Software 📦


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 four packages recently went through our onboarding process and has been approved!

The following two packages were recently submitted:

On the blog

main blog

Steffi LaZerte wrote about her package weathercan recently onboarded with rOpenSci: Integrating data from weathercan

Charles Gray wrote about her experience in reviewing her first R package: An Ode to Testing, my first review.

The rOpenSci Editors wrote a post Thanking Your Reviewers: Gratitude through Semantic Metadata announcing that we can now include reviewers in the Authors section of an R package’s DESCRIPTION file. Yay!

David Winter wrote a post (A rentrez paper, and how to use the NCBI’s new API keys) about his package rentrez for interacting with NCBI data. He discussed a recently published paper on rentrez and support for API keys for NCBI.

Use cases

If you’ve used rOpenSci software in a blog post or a paper, tell us on the discussion forum and we’ll share it with our community here.

The following 15 works use/cite rOpenSci software:

In the news

David Clark shared a screenshot of packages he was using for a project, including rOpenSci’s geojsonio package to do GeoJSON I/O (input/output):

Ciera Martinez and Caryn Johansen describe in a blog post how to use our neotoma package to access and explore mammal bone records

Keep up with rOpenSci


  1. Borcard D., Gillet F., Legendre P. (2018) Community Diversity. In: Numerical Ecology with R. Use R! Springer, Cham 

  2. Cho, H., & Yu, Y. (2018). Link prediction for interdisciplinary collaboration via co-authorship network. arXiv preprint arXiv:1803.06249. 

  3. Nabout, J. C., Teresa, F. B., Machado, K. B., do Prado, V. H. M., Bini, L. M., & Diniz-Filho, J. A. F. (2018). Do traditional scientometric indicators predict social media activity on scientific knowledge? An analysis of the ecological literature. Scientometrics. 

  4. Sanyal, A., Lenoir, J., O’Neill, C., Dubois, F., & Decocq, G. (2018). Intraspecific and interspecific adaptive latitudinal cline in Brassicaceae seed oil traits. American Journal of Botany, 105(1), 85–94. 

  5. Lakiotaki, K., Vorniotakis, N., Tsagris, M., Georgakopoulos, G., & Tsamardinos, I. (2018). BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology. Database, 2018. 

  6. Vieilledent, G., Fischer, F. J., Chave, J., Guibal, D., Langbour, P., & Gérard, J. (2018). New formula and conversion factor to compute tree species basic wood density from a global wood technology database. bioRxiv, 274068. 

  7. Foster, Z. S. L., Chamberlain, S., & Grünwald, N. J. (2018). Taxa: An R package implementing data standards and methods for taxonomic data. F1000Research, 7, 272. 

  8. Farquharson, K. A., Hogg, C. J., & Grueber, C. E. (2018). A meta-analysis of birth-origin effects on reproduction in diverse captive environments. Nature Communications, 9(1). 

  9. Bemmels, J. B., Wright, S. J., Garwood, N. C., Queenborough, S. A., Valencia, R., & Dick, C. W. (2018). Filter-dispersal assembly of lowland Neotropical rainforests across the Andes. Ecography. 

  10. Ng, P. K.-S., Li, J., Jeong, K. J., Shao, S., Chen, H., Tsang, Y. H., … Mills, G. B. (2018). Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell, 33(3), 450–462.e10. 

  11. Bennett, J. M., Calosi, P., Clusella-Trullas, S., Martínez, B., Sunday, J., Algar, A. C., … Morales-Castilla, I. (2018). GlobTherm, a global database on thermal tolerances for aquatic and terrestrial organisms. Scientific Data, 5, 180022. 

  12. Correia, R. A., Jarić, I., Jepson, P., Malhado, A. C. M., Alves, J. A., & Ladle, R. J. (2018). Nomenclature instability in species culturomic assessments: Why synonyms matter. Ecological Indicators, 90, 74–78. 

  13. Reibe, S., Hjorth, M., Febbraio, M. A., & Whitham, M. (2018). GeneXX: An online tool for the exploration of transcript changes in skeletal muscle associated with exercise. Physiological genomics. 

  14. Sinval, J., Pasian, S., Queirós, C., & Marôco, J. (2018). Brazil-Portugal Transcultural Adaptation of the UWES-9: Internal Consistency, Dimensionality, and Measurement Invariance. Frontiers in Psychology, 9. 

  15. Bergmann, A. J., Scott, R. P., Wilson, G., & Anderson, K. A. (2018). Development of quantitative screen for 1550 chemicals with GC-MS. Analytical and Bioanalytical Chemistry, 1-10.