Software 📦

CRAN: GitHub:

New packages

Releases

  • A new version (v1.0.3) of skimr is on CRAN - a simple to use summary function that can be used with pipes and displays nicely in the console. See the skimr NEWS for changes. Check out the skimr vignettes to get started.

    use skim_with()` with a nested list of functions

  • A new version (v0.2.2) of tabulizer is on CRAN. See the tabulizer NEWS for changes. Check out the tabulizer vignette to get started.

    extract_tables() gets outdir argument

  • A new version (v1.0.13) of lingtypology is on CRAN - a package for linguistic cartography and typological databases search. See the lingtypology release notes for changes. Check out the lingtypology docs to get started.

    account for leaflet updates, many new arguments

  • A new version (v0.2.1) of bomrang is on CRAN - Australian Government Bureau of Meteorology Data From R. See the bomrang release notes for changes. Check out the bomrang docs to get started.

    deprecated fxns gone, docs better

  • A new version (v0.2.4) of getCRUCLdata is on CRAN - explore CRU CL v. 2.0 Climatology Elements in R. See the getCRUCLdata release notes for changes. Check out the getCRUCLdata docs to get started.

    docs better, minor bug

  • A new version (v1.2.1) of GSODR is on CRAN - Global Summary Daily Weather Data in R. See the GSODR release notes for changes. Check out the GSODR docs to get started.

    docs cleanup, cleanup internal station metadata, bug fixes

  • A new version (v0.3.0) of nomisr is on CRAN - access UK official statistics from the Nomis database. See the nomisr release notes for changes. Check out the nomisr docs to get started.

    new function nomis_codelist(), a deprecated arg in two functions

  • A new version (v0.2.0) of geoops is on CRAN - a package for doing spatial operations on GeoJSON. See the geoops release notes for changes. Check out the geoops vignette to get started.

    updates the JSON C++ lib, add jsonlite to Suggests

  • A new version (v0.4.0) of rdryad is on CRAN - an R client for Dryad. See the rdryad release notes for changes. Check out the rdryad README to get started.

    new fxns dryad_metadata/dryad_package_dois, download_url defunct (use dryad_files)



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 five packages were recently submitted:



On the blog

rOpenSci Unconference

A series of posts recaping our recent rOpenSci Unconference:

Stefanie Butland wrote a high level overview of the unconference, and included a wrap-up of blog posts about the event by the community: Exploring, experimenting, and building software and trust at rOpenSci’s unconf18

Our team wrote a series of four blog posts recapping the projects that happened at the unconference. Also check out Stefanie’s blog post for links to other blog posts about the event.

.rprofile series

We have another post in our .rprofile series conducted by Kelly O’Briant - .rprofile: Julia Silge

Keep an eye out for more posts in this series.

Onboarding

Jorge Cimentada wrote a blog post (Exploring European attitudes and behaviours using the European Social Survey) introducing his recently onboarded package essurvey.

technotes

Jeroen Ooms wrote about The ssh Package: Secure Shell (SSH) Client for R - The taxize package has been around for seven years now. This post covers some of the noteable milestones and covers some upcoming changes.

library(ssh)
session <- ssh_connect("<your host>")
out <- ssh_exec_wait(session, command = 'whoami')
##  jane



Use cases

The following six works use/cite rOpenSci software:



In the news


Sam Albers ran a workshop recently Introduction to R and the tidyverse in Hydrology using the package he maintains that’s part of the rOpenSci suite: [tidyhydat][]


Matt Dray used our magick package for Animating Changes in Football Kits using R

Torkild Lyngstad made an animated figure exploring data from our recently onboarded package essurvey

Paul Oldham wrote a thorough guide to API Resources for the Scientific Literature in R and Python, including many rOpenSci R packages

Shannon Dunnigan wrote about [magick]-ally adding images to figures using our magick package

Najko Jahn maintains an R Shiny web app called the Hybrid OA Journal Monitor that uses the rOpenSci package rcrossref






Keep up with rOpenSci


Footnotes

  1. Machado, V. N., Collins, R. A., Ota, R. P., Andrade, M. C., Farias, I. P., & Hrbek, T. (2018). One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognised diversity in the Amazon. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-26550-x 

  2. Richmond, M. (2018). Evaluation of Craniofacial Superimposition as a Technique for Measuring Mountain Gorilla Facial Soft Tissue Depth and Implications for Hominid Facial Approximation (Masters dissertation, The George Washington University). https://search.proquest.com/openview/bea2b5bf21b62cb1e5e08b6a6e2354a3/1?pq-origsite=gscholar&cbl=18750&diss=y 

  3. Rastrojo, A., García-Hernández, R., Vargas, P., Camacho, E., Corvo, L., Imamura, H., … Requena, J. M. (2018). Genomic and transcriptomic alterations in Leishmania donovani lines experimentally resistant to antileishmanial drugs. International Journal for Parasitology: Drugs and Drug Resistance, 8(2), 246–264. https://doi.org/10.1016/j.ijpddr.2018.04.002 

  4. Simchon, A., & Gilead, M. (2018). A Psychologically Informed Approach to CLPsych Shared Task 2018. In Proceedings of the Fifth Workshop on Computational Linguistics and Clinical Psychology: From Keyboard to Clinic (pp. 113-118). http://www.aclweb.org/anthology/W18-0612 

  5. Sun, B. B., Maranville, J. C., Peters, J. E., Stacey, D., Staley, J. R., Blackshaw, J., … Butterworth, A. S. (2018). Genomic atlas of the human plasma proteome. Nature, 558(7708), 73–79. https://doi.org/10.1038/s41586-018-0175-2 

  6. Nousiainen, K., Kanduri, K., Ricaño-Ponce, I., Wijmenga, C., Lahesmaa, R., Kumar, V., & Lähdesmäki, H. (2018). snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty460