2020-12-14

rOpenSci HQ

Community Calls

Join us for our next Community Call - The Wild World of Data Repositories - this Wednesday, December 16th, 2020 (10-11 AM PST). This call will be moderated by Kara Woo with speakers Daniella Lowenberg, Matt Jones, Carl Boettiger and Karthik Ram.

Software 📦

CRAN: GitHub:

New Packages

The first version (v0.1.1) of outsider is on CRAN - “Install and Run Programs, Outside of R, Inside of R”. Checkout the docs to get started.
The first version (v0.0.2) of allcontributors is on CRAN - Acknowledge all Contributors to a Project. Checkout the docs to get started.

New Versions

A new version (v0.6.0) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started.
A new version (v0.0.4) of medrxivr is on CRAN - access and search MedRxiv and BioRxiv preprint data. See the release notes for changes. Checkout the docs to get started.
A new version (v3.0.1) of hunspell is on CRAN - High-Performance stemmer, tokenizer, and spell checker. See the release notes for changes. Checkout the vignette to get started.
A new version (v0.3.1) of tacmagic is on CRAN - positron emission tomography time-activity curve analysis. See the release notes for changes. Checkout the vignette to get started.
A new version (v0.7.4) 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.
A new version (v1.13) of mcbette is on CRAN - model comparison using babette. See the release notes for changes. Checkout the docs to get started.
A new version (v0.2.0) of prism is on CRAN - Data from the Oregon State Prism Climate Project. See the release notes for changes. Checkout the vignette to get started.
A new version (v3.4.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started.
A new version (v0.3.0) of jaod is on CRAN - Directory of Open Access Journals client. See the release notes for changes. Checkout the docs to get started.
A new version (v1.1.1) of rnpn is on CRAN - Interface to the National Phenology Network API. See the release notes for changes. Checkout the docs to get started.
A new version (v0.7.3) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started.
A new version (v0.7.1) of rdhs is on CRAN - Client for Demographic and Health Survey (DHS) Data. See the release notes for changes. Checkout the docs to get started.
A new version (v0.4.3) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started.
A new version (v0.0.10) of phonfieldwork is on CRAN - linguistic phonetic fieldwork tools. See the release notes for changes. Checkout the docs to get started.
A new version (v1.3.6) 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.

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 packages were recently submitted:

censo2017 > Base de Datos de Facil Acceso del Censo 2017 de Chile (2017 Chilean Census Easy Access Database)
- Author: Pachá
- Issue: ropensci/software-review#414
- Reviewers:
  - Frans van Dunné
  - Ana Laura Diedrichs
terrainr > Retrieve Data from the USGS National Map and Transform it for 3D Landscape Visualizations
- Author: Michael Mahoney
- Issue: ropensci/software-review#416
- Reviewers: not yet assigned

On the blog

Richèl Bilderbeek wrote about using his mcbette package for: Selecting the Best Phylogenetic Evolutionary Model

Dennis Irorere wrote a post about solving a problem using a GraphQL service using the rOpenSci package ghql: Accessing GrahpQL from R

Citations

The following 22 works use/cite rOpenSci software:

