rOpenSci

Stefanie Butland

### rOpenSci HQ

- rOpenSci [received a \$678K
  award](/blog/2019/07/15/expanding-software-review/) from the Sloan
  Foundation to expand Software Peer Review.
- [We are hiring](/blog/2019/07/18/ropensci-hiring/) for a new position
  in statistical software testing and peer review.
- Join our next [Community Call on Reproducible Workflows at Scale with
  drake](/blog/2019/08/08/commcall-sep2019/) September 24th.
- Videos, speakers' slides, resources and collaborative notes from our
  Community Calls on [Involving Multilingual
  Communities](/commcalls/2019-06-28/) and [Reproducible Research with
  R](/commcalls/2019-07-30/) are posted.

### Software Peer Review

5 community-contributed packages passed [software peer
review](/software-review/).

**[gitignore](https://docs.ropensci.org/gitignore/)** - Create useful
.gitignore files for your project. Author: [Philippe
Massicotte](https://github.com/PMassicotte); Reviewers: [Amanda
Dobbyn](https://github.com/aedobbyn), [Mauro
Lepore](https://github.com/maurolepore);
[Review](https://github.com/ropensci/software-review/issues/303)

**[grainchanger](https://docs.ropensci.org/grainchanger/)** -
Moving-Window and Direct Data Aggregation. Author: [Laura Jane
Graham](https://github.com/laurajanegraham); Reviewers: [Max
Joseph](https://github.com/mbjoseph), [John
Baumgartner](https://github.com/johnbaums);
[Review](https://github.com/ropensci/onboarding/issues/289)

**[popler](https://github.com/ropensci/popler)** - Browse and query the
popler database. Author: [Aldo
Compagnoni](https://github.com/AldoCompagnoni); Reviewers: [Corinna
Gries](https://github.com/cgries), [Ben
Bond-Lamberty](https://github.com/bpbond);
[Review](https://github.com/ropensci/software-review/issues/254)

**[tidypmc](https://docs.ropensci.org/tidypmc/)** - Parse full text XML
documents from PMC. Author: [Chris
Stubben](https://github.com/cstubben); Reviewers: [Julia
Silge](https://github.com/juliasilge), [Toph
Allen](https://github.com/toph-allen);[Review](https://github.com/ropensci/software-review/issues/290)

**[UCSCXenaTools](https://github.com/ropensci/UCSCXenaTools)** -
Download and Explore Datasets from UCSC Xena Data Hubs. Author:
[Shixiang Wang](https://github.com/ShixiangWang); Reviewers: [Christine
Stawitz](https://github.com/ChristineStawitz-NOAA), [Carl
Ganz](https://github.com/carlganz);
[Review](https://github.com/ropensci/software-review/issues/315)

*Consider [submitting your
package](https://devguide.ropensci.org/softwarereviewintro.html) or
[volunteering to
review](https://devguide.ropensci.org/softwarereviewintro.html#whyreview).*

### Software

3 new packages from the community are on CRAN.

- [git2rdata](https://docs.ropensci.org/git2rdata/) - store and retrieve
  data.frames in a Git repository
- [tidypmc](https://docs.ropensci.org/tidypmc/) - parse full text XML
  documents from PubMed Central
- [UCSCXenaTools](https://github.com/ropensci/UCSCXenaTools) - download
  and explore datasets from UCSC Xena data hubs

### On the Blog

#### From the rOpenSci team

- [Taking over maintenance of a software
  package](/blog/2019/06/12/taking-over-maint/)
- [rOpenSci Contributors at useR!2019](/blog/2019/07/08/user2019/)
- [2 Months in 2 Minutes - rOpenSci News, June
  2019](/blog/2019/06/20/news-jun2019/)

#### From the community

- [Aggregating spatial data with the grainchanger
  package](/blog/2019/07/16/grainchanger/) -- [Laura Jane
  Graham](/authors/laura-graham/)

<figure>
<img src="/img/blog-images/2019-07-16-grainchanger/logo.png" width="150"
alt="Image: hex sticker for grainchanger package" />
</figure>

### Use Cases

- 51 published works cited or used rOpenSci software (listed in
  individual newsletters)
- 6 use cases for our packages or resources were posted in our
  [discussion forum](https://discuss.ropensci.org/c/usecases)

**Example**: [Dan Quintana](https://twitter.com/dsquintana) gave a short
video demonstration of using
[europepmc](https://github.com/ropensci/europepmc/), a package
maintained by [Najko Jahn](https://github.com/njahn82)

> Ever wanted to visualize the popularity of a research topic over time?
> Here\'s how, using the \'europepmc\'
> [\#Rstats](https://twitter.com/hashtag/Rstats?src=hash&ref_src=twsrc%5Etfw)
> package  
>   
> YouTube link: <https://t.co/fI5B6PLDco>  
> Code: <https://t.co/hSnYiBrUh8>  
> Thread 👇 [pic.twitter.com/Ezsh9jUJul](https://t.co/Ezsh9jUJul)
>
> --- Dan Quintana (@dsquintana) [July 23,
> 2019](https://twitter.com/dsquintana/status/1153765004606394372?ref_src=twsrc%5Etfw)

*Have you used an rOpenSci package? [Share your use
case](https://discuss.ropensci.org/c/usecases) and we'll tweet about
it.*

### Keep up with rOpenSci

We create a newsletter every two weeks. You can subscribe via rss feed
in [XML](https://news.ropensci.org/feed.xml) or
[JSON](https://news.ropensci.org/feed.json) or via our one-way [mailing
list](/#subscribe).

