Aug 28, 2017
rOpenSci HQ
Community Calls
We’ll have our next community call on September 13th, on rOpenSci Software Review and Onboarding.
Save the date! https://github.com/ropensci/commcalls/issues/15
We hope past authors and reviewers will attend, as well as people considering volunteering to review rOpenSci packages or people considering submitting their package for review.
Discussion forum
Recently, on our discussion forum https://discuss.ropensci.org:
- Retiring rOpenSci packages?
- Best practice for documenting raw data in a package?
- NCEAS Data Science Fellowship
Software
Releases
- A new version (
v1.6
) oftesseract
is on CRAN. See the release notes for details. Check out the tesseract README to get started. Repository on GitHub - A new version (
v0.6.0
) ofrvertnet
is on CRAN. This version switches to using crul for HTTP requests and adds a new functiontraitsearch
for getting VertNet trait data. See the release notes for details. Check out the rvertnet vignette to get started. Repository on GitHub - A new version (
v1.0.6
) oflingtypology
is on CRAN. See the release notes for details. Check out the lingtypology vignette to get started. Repository on GitHub - A new version (
v0.0.4
) ofbikedata
is on CRAN. See the release notes for details. Check out the bikedata vignette to get started. Repository on GitHub - A new version (
v0.14.20
) ofRefManageR
is on CRAN. See the release notes for details. Check out the RefManageR vignettes to get started. Repository on GitHub - A new version (
v1.11.0
) ofecoengine
is on CRAN. See the release notes for details. Check out the README to get started. Repository on GitHub - A new version (
v2.4.6
) ofFedData
is on CRAN. See the NEWS for details. Check out the FedData docs to get started. Repository on GitHub - A new version (
v1.0.5
) ofGSODR
is on CRAN. See the release notes for details. Check out the GSODR vignettes to get started. Repository on GitHub - A new version (
v0.1.9
) ofgetCRUCLdata
is on CRAN. See the NEWS for details. Check out the getCRUCLdata vignette to get started. Repository on GitHub - A new version (
v0.4.0
) ofgeojsonio
is on CRAN. This version gains a suite of new funtions for working with TopoJSON data. See the release notes for details. Check out the geojsonio vignettes to get started. Repository on GitHub - A new version (
v0.2.0
) ofworrms
is on CRAN. This version adds sister functions to most of the main exported functions to allow passing in many inputs (scientific names or WoRMS AphiaIDs). See the release notes for details. Check out the worrms vignettes to get started. Repository on GitHub - A new version (
v0.4.0
) ofrredlist
is on CRAN. This version adds new functions for getting IUCN Redlist growth form data and does many small improvements. See the release notes for details. Check out the rredlist README to get started. Repository on GitHub - A new version (
v1.2
) ofmagick
is on CRAN. See the release notes for details. Check out the magick vignette to get started. Repository on GitHub
Onboarding
We accept community contributed packages via our onboarding system - a software review system, sorta like scholarly paper review, but way better. We’ll highlight new packages here that have come through this system. 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 we have a new form you can fill out, and we’ll ping you when there’s a submission that fits in your area of expertise.
The following package was recently submitted to our onboarding process:
- rperseus > Gets texts from the Perseus Digital Library
- Author: David Ranzolin
- Issue: ropensci/onboarding#145
- Reviewers: not assigned yet
The following package recently went through our onboarding process and has been approved!
