Software 📦

CRAN: GitHub:

New packages

  • The first version (v1.0) of jenkins is on CRAN - Simple Jenkins Client for R. Checkout the README to get started. jenkins jenkins
  • The first version (v2.0.14) of beastier is on CRAN - Provides a way to call BEAST2 from R. Checkout the docs to get started. beastier beastier
  • The first version (v0.1.0) of colocr is on CRAN - conduct co-localization analysis of fluorescence microscopy images. Checkout the vignette to get started. colocr colocr
  • The first version (v0.0.2) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. Checkout the vignette to get started. plotdap plotdap
  • The first version (v0.2.0) of ramlegacy is on CRAN - download and read RAM legacy stock assessment database. Checkout the docs to get started. ramlegacy ramlegacy
  • The first version (v0.1.0) of rromeo is on CRAN - access publisher copyright & self-archiving policies via the SHERPA/RoMEO API. Checkout the docs to get started. rromeo rromeo
  • The first version (v0.1.1) of tidync is on CRAN - a tidy approach to NetCDF data exploration and extraction. Checkout the docs to get started. tidync tidync

New Versions

  • A new version (v2.0.0) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. ijtiff ijtiff

    a few fxns changed names

  • A new version (v7.4.0) 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

    data splitting; URL tracking; advanced memory management

  • A new version (v0.2.6) 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

    bug fixes for nearest_neighbours() and indicator_order()

  • A new version (v0.5.0) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started. rorcid rorcid

    now works with ORCID’s v3 API (& new fxns); new fxns orcid_citations and orcid_search; many fixes

  • A new version (v0.3.0) of tacmagic is on CRAN - positron emission tomography time-activity curve analysis. See the release notes for changes. Checkout the vignette to get started. tacmagic tacmagic

    radioactivity unit conversion for tac objects and numeric objects; conversion of a tac object to standardized uptake value (SUV) by controlling for weight and injected dose

  • A new version (v0.4.0) of traits is on CRAN - species trait data from around the web. See the release notes for changes. Checkout the README to get started. traits traits

    many updates for betydb fxns; EOL Traitbank completely changed; bug fixes

  • A new version (v1.2) of hydroscoper is on CRAN - interface to the Greek National Data Bank for Hydrological and Meteorological Information http://www.hydroscope.gr/. See the release notes for changes. Checkout the vignettes to get started. hydroscoper hydroscoper

    removes plyr dependency

  • A new version (v1.3.1) of MtreeRing is on CRAN - a shiny application for automatic measurements of tree-ring widths on digital images. See the release notes for changes. Checkout the docs to get started. MtreeRing MtreeRing

    add plot parameter to ring_read; all exported fxns renamed to snake_case style

  • A new version (v1.0.6) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. skimr skimr
  • A new version (v0.3.1) of cRegulome is on CRAN - access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer. See the release notes for changes. Checkout the vignettes to get started. cRegulome cRegulome

    fix a test

  • A new version (v2.0.0) of rdataretriever is on CRAN - R interface to the Data Retriever. See the release notes for changes. Checkout the README to get started. rdataretriever rdataretriever

    new author Hashit Bansal; add spatial support; now using reticulate; new get_citation fxn

  • A new version (v1.0.1) of rcites is on CRAN - access the CITES Speciesplus database. See the release notes for changes. Checkout the docs to get started. rcites rcites

    now using cli pkg; bug fixes

  • A new version (v1.1.1) of bib2df is on CRAN - parse a BibTeX file to a data frame. See the release notes for changes. Checkout the vignette to get started. bib2df bib2df
  • A new version (v0.1.1) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started. osmdata osmdata

    bug fix in trim_osmdata function

  • A new version (v0.9.0) of biomartr is on CRAN - Genomic Data Retrieval. See the release notes for changes. Checkout the vignettes to get started. biomartr biomartr

    many new fxns and changes for existing fxns

  • A new version (v0.2.10) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. stplanr stplanr

    documentation fix

  • A new version (v1.4.0) of rtimicropem is on CRAN - supports the analysis of RTI MicroPEM output files. See the release notes for changes. Checkout the docs to get started. rtimicropem rtimicropem

    change dependency on pathological to fs



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 packages were recently submitted:

The following packages recently went through our onboarding process and have been approved:



On the blog

Main blog

We’re excited to announce the release of rOpenSci Dev Guide 0.2.0: Updates Inside and Out - authored by the rOpenSci Editors.

Software Review

Adam Sparks wrote a post POWER to the People about the nasapower package he maintains. The post includes how the package came about, some lessons learned during package development, and some cool usage examples.


Kshitiz Gupta and Carl Boettiger wrote a post on ramlegacy: a package for RAM Legacy Database for the ramlegacy package.


Matthias Grenié and Hugo Gruson wrote a post on Access Publisher Copyright & Self-Archiving Policies via the SHERPA/RoMEO API for their rromeo package.

Tech notes

Maëlle Salmon wrote a blog post about rodev: helpers for rOpenSci package authors. Check out the package.


Jeroen Ooms wrote about a significant piece infrastructure he’s been working on: Introducing the new rOpenSci docs server - a new service to automatically build and host documentation for all rOpenSci packages.



