2020-06-08

rOpenSci HQ

rOpenSci, together with many of our community members, put together a guide to help researchers find open data available in R: When Field or Lab Work is not an Option - Leveraging Open Data Resources for Remote Research. The blog post has information on a few topical areas, as well as a table of rOpenSci packages for access to research data.

Software 📦

CRAN: GitHub:

New Versions

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 (v1.0.4) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the docs to get started.
A new version (v0.3.9) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.
A new version (v7.12.2) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.
A new version (v1.3.8) of skynet is on CRAN - Bureau of Transport Statistics Data client. See the release notes for changes. Checkout the docs to get started.
A new version (v0.4) of europepmc is on CRAN - Interface to the Europe PubMed Central RESTful web service. See the release notes for changes. Checkout the docs to get started.
A new version (v0.7.4) 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 (v2.3) 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 (v1.0.0) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started.
A new version (v2.2) of jsonld is on CRAN - JSON for linking data. See the release notes for changes. Checkout the README to get started.
A new version (v0.9.1) of hddtools is on CRAN - Hydrological Data Discovery Tools. See the release notes for changes. Checkout the docs to get started.
A new version (v2.3.1) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started.
A new version (v3.1.3) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started.
A new version (v0.9.96) 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 (v0.3.0) of geoops is on CRAN - GeoJSON topology calculations and operations. See the release notes for changes. Checkout the docs to get started.
A new version (v1.4.2) of xslt is on CRAN - extensible style-sheet language transformations. See the release notes for changes. Checkout the README to get started.
A new version (v1.0.0) of natserv is on CRAN - NatureServe R Interface. See the release notes for changes. Checkout the docs to get started.
A new version (v0.1.5) of textreuse is on CRAN - detect text reuse and document similarity. See the release notes for changes. Checkout the docs to get started.
A new version (v0.2.4) of tidync is on CRAN - a tidy approach to NetCDF data exploration and extraction. See the release notes for changes. Checkout the docs to get started.
A new version (v2.0-15) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. 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 two packages were recently submitted:

medrxivr > Access MedRxiv Preprint Data
- Author: Luke McGuinness
- Issue: ropensci/software-review#380
- Reviewers: not yet assigned
coder > Deterministic Categorization of Items Based on External Code Data
- Author: Erik Bülow
- Issue: ropensci/software-review#381
- Reviewers: not yet assigned

On the blog

Technical notes

Jeroen Ooms wrote about a new version of the rsvg package: Superior svg graphics rendering in R, and why it matters.

Use Cases

The following 26 works use/cite rOpenSci software:

Perez‐Lamarque et al. used rotl in their paper Cheating in arbuscular mycorrhizal mutualism: a network and phylogenetic analysis of mycoheterotrophy ¹
Larson et al. used brranching in their paper Ecological strategies begin at germination: Traits, plasticity and survival in the first 4 days of plant life ²
Rodrigues & Boscolo used taxize in their paper Do bipartite binary antagonistic and mutualistic networks have different responses to the taxonomic resolution of nodes? ³
Manel et al. used rfishbase in their paper Global determinants of freshwater and marine fish genetic diversity ⁴
Thompson used taxize and rentrez in their paper Experimental hybridization studies suggest that pleiotropic alleles commonly underlie adaptive divergence between natural populations ⁵
Gent et al. used taxize in their paper Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations ⁶
Bagheri used biomartr in their paper Domain-specific language and infrastructure for genomics ⁷
Heisel used rotl in their paper Ecological, Genomic, and Social Factors Impacting Wildlife Conservation ⁸
Hannah et al. used rgbif in their paper 30% land conservation and climate action reduces tropical extinction risk by more than 50% ⁹
Ryt-Hansen et al. used treeio in their paper Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses ¹⁰
Armitage & Jones used CoordinateCleaner in their paper Barriers to coexistence limit the poleward range of a globally-distributed plant ¹¹
M. et al. used rredlist in their paper Threatened Flora of Jammu and Kashmir State ¹²
Kaczvinsky & Hardy used taxize in their paper Do major host shifts spark diversification in butterflies? ¹³
Zizka et al. used taxize and rgbif and CoordinateCleaner in their paper Transitions between biomes are common and directional in Bombacoideae (Malvaceae) ¹⁴
Jung et al. used rgbif in their paper Comparative drought resistance of temperate grassland species: testing performance trade-offs and the relation to distribution ¹⁵
Howard & Cellinese used rgbif in their paper Tunicate bulb size variation in monocots explained by temperature and phenology ¹⁶
Du et al. used rgbif in their paper High correlation of species diversity patterns between specialist herbivorous insects and their specific hosts ¹⁷
Long & Turner used skimr in their paper Applied R in the Classroom ¹⁸
Reyes & Lira-Noriega used spocc in their paper Current and future global potential distribution of the fruit fly Drosophila suzukii (Diptera: Drosophilidae) ¹⁹
Lara-Lizardi et al. used osmdata in their paper Shark movements in the Revillagigedo Archipelago and connectivity with the Eastern Tropical Pacific ²⁰
Cichosz used hunspell in their paper Unsupervised modeling anomaly detection in discussion forums posts using global vectors for text representation ²¹
Pietzke & Vazquez used writexl in their paper Metabolite AutoPlotter–an application to automatically process and visualise metabolite data in the web-browser ²²
Kusumoto et al. used rgbif in their paper Global distribution of coral diversity: Biodiversity knowledge gradients related to spatial resolution ²³
Potter used rfishbase in their paper Machine learning for resource economics; a review of modern computational statistics with empirical applications in fisheries management ²⁴
Marshall et al. used rotl in their paper Developmental cost theory predicts thermal environment and vulnerability to global warming ²⁵
Amiri Roudbar et al. used rsnps in their paper Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls ²⁶

