Feb 19, 2019
Software 📦
CRAN: GitHub:
New packages
- The first version (
v0.1.0
) ofrcitoid
is on CRAN - Client for Citoid, Wikipedia’s citation data. Checkout the README to get started.
New Versions
- A new version (
v1.0.7
) ofnasapower
is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started.minor changes
- A new version (
v0.2-7
) ofdbhydroR
is on CRAN - DBHYDRO hydrologic and water quality data. See the release notes for changes. Checkout the docs to get started.fixed critical bug in
get_hydro
causing data parsing failure in all cases - A new version (
v3.0.7
) ofrotl
is on CRAN - an interface to the Open Tree of Life API. See the release notes for changes. Checkout the vignettes to get started.update vignette to address change to OTL TNRS endpoint
- A new version (
v0.2.0
) ofstats19
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 (
v0.5.3
) ofvisdat
is on CRAN - create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using ggplot2. See the release notes for changes. Checkout the docs to get started.updates to
vis_cor()
; useglue
instead ofpaste
- A new version (
v0.2.6
) ofvcr
is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started.new vcr setup fxn
use_vcr()
; support all recording modes!; many fixes to support httr integration;use_cassette()
error blocks no longer include secrets - A new version (
v0.3.4
) ofwebmockr
is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started.to_return_()
/wi_th_()
defunct;to_return()
gains.list
param; bug fixes 🐞 - A new version (
v0.3.0
) ofgeojsonlint
is on CRAN - Tools for Validating GeoJSON. See the release notes for changes. Checkout the vignette to get started.update JS library geojsonhint to
v2.1
; usecrul
for HTTP - A new version (
v0.0.10
) ofpiggyback
is on CRAN - Managing larger data on a GitHub repository. See the release notes for changes. Checkout the docs to get started.improve interface for overwrite files on upload; bug fixes
- A new version (
v2.1
) ofjsonld
is on CRAN - JSON for linking data. See the release notes for changes. Checkout the README to get started.refactor async code to work with V8 package changes
Software Review ✔
We accept community contributed packages via our onboarding 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 recently went through our onboarding process and has been approved:
- emld > Ecological Metadata as Linked Data
- Author: Carl Boettiger
- Issue: ropensci/onboarding#269
- Reviewers:
The following two packagess were recently submitted:
- CytoRSuite > Compensation, Gating & Visualisation Toolkit for Analysis of Flow Cytometry Data
- Author: Dillon Hammill
- Issue: ropensci/onboarding#281
- Reviewers: not yet assigned
- outsider > Install and run programs, outside of R, inside of R
- Author: Dom Bennett
- Issue: ropensci/onboarding#282
- Reviewers: not yet assigned
On the blog
Community
Dan Sholler wrote a summary of his recent rOpenSci Community Call: Community Call Follow-up - Governance of Open Source Research Software Organizations.
Tech notes
Jeroen Ooms wrote about A Major Upgrade of the V8 package in his recent rOpenSci tech note. The V8 package provides an embedded JavaScript engine that can be used inside of R.
Use Cases
The following 14 works use/cite rOpenSci software:
- Lee, et al. used RSelenium and hunspell in their paper Investigating the association between mating-relevant self-concepts and mate preferences through a data-driven analysis of online personal descriptions 1
- Lu & Hedin used rgbif in their paper Global plant–symbiont organization and emergence of biogeochemical cycles resolved by evolution-based trait modelling 2
- Zizka et al. referenced opencage, rgbif, rnaturalearth, and scrubr in their paper CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases 3
- Rice et al. used rgbif, rnaturalearthdata and CoordinateCleaner in their paper The global biogeography of polyploid plants 4
- Sellgren et al. used plotly in their paper Peripheral and central levels of kynurenic acid in bipolar disorder subjects and healthy controls 5
- Gill et al. used brranching Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna 6
- Hicks et al. used rcrossref in their paper Network analysis to evaluate the impact of research funding on research community consolidation 7
- Jovanović et al. used plotly Introducing of modeling techniques in the research of POPs in breast milk – A pilot study 8
- Kay et al. used plotly in their paper Agroforestry is paying off – Economic evaluation of ecosystem services in European landscapes with and without agroforestry systems 9
- Marcos et al. used MODIStsp in their paper Improving the detection of wildfire disturbances in space and time based on indicators extracted from MODIS data: a case study in northern Portugal 10
- Martins et al. used plotly in their paper HABIT - a webserver for interactive T cell neoepitope discovery 11
- Nadal-Ribelles et al. used plotly in their paper Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations 12
- Rigg et al. used MODIStsp in their paper Malaria infection rates in Anopheles albimanus (Diptera: Culicidae) at Ipetí-Guna, a village within a region targeted for malaria elimination in Panamá 13
- Briz-Redón used osmdata in their paper SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks 14
In The News
Some nice words about bib2df from community member Philipp Ottolinger.
Thank you @0ttlngr and collaborators for making the bib2df-package for R!
