback ¹⁷
Salgado & Oancea used RSelenium in their paper On new data sources for the production of official statistics ¹⁸
Jézéquel et al. used rfishbase in their paper A database of freshwater fish species of the Amazon Basin ¹⁹
Chapman et al. used rgbif in their paper Developing Standards for Improved Data Quality and for Selecting Fit for Use Biodiversity Data ²⁰
Hamilton & Lahne used hunspell in their paper Fast and automated sensory analysis: Using natural language processing for descriptive lexicon development ²¹
Ranghetti et al. used geojsonio in their paper sen2r”: An R toolbox for automatically downloading and preprocessing Sentinel-2 satellite data ²²
Moran et al. used rotl in their paper Poor condition promotes high-risk behaviours but context-dependency is key: A systematic review and meta-analysis ²³
Lindner et al. used rotl in their paper Expression and Localization of Kcne2 in the Vertebrate Retina ²⁴
Wang et al. used iheatmapr in their paper Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model ²⁵
Hoffman et al. used ijtiff in their paper Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid ²⁶
Bastide et al. used treeio in their paper Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees ²⁷

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.

Many new use cases were shared in the forum over the past month since our last newsletter:

Iván Mauricio Cely Toro shared: Create a time-lapse video using av package; it leveraged the av package, an rOpenSci package maintained by Jeroen Ooms
André Ourednik shared: Scrape an image from DeepZoom with R and magick, recomposing a single image from multiple tiles; it leveraged the magick package, an rOpenSci package maintained by Jeroen Ooms
Jay Timm shared: US lawmakers on Twitter during a pandemic: some corpus linguistics methods; it leveraged the rtweet package, an rOpenSci package maintained by Michael Kearney
Dave Parr shared: Testing an API wrapper with webmockr and vcr; it leveraged the webmockr and vcr rOpenSci packages

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 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 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
rinat: now maintained by Stéphane Guillou

We’ve got one package in need of a new maintainer:

rflybase: The current maintainer is looking for a new maintainer. Email Scott if you’re interested.

