Sep 28, 2020
Software đŠ
CRAN:
GitHub:
New Packages
- The first version (
v0.0.3
) ofmedrxivr
is on CRAN - access and search MedRxiv and BioRxiv preprint data. Checkout the docs to get started. This package recently went through rOpenSci software review.
New Versions
- A new version (
v0.7.1
) ofbomrang
is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.5.1
) ofemld
is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.2.0
) ofopencv
is on CRAN - bindings to the OpenCV computer vision library. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.0.0
) ofnasapower
is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.2.0
) ofgutenbergr
is on CRAN - Download and process public domain works from Project Gutenberg. See the release notes for changes. Checkout the vignette to get started. - A new version (
v2.1.2
) ofGSODR
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 (
v2.0.3
) ofMODIStsp
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 (
v0.0.6
) ofarkdb
is on CRAN - archive and unarchive databases as flat text files. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.0.1
) ofrppo
is on CRAN - access the Global Plant Phenology Data portal. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.9.98
) oftaxize
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
) 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 (
v3.0.0
) ofrdataretriever
is on CRAN - R interface to the Data Retriever. See the release notes for changes. Checkout the docs 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.
The following two packages were recently approved:
- treedata.table > A Wrapper For data.table For Fast Manipulation Of Phylogenetic Trees Matched To Data
- Author: Josef Uyeda
- Issue: ropensci/software-review#367
- Reviewers:
- medrxivr > Access and Search MedRxiv and BioRxiv Preprint Data
- Author: Luke McGuinness
- Issue: ropensci/software-review#380
- Reviewers:
On the blog
Software Review:
April Wright, Christian RomĂĄn-Palacios, and Josef Uyeda wrote about their recently rOpenSci reviewed package treedata.table: The treedata.table Package. They discuss how the package came about, why you should use the packag and a bit of high level talk on what can be done with the package.
Citations
The following 18 works use/cite rOpenSci software:
- Ehlers et al. used writexl in their paper Natural variations in brain morphology do not account for inter-individual differences in defensive responding during fear acquisition training and extinction 1
- M. et al. used writexl in their paper Method to Comparison of Cities 2
- Westfall used pdftools in their paper R Anywhere 3
- Arranz et al. used bold and taxize in their paper MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding 4
- Leonard used rentrez in their paper Engineering the gut microbiome of honey bees 5
- LeBeau & Aloe used bib2df in their paper Evolution of Statistical Software and Quantitative Methods 6
- Wieringen & Binder used fingertipsR in their paper Transfer learning of regression models from a sequence of datasets by penalized estimation 7
- Hock et al. used rgbif in their paper Native distribution characteristics rather than functional traits explain preadaptation of invasive species to highâUVâB environments 8
- Cagua used taxize in their paper Plantâpollinator communities: environmental gradients, trade-offs, and controllability 9
- Ălvarez-Noriega et al. used rotl in their paper Global biogeography of marine dispersal potential 10
- Anton used MODIStsp in their paper The Demography and Comparative Ethology of Top Predators in a Multi-Carnivore System 11
- Berkel & Cacan used pdftools and magick in their paper GAB2 and GAB3 are expressed in a tumor stage-, grade- and histotype-dependent manner and are associated with shorter progression-free survival in ovarian cancer 12
- Mallet used bomrang in their paper Meteorological normalisation of PM10 using machine learning reveals distinct increases of nearby source emissions in the Australian mining town of Moranbah 13
- Presa-Reyes et al. used dbhydroR in their paper A Water Quality Research Platform for the Near-real-time Buoy Sensor Data 14
- Dogucu & Ăetinkaya-Rundel used rtweet and robotstxt in their paper Web Scraping in the Statistics and Data Science Curriculum: Challenges and Opportunities 15
- Scott et al. used pdftools in their paper NEPA and National Trends in Federal Infrastructure Siting in the United States 16
- Waldock et al. used CoordinateCleaner in their paper Insect occurrence in agricultural landâuses depends on realized niche and geographic range properties 17
- Saleh et al. used rtweet in their paper Understanding public perception of coronavirus disease 2019 (COVID-19) social distancing on Twitter 18
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.
Four new use cases were shared in the forum over the past two weeks since our last newsletter:
- Matt Dray shared: A Twitter bot with rtweet, Mapbox and GitHub Actions; the use case employed the rtweet package, an rOpenSci package maintained by Michael Kearney
- Emilio Bruna shared two use cases employing the refsplitr package, an rOpenSci package maintained by Emilio:
- Markus Skyttner shared: Kontarion - a stack extending rocker/ml-verse for Bibliometric analytics; the use case employed many rOpenSci packages: oai, rentrez, fulltext, europepmc, refsplitr, rcrossref, citecorp, and roadoi
Related News
- One of our software review editors, Anna Krystalli, was featured in the podcast RSE Stories, in an episoded titled R for Reproducibility.
