2019-08-19

rOpenSci HQ

Join us for our next community call on Reproducible Workflows at Scale with drake on Sep 24th, 2019. The speaker is drake developer Will Landau.

Software 📦

CRAN: GitHub:

There’s very little activity in this section because CRAN submissions were closed for the last week and a half.

New Versions

A new version (v0.4.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started.

fix link to package manual; fix single method request matching
A new version (v0.5.19) of aRxiv is on CRAN - Interface to the arXiv API. See the release notes for changes. Checkout the docs to get started.

update vignette; add ORCIDs to DESCRIPTION

Software Review ✔

We accept community contributed packages via our software review 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 package was recently submitted:

c14bazAAR > Download and Prepare C14 Dates from Different Source Databases
- Author: Clemens Schmid
- Issue: ropensci/onboarding#333
- Reviewers: not yet assigned

The following package recently went through our software-review process and has been approved:

rnassqs > Access the NASS Quick Stats API
- Author: Nicholas Potter
- Issue: ropensci/onboarding#298
- Reviewers:
  - Adam Sparks
  - Neal Richardson

Use Cases

The following 19 works use/cite rOpenSci software:

Yen et al. used stplanr in their paper The morphology and circuity of walkable, bikeable, and drivable street networks in Phnom Penh, Cambodia ¹
Danella Figo et al. used taxize in their paper Cashew Tree Pollen: An Unknown Source of IgE-Reactive Molecules ²
Kanterakis et al. used hydroscoper in their paper Assessment of hydrological modelling behaviour at basin scale on the number of delineated sub-basins ³
Petrik et al. used rfishbase in their paper Bottom-up drivers of global patterns of demersal, forage, and pelagic fishes ⁴
Calderone used tokenizers in their paper A Computational Analysis of Natural Languages to Build a Sentence Structure Aware Artificial Neural Network ⁵
Uzma et al. used rgbif in their paper Timing and ecological priority shaped the diversification of sedges in the Himalayas ⁶
Baylis et al. used rerddap in their paper Important At-Sea Areas of Colonial Breeding Marine Predators on the Southern Patagonian Shelf ⁷
Nourbakhsh et al. used plotly in their paper Expression Profiling Reveals Involvement of WNT Pathway in the Malignant Progression of Sessile Serrated Adenomas ⁸
Waller used CoordinateCleaner in their paper Data Location Quality at GBIF ⁹
Shackleton et al. used rentrez in their paper Environmental DNA reveals landscape mosaic of wetland plant communities ¹⁰
Nelli et al. used MODIStsp in their paper Achieving explanatory depth and spatial breadth in infectious disease modelling: Integrating active and passive case surveillance ¹¹
Glicksberg et al. used plotly in their paper PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model ¹²
Brown et al. used tacmagic in their paper Brain Amyloid PET Tracer Delivery is Related to White Matter Integrity in Patients with Mild Cognitive Impairment ¹³
Koppelstaetter et al. used rentrez in their paper Computational Drug Screening Identifies Compounds Targeting Renal Age-associated Molecular Profiles ¹⁴
Calero Valdez & Ziefle used pdftools in their paper Trends and Changes in the Field of HCI the Last Decade from the Perspective of HCII Conference ¹⁵
Alfaro et al. used rfishbase in their paper The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae). Integrative and comparative biology ¹⁶
Butterfield et al. used rgbif and CoordinateCleaner in their paper Life history traits predict colonization and extinction lags of desert plant species since the Last Glacial Maximum ¹⁷
Kovalenko et al. used rfishbase in their paper Hotspots and bright spots in functional and taxonomic fish diversity ¹⁸
Ferraz et al. used rentrez in their paper Oviductal extracellular vesicles interact with the spermatozoon’s head and mid-piece and improves its motility and fertilizing ability in the domestic cat ¹⁹

In the News

In a recent blog post Being a better programmer and scientist with rOpenSci Matt Boone of the Mablab at University of Florida (and an author on the refnet package under rOpenSci review) wrote about R and programming, and did a nice job of describing our software review system.

In an August 15th article in Forbes Restrict Twice-As-Deadly SUVs In U.K. Cities, Urge Transport Data Scientists, the data used was from the stplanr package maintained by Robin Lovelace and others. See also Robin’s tweet about the article.

From the Forum

We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.

The Trafford Data Lab supports government decision-making in Trafford, Greater Manchester, UK. They shared use cases for ropenaq to retrieve air quality information from the Manchester Piccadilly monitoring station, fingertipsR to access public health data on the rate of antidepressant prescribing, and ghql to query linked data to map hot and cold spots of worklessness and improve public services.

fingertips_use_case

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:

RSelenium: now maintained by Ju Kim
chromer: now maintained by Paula Andrea
qualtRics: now maintained by Julia Silge
rsnps: now maintained by Julia Gustavsen and Sina Rüeger
rdpla: now maintained by Alyssa Columbus
webchem: now maintained by Erik Sapper