Use Cases

The following 17 works use/cite rOpenSci software:

There’s four recent use cases in the Use Cases section of the rOpenSci discussion forum:



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. Checkout our Contributing Guide for why and how to contribute to rOpenSci.

We’ve had six recent examples of maintainer transitions within rOpenSci:

We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.








Keep up with rOpenSci


Footnotes

  1. Van den Berg, S. J. P., Baveco, H., Butler, E., De Laender, F., Focks, A., Franco, A., … Van den Brink, P. J. (2019). Modeling the Sensitivity of Aquatic Macroinvertebrates to Chemicals Using Traits. Environmental Science & Technology. https://doi.org/10.1021/acs.est.9b00893 

  2. Van Strien, M. J., Huber, S. H., Anderies, J. M., & Grêt-Regamey, A. (2019). Resilience in social-ecological systems: identifying stable and unstable equilibria with agent-based models. Ecology and Society, 24(2). https://doi.org/10.5751/es-10899-240208 

  3. Bayer, D., & Michael, S. (2019). Exploring the Daschle Collection using Text Mining. arXiv preprint arXiv:1904.12623 https://arxiv.org/pdf/1904.12623 

  4. Ruiz, J. L., & Gómez-Díaz, E. (2019). The second life of Plasmodium in the mosquito host: gene regulation on the move. Briefings in functional genomics. https://www.ncbi.nlm.nih.gov/pubmed/31058281 

  5. Baliga, V. B., & Mehta, R. S. (2019). Morphology, ecology, and biogeography of independent origins of cleaning behavior around the world. Integrative and comparative biology. https://doi.org/10.1093/icb/icz030 

  6. Estrela, M. J. (2019) JCSP 44 PCEMI 44 Master of Defence Studies Maîtrise en études de la défense. https://www.cfc.forces.gc.ca/papers/csc/csc44/mds/estrela.pdf 

  7. Falster, D. S., FitzJohn, R. G., Pennell, M. W., & Cornwell, W. K. (2019). Datastorr: a workflow and package for delivering successive versions of “evolving data” directly into R. GigaScience, 8(5). https://doi.org/10.1093/gigascience/giz035 

  8. Barnett, A. G., & Moher, D. (2019). Turning the tables: A university league-table based on quality not quantity. F1000Research, 8, 583. https://doi.org/10.12688/f1000research.18453.1 

  9. Kovacevic, A., Latombe, G., & Chown, S. L. (2019). Rate dynamics of ectotherm responses to thermal stress. Proceedings of the Royal Society B: Biological Sciences, 286(1902), 20190174. https://doi.org/10.1098/rspb.2019.0174 

  10. Schindler, D., Yordanova, K., & Krüger, F. An annotation scheme for references to research artefacts in scientific publications. https://h-suwa.github.io/percomworkshops2019/papers/p52-schindler.pdf 

  11. Piccione, P. M., Baumeister, J., Salvesen, T., Grosjean, C., Flores, Y., Groelly, E., … Lothschütz, C. (2019). Solvent Selection Methods and Tool. Organic Process Research & Development, 23(5), 998–1016. https://doi.org/10.1021/acs.oprd.9b00065 

  12. Łagód, G., Duda, S. M., Majerek, D., Szutt, A., & Dołhańczuk-Śródka, A. (2019). Application of Electronic Nose for Evaluation of Wastewater Treatment Process Effects at Full-Scale WWTP. Processes, 7(5), 251. https://doi.org/10.3390/pr7050251 

  13. Kirsch, S. A., & Böckmann, R. A. (2019). Coupling of Membrane Nanodomain Formation and Enhanced Electroporation near Phase Transition. Biophysical Journal. https://doi.org/10.1016/j.bpj.2019.04.024 

  14. Evans, K. M., Vidal-García, M., Tagliacollo, V. A., Taylor, S. J., & Fenolio, D. B. (2019). Bony Patchwork: Mosaic Patterns of Evolution in the Skull of Electric Fishes (Apteronotidae: Gymnotiformes). Integrative and Comparative Biology. https://doi.org/10.1093/icb/icz026 

  15. Jeremy Forbes, Dianne Cook, Rob J Hyndman. 2019. Spatial modelling of the two-party preferred vote in Australian federal elections: 2001-2016. Monash Econometrics and Business Statistics Working Papers 8/19, Monash University, Department of Econometrics and Business Statistics. https://ideas.repec.org/p/msh/ebswps/2019-8.html 

  16. Colli‐Silva, M., Vasconcelos, T. N. C., & Pirani, J. R. (2019). Outstanding plant endemism levels strongly support the recognition of campo rupestre provinces in mountaintops of eastern South America. Journal of Biogeography. https://doi.org/10.1111/jbi.13585 

  17. Bhattarai, N., Mallick, K., Stuart, J., Vishwakarma, B. D., Niraula, R., Sen, S., & Jain, M. (2019). An automated multi-model evapotranspiration mapping framework using remotely sensed and reanalysis data. Remote Sensing of Environment, 229, 69–92. https://doi.org/10.1016/j.rse.2019.04.026