— Hedvig (@Laserhedvig) February 8, 2019
So practical to be able to read in #bibtex syntax into neat complete dataframes, including quirky @clld_dot_org #Glottolog specific field types without complaints of non-complete entries#rstats
Someone found NLMR and landscapetools very useful! From community member Marco Sciaini
Using the excellent @rOpenSci NLMR and landscapetools 📦s by @msciain et al. to create correlated spatial features for model simulation. Incredibly useful! pic.twitter.com/FdK0dMf3Mm
— Matt Harris (@Md_Harris) January 30, 2019
Brodie Gaslam wrote a blog post using our magick package (by Jeroen Ooms) Favicons From the Comfort of Your R Session
Call For Contributors
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. We’ve had three 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
We’ve still got two packages in need of new maintainers:
- webchem: The current maintainer of webchem, Eduard Szöcs, is looking for a new maintainer. See issue #155. Do ping Eduard in that issue and/or email us at info@ropensci.org
- rsnps: The current maintainer would like to hand it over to someone with more expertise in the domain. Please get in touch with Scott if you’re interested.
Related News
- The Red Hat Women in Open Source Award vote ends on February 25th. Gabriela de Gueiroz is one of the options: she’s the founder of R-Ladies. You can vote here: https://www.redhat.com/en/about/women-in-open-source
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
-
Lee, A. J., Jones, B. C., & DeBruine, L. M. (2019, January 21). Investigating the association between mating-relevant self-concepts and mate preferences through a data-driven analysis of online personal descriptions. https://doi.org/10.31234/osf.io/38zef ↩
-
Lu, M., & Hedin, L. O. (2019). Global plant–symbiont organization and emergence of biogeochemical cycles resolved by evolution-based trait modelling. Nature Ecology & Evolution, 3(2), 239–250. https://doi.org/10.1038/s41559-018-0759-0 ↩
-
Zizka, A., Silvestro, D., Andermann, T., Azevedo, J., Duarte Ritter, C., Edler, D., … Antonelli, A. (2019). CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13152 ↩
-
Rice, A., Šmarda, P., Novosolov, M., Drori, M., Glick, L., Sabath, N., … Mayrose, I. (2019). The global biogeography of polyploid plants. Nature Ecology & Evolution, 3(2), 265–273. https://doi.org/10.1038/s41559-018-0787-9 ↩
-
Sellgren, C. M., Gracias, J., Jungholm, O., Perlis, R. H., Engberg, G., Schwieler, L., … Erhardt, S. (2019). Peripheral and central levels of kynurenic acid in bipolar disorder subjects and healthy controls. Translational Psychiatry, 9(1). https://doi.org/10.1038/s41398-019-0378-9 ↩
-
Gill, B. A., Musili, P. M., Kurukura, S., Hassan, A. A., Goheen, J. R., Kress, W. J., … Kartzinel, T. R. (2019). Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13001 ↩
-
Hicks, D. J., Coil, D. A., Stahmer, C. G., & Eisen, J. A. (2019). Network analysis to evaluate the impact of research funding on research community consolidation. https://doi.org/10.1101/534495 ↩
-
Jovanović, G., Romanić, S. H., Stojić, A., Klinčić, D., Sarić, M. M., Letinić, J. G., & Popović, A. (2019). Introducing of modeling techniques in the research of POPs in breast milk – A pilot study. Ecotoxicology and Environmental Safety, 172, 341–347. https://doi.org/10.1016/j.ecoenv.2019.01.087 ↩
-
Kay, S., Graves, A., Palma, J. H. N., Moreno, G., Roces-Díaz, J. V., Aviron, S., … Herzog, F. (2019). Agroforestry is paying off – Economic evaluation of ecosystem services in European landscapes with and without agroforestry systems. Ecosystem Services, 36, 100896. https://doi.org/10.1016/j.ecoser.2019.100896 ↩
-
Marcos, B., Gonçalves, J., Alcaraz-Segura, D., Cunha, M., & Honrado, J. P. (2019). Improving the detection of wildfire disturbances in space and time based on indicators extracted from MODIS data: a case study in northern Portugal. International Journal of Applied Earth Observation and Geoinformation, 78, 77–85. https://doi.org/10.1016/j.jag.2018.12.003 ↩
-
Martins, J., Magalhaes, C., Vieira, V., Rocha, M., & Osorio, N. S. (2019). HABIT - a webserver for interactive T cell neoepitope discovery. https://doi.org/10.1101/535716 ↩
-
Nadal-Ribelles, M., Islam, S., Wei, W., Latorre, P., Nguyen, M., de Nadal, E., … Steinmetz, L. M. (2019). Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations. Nature Microbiology. https://doi.org/10.1038/s41564-018-0346-9 ↩
-
Rigg, C. A., Hurtado, L. A., Calzada, J. E., & Chaves, L. F. (2019). Malaria infection rates in Anopheles albimanus (Diptera: Culicidae) at Ipetí-Guna, a village within a region targeted for malaria elimination in Panamá. Infection, Genetics and Evolution, 69, 216–223. https://doi.org/10.1016/j.meegid.2019.02.003 ↩
-
Briz-Redón, Á. (2019). SpNetPrep: An R package using Shiny to facilitate spatial statistics on road networks. Research Ideas and Outcomes, 5. https://doi.org/10.3897/rio.5.e33521 ↩