2020-10-12

Software 📦

CRAN: GitHub:

New Packages

The first version (v0.1.0) of treedata.table is on CRAN - manipulation of matched phylogenies and data using data.table. Checkout the docs to get started.

New Versions

A new version (v0.1.3) of dittodb is on CRAN - a test environment for database requests. See the release notes for changes. Checkout the docs to get started.
A new version (v7.12.6) 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 (v2.2.1) of ijtiff 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 (v3.0.0) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started.
A new version (v0.5.1) of tidyhydat is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the vignettes to get started.
A new version (v0.2.0) of parzer is on CRAN - parse messy geographic coordinates. See the release notes for changes. Checkout the docs to get started.
A new version (v0.3.0) of pleiades is on CRAN - interface to the Pleiades archeological database. See the release notes for changes. Checkout the docs to get started.
A new version (v1.4.0) 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 (v0.2.0) of taxlist is on CRAN - handling taxonomic lists. See the release notes for changes. Checkout the docs to get started.
A new version (v1.2.0) 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 (v1.1-4) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started.
A new version (v1.1.4) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started.
A new version (v0.1.2) of binman is on CRAN - a binary download manager. See the release notes for changes. Checkout the vignette to get started.
A new version (v1.1.0) of rcrossref is on CRAN - R client for the Crossref API. See the release notes for changes. Checkout the docs to get started.
A new version (v1.1.0) 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 (v1.3.0) of stats19 is on CRAN - Work with Open Road Traffic Casualty Data from Great Britain. See the release notes for changes. Checkout the docs to get started.
A new version (v1.3.4) of UCSCXenaTools 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 (v0.7.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started.
A new version (v0.5.1) of av is on CRAN - working with audio and video. See the release notes for changes. Checkout the docs to get started.
A new version (v0.7.1) of bomrang 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 (v0.0.3) of medrxivr is on CRAN - access and search MedRxiv and BioRxiv preprint data. See the release notes for changes. Checkout the docs to get started.

Software Review ✔

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 approved:

mcbette > Model Comparison Using babette
- Author: Richel Bilderbeek
- Issue: ropensci/onboarding#360
- Reviewers:
  - Vikram Baliga
  - bjoelle

The following package was recently submitted:

osmextract > Download and Read OpenStreetMap Data Extracts
- Author: Andrea Gilardi
- Issue: ropensci/software-review#395
- Reviewers: not yet assigned

On the blog

Our community manager Stefanie Butland wrote the post Hacktober? Any Month is a Good Month to Contribute to rOpenSci - with guidance on how to make your package easier to contribute to, and lots of details on how to contribute to packages any time of year.

Software Review

Mark Padgham wrote about his recently rOpenSci reviewed package mapscanner: Rectifying Hand-Drawn Marks on Maps With the mapscanner Package . He discusses the motivation behind the package, and highlights three uses cases for mapscanner.

Citations

The following 19 works use/cite rOpenSci software:

Costa-Neto et al. used nasapower in their paper Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials ¹
Ponce & Sandhel used rentrez in their paper covid19. analytics: An R Package to Obtain, Analyze and Visualize Data from the Corona Virus Disease Pandemic ²
Anderson & Gillooly used rfishbase in their paper Predicting egg size across temperatures in marine teleost fishes ³
Stevens et al. used fingertipsR in their paper Key factors driving obesity in the UK ⁴
Schertler et al. used rgbif in their paper The potential current distribution of the coypu (Myocastor coypus) in Europe and climate change induced shifts in the near future ⁵
Dion et al. used rcrossref in their paper Gender, seniority, and self-citation practices in political science ⁶
Bailey et al. used biomartr in their paper RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge ⁷
Tressel used rnaturalearth in their paper A Morphological and Molecular Taxonomic Review of the Trifolium Depauperatum (Fabaceae) Species Complex ⁸
Guiterman et al. used MtreeRing in their paper dfoliatR: An R package for detection and analysis of insect defoliation signals in tree rings ⁹
Bauder et al. used rnoaa in their paper Identifying and Controlling for Variation in Canid Harvest Data ¹⁰
Çetinkaya-Rundel & Ellison used gutenbergr in their paper A Fresh Look at Introductory Data Science ¹¹
Duarte et al. used rentrez in their paper Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions ¹²
Dupont et al. used NLMR in their paper Optimal sampling design for spatial capture-recapture ¹³
Buil-Gil used essurvey in their paper Small Area Estimation for Crime Analysis ¹⁴
Xaudiera & Cardenal used rtweet in their paper Ibuprofen Narratives in Five European Countries During the COVID-19 Pandemic ¹⁵
Ferster et al. used rtweet in their paper From advocacy to acceptance: Social media discussions of protected bike lane installations ¹⁶
Sampath et al. used rentrez in their paper Roles of dietary taurine in fish nutrition ¹⁷
Grenn et al. used rentrez in their paper The Parkinson’s Disease Genome‐Wide Association Study Locus Browser. Movement Disorders ¹⁸
Tang et al. used nlrx in their paper Code Reusability and Transparency of Agent-Based Modeling: A Review from a Cyberinfrastructure Perspective ¹⁹