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:

Isabella Velásquez shared: Package for downloading shapefiles using piggyback; it leveraged piggyback, an rOpenSci package maintained by Carl Boettiger
Adam Sparks shared: bomrang with a third party package, stationaRy, to get hourly weather data and clifro to plot wind roses; it leveraged bomrang and clifro, rOpenSci packages maintained by Adam Sparks and Blake Seers, respectively
Edwin Thoen shared: Using {drake} for machine learning; it leveraged drake, an rOpenSci package maintained by Will Landau
Sam Albers shared: Detecting the Effects of Sustained Glacier Wastage on Streamflow in Variably Glacierized Catchments; the use case is from a research article (Detecting the Effects of Sustained Glacier Wastage on Streamflow in Variably Glacierized Catchments) that uses tidyhydat

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 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

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

Perez‐Lamarque, B., Selosse, M., Öpik, M., Morlon, H., & Martos, F. (2020). Cheating in arbuscular mycorrhizal mutualism: a network and phylogenetic analysis of mycoheterotrophy. New Phytologist. https://doi.org/10.1111/nph.16474 ↩
Larson, J. E., Anacker, B. L., Wanous, S., & Funk, J. L. (2020). Ecological strategies begin at germination: Traits, plasticity and survival in the first 4 days of plant life. Functional Ecology. https://doi.org/10.1111/1365-2435.13543 ↩
Rodrigues, B. N., & Boscolo, D. (2020). Do bipartite binary antagonistic and mutualistic networks have different responses to the taxonomic resolution of nodes? Ecological Entomology. https://doi.org/10.1111/een.12844 ↩
Manel, S., Guerin, P.-E., Mouillot, D., Blanchet, S., Velez, L., Albouy, C., & Pellissier, L. (2020). Global determinants of freshwater and marine fish genetic diversity. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14409-7 ↩
Thompson, K. A. (2020). Experimental hybridization studies suggest that pleiotropic alleles commonly underlie adaptive divergence between natural populations. The American Naturalist. https://doi.org/10.1086/708722 ↩
Gent, D. H., Claassen, B. J., Gadoury, D. M., Grünwald, N. J., Knaus, B. J., Radišek, S., … Wolfenbarger, S. N. (2020). Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations. Phytopathology, PHYTO–12–19–044. https://doi.org/10.1094/phyto-12-19-0448-r ↩
Bagheri, H. 2019. Domain-specific language and infrastructure for genomics. Graduate Theses and Dissertations. 17641. https://lib.dr.iastate.edu/etd/17641 ↩
Heisel, S. E. (2019). Ecological, Genomic, and Social Factors Impacting Wildlife Conservation (Doctoral dissertation, University of Georgia). https://search.proquest.com/docview/2357432037 ↩
Hannah, L., Roehrdanz, P. R., Marquet, P. A., Enquist, B. J., Midgley, G., Foden, W., … Svenning, J. (2020). 30% land conservation and climate action reduces tropical extinction risk by more than 50%. Ecography. https://doi.org/10.1111/ecog.05166 ↩
Ryt-Hansen, P., Pedersen, A. G., Larsen, I., Kristensen, C. S., Krog, J. S., Wacheck, S., & Larsen, L. E. (2020). Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses. Viruses, 12(2), 248. https://doi.org/10.3390/v12020248 ↩
Armitage, D. W., & Jones, S. E. (2020). Barriers to coexistence limit the poleward range of a globally-distributed plant. https://doi.org/10.1101/2020.02.24.946574 ↩
