rOpenSci HQ


Software 📦

CRAN: GitHub:

New packages

  • The first version (v0.2.0) of emld is on CRAN - ecological metadata as linked data. The package recently went through rOpenSci software review, check out the review. Checkout the vignette to get started. emld emld
  • The first version (v0.2.1) of tacmagic is on CRAN - positron emission tomography time-activity curve analysis. The package recently went through rOpenSci software review, check out the review. Checkout the vignette to get started. tacmagic tacmagic

New Versions

  • A new version (v0.25.1) of git2r is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the README to get started. git2r git2r

    fixed significant warning from ‘R CMD check’

  • A new version (v0.4.8) of iheatmapr is on CRAN - Interactive and complex heatmaps. See the release notes for changes. Checkout the docs to get started. iheatmapr iheatmapr

    fix for sample; fixes for add_col_groups, iheatmapr_event, show_colorbar, save_iheatmap

  • A new version (v0.15.6) of DataPackageR is on CRAN - construct reproducible analytic data sets as R packages. See the release notes for changes. Checkout the vignettes to get started. DataPackageR DataPackageR

    fixes for writing to users dir; fixes to update_news()

  • A new version (v0.1.7) of codemetar is on CRAN - Generate codemeta metadata for R packages. See the release notes for changes. Checkout the docs to get started. codemetar codemetar

    jsonld to Suggests; write_codemeta() gains new arg. use_githook; create_codemeta() & write_codemeta() gain new arg. use_filesize

  • A new version (v3.0.3) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started. rfishbase rfishbase

    fix bug in sealifebase name resolution

  • A new version (v2.1) of spelling is on CRAN - tools for spell checking. See the release notes for changes. Checkout the README to get started. spelling spelling

    pre-filter script/style/img tags when checking html files; treat input files in spell_check_files() as UTF-8 on all platforms; fix sorting bug in spell_check_files()

  • A new version (v7.0.0) 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. drake drake

    many breaking changes; some bug fixes; new features including DSL for generating large plans; many enhancements including a large speed boost

  • A new version (v2.2) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started. pdftools pdftools

    import new qpdf pkg; document new PPA for Ubuntu 16.04 and 18.04 with poppler 0.74

  • A new version (v1.3.8) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started. MODIStsp MODIStsp

    fix for incorrect application of scale/offset values on GDAL verions > 2.3; added support for more MODIS products

  • A new version (v0.2.1) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started. fingertipsR fingertipsR

    change in deprivation_decile(); bug fix for fingertips_data()

  • A new version (v1.1) of qpdf is on CRAN - Split, combine and compress PDF files. See the release notes for changes. Checkout the README to get started. qpdf qpdf

    add configure script to allow building with system libqpdf; fix solaris build

Archived

  • The rdefra has been archived on CRAN - we’re hoping to get it back on CRAN soon. rdefra rdefra



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 two packagess were recently submitted:



On the blog

Community calls

Stefanie Butland wrote about our upcoming community call: Community Call - Research Applications of rOpenSci Taxonomy and Biodiversity Tools.

Tech notes

Will Landau wrote about a new version (v7) of drake in a tech note drake transformed. drake is an R-focused pipeline toolkit for reproducibility and high-performance computing.



Use Cases

The following eight works use/cite rOpenSci software:



In The News

We’ve introduced a template in our UseCases category in our discussion forum to make it easy to share how folks are using rOpenSci tools. Check out a recent one by Sharla Gelfand #visdat, #skimr, and #assertr use case: Exploring and understanding a new data set to find top 5 causes for delays on the TTC subway and SRT in 2018.


Stephanie Hazlitt wrote a blog post using the rOpenSci package weathercan triggered by her fence being blown over!


Guangchuang Yu is writing a bookdown book wrote Data Integration, Manipulation and Visualization of Phylogenetic Trees, in which he includes a section of a chapter on the rOpenSci package treeio



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:

We’ve got three 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.
  • rdpla: 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.






Keep up with rOpenSci


Footnotes

  1. Karger, D. N., Kessler, M., Conrad, O., Weigelt, P., Kreft, H., König, C., & Zimmermann, N. E. (2019). Why tree lines are lower on islands-Climatic and biogeographic effects hold the answer. Global Ecology and Biogeography. https://doi.org/10.1111/geb.12897 

  2. Olsson-Collentine, A., van Assen, M. A. L. M., & Hartgerink, C. H. J. (2019). The Prevalence of Marginally Significant Results in Psychology Over Time. Psychological Science, 095679761983032. https://doi.org/10.1177/0956797619830326 

  3. Poulin, R., Hay, E., & Jorge, F. (2019). Taxonomic and geographic bias in the genetic study of helminth parasites. International Journal for Parasitology. https://doi.org/10.1016/j.ijpara.2018.12.005 

  4. Piñar, G., Poyntner, C., Tafer, H., & Sterflinger, K. (2019). A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues. Annals of Microbiology. https://doi.org/10.1007/s13213-019-1446-3 

  5. Dreyer, J. B. B., Higuchi, P., & Silva, A. C. (2019). Ligustrum lucidum W. T. Aiton (broad-leaf privet) demonstrates climatic niche shifts during global-scale invasion. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-40531-8 

  6. Ludt, W. B., Bernal, M. A., Kenworthy, E., Salas, E., & Chakrabarty, P. (2019). Genomic, ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes. Ecology and Evolution. https://doi.org/10.1002/ece3.5029 

  7. Peruffo, E. Improving predictive maintenance classifiers of industrial sensors’ data using entropy. A case study. http://trap.ncirl.ie/3429/1/eleonoraperuffo.pdf 

  8. Free, C. M., Thorson, J. T., Pinsky, M. L., Oken, K. L., Wiedenmann, J., & Jensen, O. P. (2019). Impacts of historical warming on marine fisheries production. Science, 363(6430), 979–983. https://doi.org/10.1126/science.aau1758