Follow [@rOpenSci](https://twitter.com/ropensci) on Twitter.

Find out how you can
[contribute](https://devguide.ropensci.org/contributingguide.html) to
rOpenSci as a user or developer.


rOpenSci HQ rOpenSci received a $678K award from the Sloan Foundation to expand Software Peer Review.We are hiring for a new position in statistical software testing and peer review.Join our next Community Call on Reproducible Workflows at Scale with drake September 24th.Videos, speakers’ slides, resources and collaborative notes from our Community Calls on Involving Multilingual Communities and Reproducible Research with R are posted.Software

2 Months in 2 Minutes - rOpenSci News, August 2019

### rOpenSci HQ 👨🏽‍💻👩🏼‍💻 🏗️ {#ropensci-hq--}

- Join our next [Community Call on Involving Multilingual
  Communities](/commcalls/2019-06-28/) June 28th.
- Video of our [Community Call on Security for
  R](/commcalls/2019-05-07/) is up, with a long list of resources.
- Our Community Manager, Stefanie Butland, spoke at R-Ladies Seattle and
  Fred Hutch about rOpenSci, Learning R, and Building Community May
  22nd.

### Software Peer Review ✔

6 community-contributed packages passed [software peer
review](/software-review/)

- [nbaR](https://docs.ropensci.org/nbaR/) - R Package Client for the
  Netherlands Biodiversity API
  - Author: [Hannes Hettling](https://github.com/hettling)
  - Issue:
    [ropensci/onboarding#257](https://github.com/ropensci/onboarding/issues/257)
  - Reviewers:
    - [Dom Bennett](https://github.com/DomBennett)
    - [Max Joseph](https://github.com/mbjoseph)
- [git2rdata](https://docs.ropensci.org/git2rdata/) - Store and Retrieve
  Data.frames in a Git Repository
  - Author: [Thierry Onkelinx](https://github.com/ThierryO)
  - Issue:
    [ropensci/onboarding#263](https://github.com/ropensci/onboarding/issues/263)
  - Reviewers:
    - [Jenny Bryan](https://github.com/jennybc)
    - [Brodie Gaslam](https://github.com/brodieG)
- [citesdb](https://docs.ropensci.org/citesdb/) - A high-performance
  database of shipment-level CITES trade data
  - Author: [Noam Ross](https://github.com/noamross)
  - Issue:
    [ropensci/onboarding#292](https://github.com/ropensci/onboarding/issues/292)
  - Reviewers:
    - [pachamaltese](https://github.com/pachamaltese)
    - [Xavier Rotllan-Puig](https://github.com/xavi-rp)
- [MtreeRing](https://docs.ropensci.org/MtreeRing/) - A Shiny
  Application for Automatic Measurements of Tree-Ring Widths on Digital
  Images
  - Author: [Jingning Shi](https://github.com/JingningShi)
  - Issue:
    [ropensci/onboarding#287](https://github.com/ropensci/onboarding/issues/287)
  - Reviewers:
    - [Brandon Hurr](https://github.com/bhive01)
    - [Rory Nolan](https://github.com/rorynolan)
- [rromeo](https://docs.ropensci.org/rromeo/) - An R Client for
  SHERPA/RoMEO API
  - Author: [Matthias Grenié](https://github.com/Rekyt)
  - Issue:
    [ropensci/onboarding#285](https://github.com/ropensci/onboarding/issues/285)
  - Reviewers:
    - [Philipp Ottolinger](https://github.com/ottlngr)
    - [Bruna Wundervald](https://github.com/brunaw)
- [tidync](https://docs.ropensci.org/tidync/) - A Tidy Approach to
  'NetCDF' Data Exploration and Extraction
  - Author: [Michael Sumner](https://github.com/mdsumner)
  - Issue:
    [ropensci/onboarding#174](https://github.com/ropensci/onboarding/issues/174)
  - Reviewers:
    - [Tim Lucas](https://github.com/timcdlucas)
    - [Jakub Nowosad](https://github.com/Nowosad)

*Consider [submitting your
package](https://devguide.ropensci.org/softwarereviewintro.html) or
[volunteering to
review](https://devguide.ropensci.org/softwarereviewintro.html#whyreview).*