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 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
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

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

monkeylearn: The current maintainer is looking for a new maintainer. Comment on this thread 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

Costa-Neto, G., Fritsche-Neto, R., & Crossa, J. (2020). Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials. Heredity. https://doi.org/10.1038/s41437-020-00353-1 ↩
Ponce, M., & Sandhel, A. (2020). covid19. analytics: An R Package to Obtain, Analyze and Visualize Data from the Corona Virus Disease Pandemic. arXiv preprint arXiv:2009.01091 https://arxiv.org/pdf/2009.01091. ↩
Anderson, D. M., & Gillooly, J. F. (2020). Predicting egg size across temperatures in marine teleost fishes. Fish and Fisheries, 21(5), 1027–1033. https://doi.org/10.1111/faf.12486 ↩
Stevens, M. C., Chen, Y., Stringer, A., Clemmow, C., & Jones, L. A. (2020). Key factors driving obesity in the UK. http://london.gisruk.org/gisruk2020_proceedings/GISRUK2020_paper_17.pdf ↩
Schertler, A., Rabitsch, W., Moser, D., Wessely, J., & Essl, F. (2020). The potential current distribution of the coypu (Myocastor coypus) in Europe and climate change induced shifts in the near future. NeoBiota, 58, 129–160. https://doi.org/10.3897/neobiota.58.33118 ↩
Dion, M. L., Mitchell, S. M., & Sumner, J. L. (2020). Gender, seniority, and self-citation practices in political science. Scientometrics, 125(1), 1–28. https://doi.org/10.1007/s11192-020-03615-1 ↩
Bailey, T. W., Santos, A., Nascimento, N. C. de, Sivasankar, M. P., & Cox, A. (2020). RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge. https://doi.org/10.21203/rs.3.rs-45442/v1 ↩
Tressel, L. G. (2020). A Morphological and Molecular Taxonomic Review of the Trifolium Depauperatum (Fabaceae) Species Complex (Doctoral dissertation, Miami University). https://bit.ly/2GRqint ↩
Guiterman, C. H., Lynch, A. M., & Axelson, J. N. (2020). dfoliatR: An R package for detection and analysis of insect defoliation signals in tree rings. Dendrochronologia, 63, 125750. https://doi.org/10.1016/j.dendro.2020.125750 ↩
Bauder, J. M., Allen, M. L., Ahlers, A. A., Benson, T. J., Miller, C. A., & Stodola, K. W. (2020). Identifying and Controlling for Variation in Canid Harvest Data. The Journal of Wildlife Management, 84(7), 1234–1245. https://doi.org/10.1002/jwmg.21919 ↩
Çetinkaya-Rundel, M., & Ellison, V. (2020). A Fresh Look at Introductory Data Science. Journal of Statistics Education, 1–11. https://doi.org/10.1080/10691898.2020.1804497 ↩
Duarte, S., Vieira, P. E., & Costa, F. O. (2020). Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. Metabarcoding and Metagenomics, 4. https://doi.org/10.3897/mbmg.4.55162 ↩
Dupont, G., Royle, J. A., Nawaz, M. A., & Sutherland, C. (2020). Optimal sampling design for spatial capture-recapture. https://doi.org/10.1101/2020.04.16.045740 ↩
Buil-Gil, D. (2020). Small Area Estimation for Crime Analysis. SocArXiv. https://doi.org/10.31235/osf.io/gtbyu ↩
Xaudiera, S., & Cardenal, A. S. (2020). Ibuprofen Narratives in Five European Countries During the COVID-19 Pandemic. Harvard Kennedy School Misinformation Review. https://doi.org/10.37016/mr-2020-029 ↩
Ferster, C., Laberee, K., Nelson, T., Thigpen, C., Simeone, M., & Winters, M. (2020). From advocacy to acceptance: Social media discussions of protected bike lane installations. Urban Studies, 004209802093825. https://doi.org/10.1177/0042098020938252 ↩
Sampath, W. W. H. A., Rathnayake, R. M. D. S., Yang, M., Zhang, W., & Mai, K. (2020). Roles of dietary taurine in fish nutrition. Marine Life Science & Technology. https://doi.org/10.1007/s42995-020-00051-1 ↩
Grenn, F. P., Kim, J. J., Makarious, M. B., Iwaki, H., Illarionova, A., … Brolin, K. (2020). The Parkinson’s Disease Genome‐Wide Association Study Locus Browser. Movement Disorders. https://doi.org/10.1002/mds.28197 ↩
Tang W. et al. (2020) Code Reusability and Transparency of Agent-Based Modeling: A Review from a Cyberinfrastructure Perspective. In: Tang W., Wang S. (eds) High Performance Computing for Geospatial Applications. Geotechnologies and the Environment, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-030-47998-5_7 ↩