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

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Footnotes

Wesener, F., Szymczak, A., Rillig, M. C., & Tietjen, B. (2020). Stress priming affects fungal competition – evidence from a combined experimental and modeling study. https://doi.org/10.1101/2020.03.04.976357 ↩
Deribe, K., Simpson, H., Pullan, R. L., Bosco, M. J., Wanji, S., Weaver, N. D., … Cano, J. (2020). Predicting the Environmental Suitability and Population at Risk of Podoconiosis in Africa. https://doi.org/10.1101/2020.03.04.977827 ↩
Parravicini, V., Casey, J. M., Schiettekatte, N. M. D., Brandl, S. J., Pozas-Schacre, C., Carlot, J., … Vii, J. (2020). Global gut content data synthesis and phylogeny delineate reef fish trophic guilds. https://doi.org/10.1101/2020.03.04.977116 ↩
Vantas, K., Sidiropoulos, E., & Loukas, A. (2020). Estimating Current and Future Rainfall Erosivity in Greece Using Regional Climate Models and Spatial Quantile Regression Forests. Water, 12(3), 687. https://doi.org/10.3390/w12030687 ↩
Ashby, M. P. J. (2020, March 6). Three quarters of new criminological knowledge is hidden from policy makers. https://doi.org/10.31235/osf.io/wnq7h ↩
Yu, G. (2020). Using ggtree to Visualize Data on Tree‐Like Structures. Current Protocols in Bioinformatics, 69(1). https://doi.org/10.1002/cpbi.96 ↩
Lequime, S., Bastide, P., Dellicour, S., Lemey, P., & Baele, G. (2020). nosoi: a stochastic agent-based transmission chain simulation framework in R. https://doi.org/10.1101/2020.03.03.973107 ↩
Wei, N., Kaczorowski, R. L., Arceo-Gómez, G., O’Neill, E. M., Hayes, R. A., & Ashman, T.-L. (2020). Pollinator niche partitioning and asymmetric facilitation contribute to the maintenance of diversity. https://doi.org/10.1101/2020.03.02.974022 ↩
Fontanelli, O., & Mansilla, R. (2020). Modeling the Popularity of Twitter Hashtags with Master Equations. arXiv preprint, https://arxiv.org/pdf/2003.02672.pdf ↩
Young, N. E., Jarnevich, C. S., Sofaer, H. R., Pearse, I., Sullivan, J., Engelstad, P., & Stohlgren, T. J. (2020). A modeling workflow that balances automation and human intervention to inform invasive plant management decisions at multiple spatial scales. PLOS ONE, 15(3), e0229253. https://doi.org/10.1371/journal.pone.0229253 ↩
Allen, D., & Kim, A. Y. (2020). A permutation test and spatial cross-validation approach to assess models of interspecific competition between trees. PLOS ONE, 15(3), e0229930. https://doi.org/10.1371/journal.pone.0229930 ↩
Borgoni, R., Gilardi, A., & Zappa, D. (2020). Assessing the Risk of Car Crashes in Road Networks. Social Indicators Research. https://doi.org/10.1007/s11205-020-02295-x ↩
Dadi, B. B. (2020). Modeling malaria cases associated with environmental risk factors in Ethiopia using geographically weighted regression (Doctoral dissertation). http://repositori.uji.es/xmlui/bitstream/handle/10234/187004/TFM_Berhanu.pdf?sequence=1&isAllowed=y ↩
Pruchnik, P. (2020). Identification of Trends in the Polish Media on the Example of the Quarterly Studia Medioznawcze The Use of Big Data Tools. Media Studies, 80(1). http://yadda.icm.edu.pl/yadda/element/bwmeta1.element.desklight-e79ed2c7-fd7d-4a91-8895-c322743c8f48/c/04_Pruchnik_EN.pdf ↩
Pavlovich, S. S., Darling, T., Hume, A. J., Davey, R. A., Feng, F., Mühlberger, E., & Kepler, T. B. (2020). Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells. Frontiers in Immunology, 11. https://doi.org/10.3389/fimmu.2020.00435 ↩
Hagen, L., Neely, S., Keller, T. E., Scharf, R., & Vasquez, F. E. (2020). Rise of the Machines? Examining the Influence of Social Bots on a Political Discussion Network. Social Science Computer Review, 089443932090819. https://doi.org/10.1177/0894439320908190 ↩
Chakraborty, T. (2020). Multi-scale assessment of drought-induced forest dieback (Doctoral dissertation). https://run.unl.pt/bitstream/10362/94403/1/TGEO0243.pdf ↩
Salgado, D., & Oancea, B. (2020). On new data sources for the production of official statistics. arXiv preprint https://arxiv.org/pdf/2003.06797.pdf ↩
Jézéquel, C., Tedesco, P. A., Bigorne, R., Maldonado-Ocampo, J. A., Ortega, H., Hidalgo, M., … Oberdorff, T. (2020). A database of freshwater fish species of the Amazon Basin. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0436-4 ↩
Chapman, A., Belbin, L., Zermoglio, P., Wieczorek, J., Morris, P., Nicholls, M., … Schigel, D. (2020). Developing Standards for Improved Data Quality and for Selecting Fit for Use Biodiversity Data. Biodiversity Information Science and Standards, 4. https://doi.org/10.3897/biss.4.50889 ↩
Hamilton, L. M., & Lahne, J. (2020). Fast and automated sensory analysis: Using natural language processing for descriptive lexicon development. Food Quality and Preference, 83, 103926. https://doi.org/10.1016/j.foodqual.2020.103926 ↩
Ranghetti, L., Boschetti, M., Nutini, F., & Busetto, L. (2020). “sen2r”: An R toolbox for automatically downloading and preprocessing Sentinel-2 satellite data. Computers & Geosciences, 139, 104473. https://doi.org/10.1016/j.cageo.2020.104473 ↩
Moran, N. P., Sánchez-Tójar, A., Schielzeth, H., & Reinhold, K. (2020). Poor condition promotes high-risk behaviours but context-dependency is key: A systematic review and meta-analysis. Ecorxiv preprint. https://ecoevorxiv.org/xsehd/ ↩
Lindner, M., Gilhooley, M. J., Palumaa, T., Morton, A. J., Hughes, S., & Hankins, M. W. (2020). Expression and Localization of Kcne2 in the Vertebrate Retina. Investigative Opthalmology & Visual Science, 61(3), 33. https://doi.org/10.1167/iovs.61.3.33 ↩
Wang, Y., Zhang, X., Song, Q., Hou, Y., Liu, J., Sun, Y., & Wang, P. (2020). Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model. Alzheimer’s Research & Therapy, 12(1). https://doi.org/10.1186/s13195-020-00598-2 ↩
Hoffman, M. M., Zylla, J. S., Bhattacharya, S., Calar, K., Hartman, T. W., Bhardwaj, R. D., … Messerli, S. M. (2020). Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid. Cancers, 12(3), 756. https://doi.org/10.3390/cancers12030756 ↩
Bastide, P., Ho, L. S. T., Baele, G., Lemey, P., & Suchard, M. A. (2020). Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees. arXiv preprint arXiv:2003.10336. https://arxiv.org/pdf/2003.10336 ↩