- bomrang > Fetch Australian Government Bureau of Meteorology Data
- Author: Adam Sparks
- Issue: ropensci/onboarding#121
- Reviewers:
On the blog
We’ve had three blog posts on our main blog in the past two weeks:
- Magick 1.0: 🎩 ✨🐇 Advanced Graphics and Image Processing in R by Jeroen Ooms
- So you (don’t) think you can review a package by Mara Averick
- Onboarding visdat, a tool for preliminary visualisation of whole dataframes by Nicholas Tierney
We’ve also had two blog posts on our developer blog in the same timeframe:
- Tesseract and Magick: High Quality OCR in R by Jeroen Ooms
- FedData - Getting assorted geospatial data into R by Kyle Bocinsky
Use Cases
The following 9 works use/cite rOpenSci or rOpenSci software:
- Peter Smits cited taxize in his thesis Remodeling the Fossil Record: Analysis of Emergent Evolutionary and Ecological Patterns 1
- Leander Love-Anderegg cited taxize in their thesis On the variation of traits and tree range constraints 2
- Brown et al. cited rOpenSci in their paper NSIS and Atlantic Ecosystems Initiative to make data accessible-one dataset at a time 3
- Carota et al. cited spocc in their paper A Bayesian semi‐parametric GLMM for historical and newly collected presence‐only data: an applica on to species richness of Ross Sea Mollusca 4
- David Winter wrote a paper about his rOpenSci package rentrez, in preprint form right now: rentrez: An R package for the NCBI eUtils API 5
- Amelia McNamara and Nick Horton mentioned the rOpenSci blog post Reproducible research is still a challenge in their paper Wrangling categorical data in R 6
- Rosen cited our package gender in his paper Correlations, trends and potential biases among publicly accessible web-based student evaluations of teaching: a large-scale study of RateMyProfessors. com data 7
- Mendez et al. cited our package rerddap in their paper Geographical variation in the foraging behaviour of the pantropical red-footed booby 8
- Tennant et al. cited rOpenSci in their paper A multi-disciplinary perspective on emergent and future innovations in peer review 9
Submit news to rOpenSci
Reach out to us with your news suggestions by sending us an email info@ropensci.org or by contacting us on Twitter @ropensci
Keep up with rOpenSci news
There are a number of ways to keep up with what rOpenSci is doing:
- Mailing list: Sign up with an email address to get new blog posts sent to your inbox -> ropensci.org/#subscribe
- rOpenSci on Twitter: we’re @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.
- rOpenSci news. XML feed at https://news.ropensci.org/feed.xml - JSON feed at https://news.ropensci.org//feed.json
Footnotes
-
Smits, P. D. (2017). Remodeling the Fossil Record: Analysis of Emergent Evolutionary and Ecological Patterns (Doctoral dissertation, The University of Chicago). https://search.proquest.com/openview/2a353f0e54c8c3ee37a0d8d2bcd8ad6d/1?pq-origsite=gscholar&cbl=18750&diss=y ↩
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Love-Anderegg, L. D. (2017). On the variation of traits and tree range constraints (Doctoral dissertation, The University of Washington). https://digital.lib.washington.edu/researchworks/bitstream/handle/1773/39962/LoveAnderegg_washington_0250E_17084.pdf?sequence=1 ↩
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Brown, G., Kennedy, M., Sherin, A., Appletans, W., Mills, E. L., & Lavoilette, L. (2017). NSIS and Atlantic Ecosystems Initiative to make data accessible-one dataset at a time. Proceedings of the Nova Scotian Institute of Science. http://dalspace.library.dal.ca/bitstream/handle/10222/72817/Brown%20Kennedy%20Sherin%20Appeltans%20Mills%20%20Laviolette%20PNSIS%2049.1.pdf?sequence=1 ↩
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Carota, C., Nava, C. R., Ghiglione, C., & Schiaparelli, S. (2017). A Bayesian semi‐parametric GLMM for historical and newly collected presence‐only data: an applica on to species richness of Ross Sea Mollusca. Preprint - for submissison to Environmetrics. https://www.univda.it/UploadDocs/16975_WP2017_N15_Nava.pdf ↩
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Winter, D. J. (2017). rentrez: An R package for the NCBI eUtils API (Version 1). PeerJ Preprints. https://doi.org/10.7287/peerj.preprints.3179v1 ↩
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McNamara A, Horton NJ. (2017) Wrangling categorical data in R. PeerJ Preprints 5:e3163v1 https://doi.org/10.7287/peerj.preprints.3163v1 ↩
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Rosen, A. S. (2017). Correlations, trends and potential biases among publicly accessible web-based student evaluations of teaching: a large-scale study of RateMyProfessors. com data. Assessment & Evaluation in Higher Education, 1-14. https://sites.northwestern.edu/rosen/files/2017/02/POSTPRINT_RMP-1e3n8l9.pdf ↩
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Mendez, L., Borsa, P., Cruz, S., de Grissac, S., Hennicke, J., Lallemand, J., … Weimerskirch, H. (2017). Geographical variation in the foraging behaviour of the pantropical red-footed booby. Marine Ecology Progress Series, 568, 217–230. https://doi.org/10.3354/meps12052 ↩
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Tennant, J. P., Dugan, J. M., Graziotin, D., Jacques, D. C., Waldner, F., Mietchen, D., … Colomb, J. (2017). A multi-disciplinary perspective on emergent and future innovations in peer review. F1000Research, 6, 1151. https://doi.org/10.12688/f1000research.12037.1 ↩