2019-10-14

rOpenSci HQ

What would you like to hear about in an rOpenSci Community Call? We are soliciting your “votes” and new ideas for Community Call topics and speakers. Find out how you can influence us by checking out our new Community Calls repository.
One of our next Community Calls will be about testing. Tell us what you want to know about it or who you’d like to hear from by commenting in our new Community Calls repository.
Help wanted! We encourage rOpenSci package authors to help us help you get more contributors to your package. If you label an issue “help wanted” (no hyphen or emojis), those issues can be found in a search of the rOpenSci organization; and on the rOpenSci GitHub landing page https://github.com/ropensci the number of open help wanted issues is highlighted for each package that has them.

Software 📦

CRAN: GitHub:

New Packages

The first version (v0.1.2) of chlorpromazineR is on CRAN - convert antipsychotic doses to chlorpromazine equivalents. Checkout the docs to get started. This package recently went through rOpenSci software review.
The first version (v2.0.0) of rmangal is on CRAN - interface to the Mangal database of ecological networks. Checkout the docs to get started. This package recently went through rOpenSci software review.

New Versions

A new version (v0.4.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

family of new fxns for adding new nodes to routes, route networks and sfNetwork objects; other new fxns
A new version (v0.4.0) of ckanr is on CRAN - R client for the CKAN API. See the release notes for changes. Checkout the docs to get started.

^^ improvements to ckan_fetch fxn (thanks Sharla Gelfand)
A new version (v0.3.0) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the vignette to get started.

now supports EML v2.2; fixed xml parsing issue; eml_validate change
A new version (v1.2.7) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started.

vignette updated; new datasets added; bug fixes
A new version (v1.4.2) 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.

Update GitHub links in ring_app_launch function

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:

taxadb > A High-Performance Local Taxonomic Database Interface
- Author: Kari Norman
- Issue: ropensci/onboarding#344
- Reviewers:
  - Margaret Siple
  - Lindsay Platt

On the blog

There’s a new version of the rOpenSci Dev Guide out. The software review editors wrote up a post describing the accumulated changes since v0.2: rOpenSci Dev Guide 0.3.0: Updates. Some highlights:

Categories of packages we accept have been modified, make sure to read our new Aims and Scope section
Package documentation has become a lot easier for packages under rOpenSci. Read Jeroen’s post Introducing the new rOpenSci docs server and the new section on Automatic deployment of the documentation website.

Technical notes

Scott Chamberlain wrote a post on updates to the cran checks API. The API now has a route to get CRAN check results by maintainer, badges for CRAN checks with a number of different scenarios, and gives access to recent (30 day), and older (back to December 2018) checks data.

Use Cases

The following 18 works use/cite rOpenSci software:

Ayodele Benjamin et al. used writexl in their paper Data-based investigation on the performance of an independent Gas turbine for electricity generation using real power measurements and other closely related parameters ¹
Mendes et al. used plotly in their paper Point-Placement Techniques and Temporal Self-Similarity Maps for Visual Analysis of Surveillance Videos ²
Stewart et al. used plotly in their paper Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection ³
Lewis et al. used plotly in their paper Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes ⁴
Esperon‐Rodriguez et al. used taxize and rgbif in their paper Assessing the vulnerability of Australia’s urban forests to climate extremes ⁵
Lacy et al. used rfishbase in their paper Main drivers of freshwater fish diversity across extra-tropical Southern Hemisphere rivers ⁶
Gonçalves et al. used plotly in their paper Extracting spatial-temporal features that describe a team match demands when considering the effects of the quality of opposition in elite football ⁷
Urquhart-Cronish & Otto used gender in their paper Gender and language use in scientific grant writing ⁸
Wegrzyn et al. used biomartr in their paper Cyberinfrastructure and resources to enable an integrative approach to studying forest trees ⁹
Redmond et al. used brranching in their paper The cost of standing tall: wood nutrients associated with tree invasions in nutrient‐poor fynbos soils of South Africa ¹⁰
Hanna & Hanna used pdftools in their paper Topic Analysis of UK Fitness to Practise Cases: What Lessons Can Be Learnt? ¹¹
Ramagopalan et al. used hunspell in their paper Automated extraction of treatment patterns from social media posts: an exploratory analysis in renal cell carcinoma ¹²
Bayley et al. used rfishbase in their paper Evaluating the efficacy of small‐scale marine protected areas for preserving reef health: A case study applying emerging monitoring technology ¹³
Mihalitsis & Bellwood used rotl in their paper Functional implications of dentition-based morphotypes in piscivorous fishes ¹⁴
Greco et al. used pangaear in their paper Depth habitat of the planktonic foraminifera Neogloboquadrina pachyderma in the northern high latitudes explained by sea-ice and chlorophyll concentrations ¹⁵
Flower used rgbif in their paper Food Plant Biogeography of the Sonoran Desert ¹⁶
Rebolj et al. used fingertipsR in their paper Concurrent participation in screening for cervical, breast, and bowel cancer in England ¹⁷
Sun et al. used rAltmetric in their paper Reporting gaps between news media and scientific papers on outdoor air pollution–related health outcomes: A content analysis ¹⁸

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.

Matt Dray filed a use case on Can {drake} RAP? Promoting {drake} for pipeline management in UK government. The drake package is maintained by Will Landau.