- The latest epside of the Changelog Podcast was How open source saved htop. It may be of interest to readers of this newsletter as a vignette of how a project transitioned maintainers. The original htop repository, and the new one.
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 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 RĂŒeger
- 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
Weâve got one package in need of a new maintainer:
- monkeylearn: The current maintainer is looking for a new maintainer. Comment on this thread if youâre 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
-
Ehlers, M., Nold, J., Kuhn, M., Klingelhöfer-Jens, M., & Lonsdorf, T. (2020). Natural variations in brain morphology do not account for inter-individual differences in defensive responding during fear acquisition training and extinction. https://psyarxiv.com/q2kyf/download?format=pdf ↩
-
Jerabek M., Kubat J., Fabera V. (2020) Method to Comparison of Cities. In: Knapcikova L., Balog M., PerakoviÄ D., PeriĆĄa M. (eds) New Approaches in Management of Smart Manufacturing Systems. EAI/Springer Innovations in Communication and Computing. Springer, Cham. https://doi.org/10.1007/978-3-030-40176-4_7Â ↩
-
Westfall J. (2020) R Anywhere. In: Practical R 4. Apress, Berkeley, CA. https://doi.org/10.1007/978-1-4842-5946-7_8Â ↩
-
Arranz, V., Pearman, W. S., Aguirre, J. D., & Liggins, L. (2020). MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0549-9Â ↩
-
Leonard, S. P. (2020). Engineering the gut microbiome of honey bees (Doctoral dissertation). https://bit.ly/3cFfZhTÂ ↩
-
LeBeau, B. C., & Aloe, A. M. (2020). Evolution of Statistical Software and Quantitative Methods. https://doi.org/10.17077/pp.005273Â ↩
-
van Wieringen, W. N., & Binder, H. (2020). Transfer learning of regression models from a sequence of datasets by penalized estimation. arXiv preprint arXiv:2007.02117. https://arxiv.org/pdf/2007.02117Â ↩
-
Hock, M., Hofmann, R., Essl, F., PyĆĄek, P., Bruelheide, H., & Erfmeier, A. (2020). Native distribution characteristics rather than functional traits explain preadaptation of invasive species to highâUVâB environments. Diversity and Distributions. https://doi.org/10.1111/ddi.13113Â ↩
-
Cagua, F. (2020). Plantâpollinator communities: environmental gradients, trade-offs, and controllability. PhD Thesis. https://bit.ly/3kZDHrZÂ ↩
-
Ălvarez-Noriega, M., Burgess, S. C., Byers, J. E., Pringle, J. M., Wares, J. P., & Marshall, D. J. (2020). Global biogeography of marine dispersal potential. Nature Ecology & Evolution, 4(9), 1196â1203. https://doi.org/10.1038/s41559-020-1238-y ↩
-
Anton, C. (2020). The Demography and Comparative Ethology of Top Predators in a Multi-Carnivore System (Doctoral dissertation, UC Santa Cruz). https://escholarship.org/content/qt3xd9379b/qt3xd9379b.pdf ↩
-
Berkel, C., & Cacan, E. (2020). GAB2 and GAB3 are expressed in a tumor stage-, grade- and histotype-dependent manner and are associated with shorter progression-free survival in ovarian cancer. Journal of Cell Communication and Signaling. https://doi.org/10.1007/s12079-020-00582-3Â ↩
-
Mallet, M. D. (2020). Meteorological normalisation of PM10 using machine learning reveals distinct increases of nearby source emissions in the Australian mining town of Moranbah. Atmospheric Pollution Research. https://doi.org/10.1016/j.apr.2020.08.001Â ↩
-
Presa-Reyes, M., Bogosian, B., Schonhoff, B., Jerauld, C., Moreyra, C., Gardinali, P., & Chen, S. C. A Water Quality Research Platform for the Near-real-time Buoy Sensor Data. https://users.cs.fiu.edu/~chens/PDF/IRI20_Buoy.pdf ↩
-
Dogucu, M., & Ăetinkaya-Rundel, M. (2020). Web Scraping in the Statistics and Data Science Curriculum: Challenges and Opportunities. Journal of Statistics Education, 1â11. https://doi.org/10.1080/10691898.2020.1787116Â ↩
-
Scott, T. A., Ulibarri, N., & Perez Figueroa, O. (2020). NEPA and National Trends in Federal Infrastructure Siting in the United States. Review of Policy Research. https://doi.org/10.1111/ropr.12399Â ↩
-
Waldock, C. A., De Palma, A., Borges, P. A. V., & Purvis, A. (2020). Insect occurrence in agricultural landâuses depends on realized niche and geographic range properties. Ecography. https://doi.org/10.1111/ecog.05162Â ↩
-
Saleh, S. N., Lehmann, C. U., McDonald, S. A., Basit, M. A., & Medford, R. J. (2020). Understanding public perception of coronavirus disease 2019 (COVID-19) social distancing on Twitter. Infection Control & Hospital Epidemiology, 1â8. https://doi.org/10.1017/ice.2020.406Â ↩