### Software 📦

9 new packages on CRAN

- [beastier](https://docs.ropensci.org/beastier/) - provides a way to
  call BEAST2 from R
- [colocr](https://cran.rstudio.com/web/packages/colocr/vignettes/using_colocr.html) -
  conduct co-localization analysis of fluorescence microscopy images
- [conditionz](https://docs.ropensci.org/conditionz/) - control how many
  times conditions are thrown
- [jenkins](https://docs.ropensci.org/jenkins/) - Simple Jenkins Client
  for R
- [plotdap](https://cran.rstudio.com/web/packages/plotdap/vignettes/using_plotdap.html) -
  easily visualize data from ERDDAP servers via the rerddap package
- [ramlegacy](https://docs.ropensci.org/ramlegacy/) - download and read
  RAM legacy stock assessment database
- [rromeo](https://docs.ropensci.org/rromeo/) - access publisher
  copyright & self-archiving policies via the SHERPA/RoMEO API
- [suppdata](https://cran.rstudio.com/web/packages/suppdata/vignettes/suppdata-intro.pdf) -
  downloading supplementary data from published manuscripts
- [tidync](https://docs.ropensci.org/tidync/) - a tidy approach to
  NetCDF data exploration and extraction

### On the Blog ✍🏼

#### From the rOpenSci team

- [rOpenSci Dev Guide 0.2.0: Updates Inside and
  Out](/blog/2019/05/16/dev-guide-update/)
- [Introducing the new rOpenSci docs
  server](/technotes/2019/06/07/ropensci-docs/)
- [Taking over maintenance of a software
  package](/blog/2019/06/12/taking-over-maint/)
- [conditionz: control how many times conditions are
  thrown](/technotes/2019/04/24/conditionz/)
- [Join, split, and compress PDF files with
  pdftools](/technotes/2019/04/24/pdftools-22/)
- [rodev: helpers for rOpenSci package
  authors](/technotes/2019/05/21/rodev/)

<figure>
<img src="/img/blog-images/2019-06-20-news-jun2019/cover.png"
width="200"
alt="cover of rOpenSci dev guide, showing a package production line with small humans discussing, examining and promoting packages" />
</figure>

#### From the community

- [When Standards Go Wild - Software Review for a
  Manuscript](/blog/2019/04/18/wild-standards/) -- Stefanie Butland \|
  Nick Golding \| Chris Grieves \| Hugo Gruson \| Thomas White \| Hao Ye
- [Relaunching the qualtRics
  package](/blog/2019/04/30/qualtrics-relaunch/) -- Julia Silge
- [Access Publisher Copyright & Self-Archiving Policies via the
  'SHERPA/RoMEO' API](/blog/2019/06/04/rromeo/) -- Matthias Grenié \|
  Hugo Gruson
- [ramlegacy: a package for RAM Legacy
  Database](/blog/2019/05/28/ramlegacy/) -- Kshitiz Gupta \| Carl
  Boettiger
- [POWER to the People](/blog/2019/05/14/nasapower/) -- Adam Sparks
- [Open Trade Statistics](/blog/2019/05/09/tradestatistics/) -- Pachá
  (aka Mauricio Vargas Sepúlveda)

### Use Cases 📝🙋🏽‍♀️🙋🏻‍♂️ {#use-cases-}

- 38 published works cited or used rOpenSci software
- 7 use cases were posted in our [discussion
  forum](https://discuss.ropensci.org/c/usecases)

Example: [Get tweet status ID from CrossRef Event Data with our crevents
package](https://discuss.ropensci.org/t/get-tweet-status-id-from-crossref-event-data-with-crevents/1665).
Tuija Sonkkila wrote about working with altmetrics data in her post
"Everyday altmetrics". She shared her code and link to a Shiny app.

<figure>
<img
src="/img/blog-images/2019-06-20-news-jun2019/tuija_crevents_post.png"
width="400"
alt="cover of rOpenSci dev guide, showing a package production line with small humans discussing, examining and promoting packages" />
</figure>

*Have you used an rOpenSci package? [Share your use
case](https://discuss.ropensci.org/c/usecases) and we'll tweet about
it.*

### Keep up with rOpenSci 📣

We create a newsletter every two weeks. You can subscribe via rss feed
in [XML](https://news.ropensci.org/feed.xml) or
[JSON](https://news.ropensci.org/feed.json) or via our one-way [mailing
list](/#subscribe).

Follow [@rOpenSci](https://twitter.com/ropensci) on Twitter.

Learn how you can
[contribute](https://devguide.ropensci.org/contributingguide.html) to
rOpenSci as a user or developer.


rOpenSci HQ 👨🏽‍💻👩🏼‍💻 🏗️ Join our next Community Call on Involving Multilingual Communities June 28th.Video of our Community Call on Security for R is up, with a long list of resources.Our Community Manager,  Stefanie Butland, spoke at R-Ladies Seattle and Fred Hutch about rOpenSci, Learning R, and Building Community May 22nd.Software Peer Review ✔  6  community-contributed packages passed software peer reviewnbaR - R Package Client for the

Rogue Scholar Beiträge

2 Months in 2 Minutes - rOpenSci News, August 2019

2 Months in 2 Minutes - rOpenSci News, June 2019