Hamid M., Khuroo A.A., Ahmad R., Rasheed S., Malik A.H., Dar G.H. (2020) Threatened Flora of Jammu and Kashmir State. In:Dar G., Khuroo A. (eds) Biodiversity of the Himalaya:Jammu and Kashmir State. Topics in Biodiversity and Conservation, vol 18. Springer, Singapore https://doi.org/10.1007/978-981-32-9174-4_37 ↩
Kaczvinsky, C., & Hardy, N. B. (2020). Do major host shifts spark diversification in butterflies? Ecology and Evolution, 10(8), 3636–3646. https://doi.org/10.1002/ece3.6116 ↩
Zizka, A., Carvalho‐Sobrinho, J. G., Pennington, R. T., Queiroz, L. P., Alcantara, S., Baum, D. A., … Antonelli, A. (2020). Transitions between biomes are common and directional in Bombacoideae (Malvaceae). Journal of Biogeography. https://doi.org/10.1111/jbi.13815 ↩
Jung, E.-Y., Gaviria, J., Sun, S., & Engelbrecht, B. M. J. (2020). Comparative drought resistance of temperate grassland species: testing performance trade-offs and the relation to distribution. Oecologia, 192(4), 1023–1036. https://doi.org/10.1007/s00442-020-04625-9 ↩
Howard, C. C., & Cellinese, N. (2020). Tunicate bulb size variation in monocots explained by temperature and phenology. Ecology and Evolution, 10(5), 2299–2309. https://doi.org/10.1002/ece3.5996 ↩
Du, C., Chen, J., Jiang, L., & Qiao, G. (2020). High correlation of species diversity patterns between specialist herbivorous insects and their specific hosts. Journal of Biogeography. https://doi.org/10.1111/jbi.13816 ↩
Long, J. D., & Turner, D. (2020). Applied R in the Classroom. Australian Economic Review, 53(1), 139–157. https://doi.org/10.1111/1467-8462.12362 ↩
Reyes, J. A., & Lira-Noriega, A. (2020). Current and future global potential distribution of the fruit fly Drosophila suzukii (Diptera: Drosophilidae). The Canadian Entomologist, 1–13. https://doi.org/10.4039/tce.2020.3 ↩
Lara-Lizardi, F., Hoyos-Padilla, M., Hearn, A., Klimley, A. P., Galván-Magaña, F., Arauz, R., … Ketchum, J. T. (2020). Shark movements in the Revillagigedo Archipelago and connectivity with the Eastern Tropical Pacific. https://doi.org/10.1101/2020.03.02.972844 ↩
Cichosz, P. (2020). Unsupervised modeling anomaly detection in discussion forums posts using global vectors for text representation. Natural Language Engineering, 1–28. https://doi.org/10.1017/s1351324920000066 ↩
Pietzke, M., Vazquez, A. 2020. Metabolite AutoPlotter–an application to automatically process and visualise metabolite data in the web-browser. https://assets.researchsquare.com/files/6b8d169e-e621-4ebd-8c6e-ff607a788ebe/v1/Manuscript.pdf ↩
Kusumoto, B., Costello, M. J., Kubota, Y., Shiono, T., Wei, C., Yasuhara, M., & Chao, A. (2020). Global distribution of coral diversity: Biodiversity knowledge gradients related to spatial resolution. Ecological Research, 35(2), 315–326. https://doi.org/10.1111/1440-1703.12096 ↩
Potter, R. J. (2019). Machine learning for resource economics; a review of modern computational statistics with empirical applications in fisheries management (Master’s thesis). https://openaccess.nhh.no/nhh-xmlui/bitstream/handle/11250/2644607/masterthesis.pdf?sequence=1 ↩
Marshall, D. J., Pettersen, A. K., Bode, M., & White, C. R. (2020). Developmental cost theory predicts thermal environment and vulnerability to global warming. Nature Ecology & Evolution, 4(3), 406–411. https://doi.org/10.1038/s41559-020-1114-9 ↩
Amiri Roudbar, M., Mohammadabadi, M. R., Ayatollahi Mehrgardi, A., Abdollahi-Arpanahi, R., Momen, M., Morota, G., … Rosa, G. J. M. (2020). Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls. Heredity, 124(5), 658–674. https://doi.org/10.1038/s41437-020-0301-4 ↩