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’ve got one package in need of a new maintainer:

mregions: The current maintainer Scott Chamberlain is looking for a new maintainer. Email Scott if you’re interested.

Keep up with rOpenSci

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Footnotes

Ayodele Benjamin, E., Vincent, E., Claudius, A., Olatomiwa, L., & Dickson, E. (2019). Data-based investigation on the performance of an independent Gas turbine for electricity generation using real power measurements and other closely related parameters. Data in Brief, 104444. https://doi.org/10.1016/j.dib.2019.104444 ↩
Mendes, G., Paiva, J. G. S., & Schwartz, W. R. (2019, July). Point-Placement Techniques and Temporal Self-Similarity Maps for Visual Analysis of Surveillance Videos. In 2019 23rd International Conference Information Visualisation (IV) (pp. 127-132). IEEE. https://ieeexplore.ieee.org/iel7/8798596/8811888/08811966.pdf ↩
Stewart, D. B., Wright, J. R., Fowler, M., McLimans, C. J., Tokarev, V., Amaniera, I., … Lamendella, R. (2019). Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection. mSphere, 4(4). https://doi.org/10.1128/msphere.00454-19 ↩
Lewis, M. J., Barnes, M. R., Blighe, K., Goldmann, K., Rana, S., Hackney, J. A., … Pitzalis, C. (2019). Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes. Cell Reports, 28(9), 2455–2470.e5. https://doi.org/10.1016/j.celrep.2019.07.091 ↩
Esperon‐Rodriguez, M., Power, S. A., Tjoelker, M. G., Beaumont, L. J., Burley, H., Caballero‐Rodriguez, D., & Rymer, P. D. (2019). Assessing the vulnerability of Australia’s urban forests to climate extremes. Plants, People, Planet. https://doi.org/10.1002/ppp3.10064 ↩
Lacy, S. N., Corcoran, D., Alò, D., Lessmann, J., Meza, F., & Marquet, P. A. (2019). Main drivers of freshwater fish diversity across extra-tropical Southern Hemisphere rivers. Hydrobiologia. https://doi.org/10.1007/s10750-019-04044-9 ↩
Gonçalves, B., Coutinho, D., Exel, J., Travassos, B., Lago, C., & Sampaio, J. (2019). Extracting spatial-temporal features that describe a team match demands when considering the effects of the quality of opposition in elite football. PLOS ONE, 14(8), e0221368. https://doi.org/10.1371/journal.pone.0221368 ↩
Urquhart-Cronish, M., & Otto, S. P. (2019). Gender and language use in scientific grant writing. FACETS, 4(1), 442–458. https://doi.org/10.1139/facets-2018-0039 ↩
Wegrzyn, J. L., Falk, T., Grau, E., Buehler, S., Ramnath, R., & Herndon, N. (2019). Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. Evolutionary Applications. https://doi.org/10.1111/eva.12860 ↩
Redmond, M. D., Morris, T. L., & Cramer, M. C. (2019). The cost of standing tall: wood nutrients associated with tree invasions in nutrient‐poor fynbos soils of South Africa. Ecosphere, 10(9). https://doi.org/10.1002/ecs2.2831 ↩
Hanna, A., & Hanna, L.-A. (2019). Topic Analysis of UK Fitness to Practise Cases: What Lessons Can Be Learnt? Pharmacy, 7(3), 130. https://doi.org/10.3390/pharmacy7030130 ↩
Ramagopalan, S. V., Malcolm, B., Merinopoulou, E., McDonald, L., & Cox, A. (2019). Automated extraction of treatment patterns from social media posts: an exploratory analysis in renal cell carcinoma. Future Oncology. https://doi.org/10.2217/fon-2019-0406 ↩
Bayley, D. T. I., Mogg, A. O. M., Purvis, A., & Koldewey, H. J. (2019). Evaluating the efficacy of small‐scale marine protected areas for preserving reef health: A case study applying emerging monitoring technology. Aquatic Conservation: Marine and Freshwater Ecosystems. https://doi.org/10.1002/aqc.3215 ↩
Mihalitsis, M., & Bellwood, D. (2019). Functional implications of dentition-based morphotypes in piscivorous fishes. Royal Society Open Science, 6(9), 190040. https://doi.org/10.1098/rsos.190040 ↩
Greco, M., Jonkers, L., Kretschmer, K., Bijma, J., & Kucera, M. (2019). Depth habitat of the planktonic foraminifera Neogloboquadrina pachyderma in the northern high latitudes explained by sea-ice and chlorophyll concentrations. Biogeosciences, 16(17), 3425–3437. https://doi.org/10.5194/bg-16-3425-2019 ↩
Flower, C. (2019). Food Plant Biogeography of the Sonoran Desert (Doctoral dissertation, Arizona State University). https://search.proquest.com/docview/2275500833 ↩
Rebolj, M., Parmar, D., Maroni, R., Blyuss, O., & Duffy, S. W. (In press). Concurrent participation in screening for cervical, breast, and bowel cancer in England. Journal of Medical Screening. ↩
Sun, Z., Cang, J., Ruan, Y., & Zhu, D. (2019). Reporting gaps between news media and scientific papers on outdoor air pollution–related health outcomes: A content analysis. The International Journal of Health Planning and Management. https://doi.org/10.1002/hpm.2894 ↩