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

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Footnotes

Yen, Y., Zhao, P., & Sohail, M. T. (2019). The morphology and circuity of walkable, bikeable, and drivable street networks in Phnom Penh, Cambodia. Environment and Planning B: Urban Analytics and City Science, 239980831985772. https://doi.org/10.1177/2399808319857726 ↩
Danella Figo, D., De Amicis, K., Neiva Santos de Aquino, D., Pomiecinski, F., Gadermaier, G., Briza, P., … Souza Santos, K. (2019). Cashew Tree Pollen: An Unknown Source of IgE-Reactive Molecules. International Journal of Molecular Sciences, 20(10), 2397. https://doi.org/10.3390/ijms20102397 ↩
Kanterakis, G., Skoulikaris, C., & Dimitriou, E. Assessment of hydrological modelling behaviour at basin scale on the number of delineated sub-basins. Proceedings of the Seventh International Conference on Environmental Management, Engineering, Planning & Economics https://www.researchgate.net/profile/Charalampos_Skoulikaris/publication/333652500_Assessment_of_hydrological_modelling_behaviour_at_basin_scale_on_the_number_of_delineated_sub-basins/links/5cfa46ba4585157d15991da1/Assessment-of-hydrological-modelling-behaviour-at-basin-scale-on-the-number-of-delineated-sub-basins.pdf ↩
Petrik, C. M., Stock, C. A., Andersen, K. H., van Denderen, P. D., & Watson, J. R. (2019). Bottom-up drivers of global patterns of demersal, forage, and pelagic fishes. Progress in Oceanography, 176, 102124. https://doi.org/10.1016/j.pocean.2019.102124 ↩
Calderone, A. (2019). A Computational Analysis of Natural Languages to Build a Sentence Structure Aware Artificial Neural Network. arXiv preprint arXiv:1906.05491 https://arxiv.org/pdf/1906.05491.pdf ↩
Uzma, Jiménez-Mejías, P., Amir, R., Hayat, M. Q., & Hipp, A. L. (2019). Timing and ecological priority shaped the diversification of sedges in the Himalayas. PeerJ, 7, e6792. https://doi.org/10.7717/peerj.6792 ↩
Baylis, A. M. M., Tierney, M., Orben, R. A., Warwick-Evans, V., Wakefield, E., Grecian, W. J., … Brickle, P. (2019). Important At-Sea Areas of Colonial Breeding Marine Predators on the Southern Patagonian Shelf. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-44695-1 ↩
Nourbakhsh, M., Mansoor, A., Koro, K., Zhang, Q., & Minoo, P. (2019). Expression Profiling Reveals Involvement of WNT Pathway in the Malignant Progression of Sessile Serrated Adenomas. The American Journal of Pathology. https://doi.org/10.1016/j.ajpath.2019.05.009 ↩
Waller, J. (2019). Data Location Quality at GBIF. Biodiversity Information Science and Standards, 3. https://doi.org/10.3897/biss.3.35829 ↩
Shackleton, M. E., Rees, G. N., Watson, G., Campbell, C., & Nielsen, D. (2019). Environmental DNA reveals landscape mosaic of wetland plant communities. Global Ecology and Conservation, 19, e00689. https://doi.org/10.1016/j.gecco.2019.e00689 ↩
Nelli, L., Ferguson, H. M., & Matthiopoulos, J. (2019). Achieving explanatory depth and spatial breadth in infectious disease modelling: Integrating active and passive case surveillance. Statistical Methods in Medical Research, 096228021985638. https://doi.org/10.1177/0962280219856380 ↩
Glicksberg, B. S., Oskotsky, B., Thangaraj, P. M., Giangreco, N., Badgeley, M. A., Johnson, K. W., … Butte, A. J. (2019). PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz409 ↩
Brown, E. E., Rashidi‐Ranjbar, N., Caravaggio, F., Gerretsen, P., Pollock, B. G., … Mulsant, B. H. (2019). Brain Amyloid PET Tracer Delivery is Related to White Matter Integrity in Patients with Mild Cognitive Impairment. Journal of Neuroimaging. https://doi.org/10.1111/jon.12646 ↩
Koppelstaetter, C., Leierer, J., Rudnicki, M., Kerschbaum, J., Kronbichler, A., Melk, A., … Perco, P. (2019). Computational Drug Screening Identifies Compounds Targeting Renal Age-associated Molecular Profiles. Computational and Structural Biotechnology Journal, 17, 843–853. https://doi.org/10.1016/j.csbj.2019.06.019 ↩
Calero Valdez A., Ziefle M. (2019) Trends and Changes in the Field of HCI the Last Decade from the Perspective of HCII Conference. In: Kurosu M. (eds) Human-Computer Interaction. Perspectives on Design. HCII 2019. Lecture Notes in Computer Science, vol 11566. Springer, Cham https://doi.org/10.1007/978-3-030-22646-6_3 ↩
Alfaro, M. E., Karan, E., Schwartz, S. T., & Shultz, A. J. (2019). The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae). Integrative and comparative biology. https://academic.oup.com/icb/advance-article-abstract/doi/10.1093/icb/icz119/5530961 ↩
Butterfield, B. J., Holmgren, C. A., Anderson, R. S., & Betancourt, J. L. (2019). Life history traits predict colonization and extinction lags of desert plant species since the Last Glacial Maximum. Ecology. https://doi.org/10.1002/ecy.2817 ↩
Kovalenko, K. E., Johnson, L. B., Brady, V. J., Ciborowski, J. J. H., Cooper, M. J., Gathman, J. P., … Uzarski, D. G. (2019). Hotspots and bright spots in functional and taxonomic fish diversity. Freshwater Science, 000–000. https://doi.org/10.1086/704713 ↩
Ferraz, M. de A. M. M., Carothers, A., Dahal, R., Noonan, M. J., & Songsasen, N. (2019). Oviductal extracellular vesicles interact with the spermatozoon’s head and mid-piece and improves its motility and fertilizing ability in the domestic cat. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-45857-x ↩