Reimuth & Zotz used CoordinateCleaner in their paper The biogeography of the megadiverse genus Anthurium (Araceae ¹
Yu et al. used fingertipsR in their paper Impact of Vertical Integration of General Practices with an Acute Hospital on Hospital Admissions: a Retrospective Synthetic Matched Controlled Database Study. ²
Koch et al. used rgbif in their paper Bats as putative Zaire ebolavirus reservoir hosts and their habitat suitability in Africa ³
Göbel used cld2 in their paper Voting and Social Media-Based Political Participation ⁴
Larouche et al. used rfishbase in their paper Reef-associated fishes have more maneuverable body shapes at a macroevolutionary scale ⁵
De Sousa & Solberg used rgbif in their paper Conservation Gaps in Traditional Vegetables Native to Europe and Fennoscandia ⁶
Polaina et al. used rgbif and CoordinateCleaner in their paper Identifying hotspots of invasive alien terrestrial vertebrates in Europe to assist transboundary prevention and control ⁷
Ihaka & Gentleman used rentrez in their paper R: A Language for Data Analysis and Graphics ⁸
Mothes et al. used CoordinateCleaner in their paper Habitat suitability models for the imperiled wood turtle (Glyptemys insculpta) raise concerns for the species’ persistence under future climate change ⁹
Scott used skimr in their paper Spatial variation in PM2. 5 concentrations across Timaru ¹⁰
Tonnis et al. used rnoaa in their paper Peanut FAD2 Genotype and Growing Location Interactions Significantly Affect the Level of Oleic Acid in Seeds ¹¹
Da Silva Abel et al. used MODIStsp in their paper Environmental dynamics of the Juruá watershed in the Amazon. Environment, Development and Sustainability ¹²
Vantas et al. used hydroscoper in their paper Estimating Rainfall Erosivity from Daily Precipitation Using Generalized Additive Models ¹³
Weber used pangaear in their paper Digital elevation models of German waterway and navigation ¹⁴
Nania et al. used CoordinateCleaner in their paper Continuous expansion of the geographic range linked to realized niche expansion in the invasive Mourning gecko Lepidodactylus lugubris (Duméril & Bibron, 1836 ¹⁵
Keppeler et al. used rfishbase in their paper The relationship between trophic level and body size in fishes depends on functional traits ¹⁶
Doyle et al. used bomrang in their paper Unintended Consequences of Welfare Reform: Evidence from Birth Outcomes of Aboriginal Australians ¹⁷
Sass et al. used rtweet in their paper Exploring social media data to understand consumers’ perception of eggs: A multilingual study using Twitter ¹⁸
Allerton used brranching in their paper Functional Attributes of Post-Disturbance Regeneration in Puerto Rican Tropical Dry Forest ¹⁹
Davies et al. used rotl in their paper A meta-analysis of factors influencing the strength of mate-choice copying in animals ²⁰
Becker & Han used rredlist in their paper The macroecology and evolution of avian competence for Borrelia burgdorferi ²¹
Greenville et al. used rredlist in their paper Simultaneously operating threats cannot predict extinction risk ²²

Call For Maintainers

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. Check out our guidance for taking over maintenance of a package.

We’ve had eight 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
webchem: now maintained by Erik Sapper
mregions: now maintained by Lennert Schepers (VLIZ)
rWBclimate: now maintained by Sergio Ibarra-Espinosa and Amanda Rehbein
rinat: now maintained by Stéphane Guillou

Get involved with rOpenSci

We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.

Keep up with rOpenSci

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Footnotes

Reimuth, J., & Zotz, G. (2020). The biogeography of the megadiverse genus Anthurium (Araceae). Botanical Journal of the Linnean Society, 194(2), 164-176. https://doi.org/10.1093/botlinnean/boaa044 ↩
Yu, V., Wyatt, S., Woodall, M., Sultan, M., Klaire, V., Bailey, K., & Mohammed, M. A. (2020). Impact of Vertical Integration of General Practices with an Acute Hospital on Hospital Admissions: a Retrospective Synthetic Matched Controlled Database Study. https://bit.ly/3gN1omx ↩
Koch, L. K., Cunze, S., Kochmann, J., & Klimpel, S. (2020). Bats as putative Zaire ebolavirus reservoir hosts and their habitat suitability in Africa. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-71226-0 ↩
Göbel, S. (2020). Voting and Social Media-Based Political Participation. SocArXiv https://doi.org/10.31235/osf.io/sjq4g ↩
Larouche, O., Benton, B., Corn, K. A., Friedman, S. T., Gross, D., Iwan, M., … Price, S. A. (2020). Reef-associated fishes have more maneuverable body shapes at a macroevolutionary scale. Coral Reefs, 39(5), 1427–1439. https://doi.org/10.1007/s00338-020-01976-w ↩
De Sousa, K., & Solberg, S. Ø. (2020). Conservation Gaps in Traditional Vegetables Native to Europe and Fennoscandia. Agriculture, 10(8), 340. https://doi.org/10.3390/agriculture10080340 ↩
Polaina, E., Pärt, T., & Recio, M. R. (2020). Identifying hotspots of invasive alien terrestrial vertebrates in Europe to assist transboundary prevention and control. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-68387-3 ↩
Ihaka, R., & Gentleman, R. (1996). R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics, 5(3), 299–314. https://doi.org/10.1080/10618600.1996.10474713 ↩
Mothes, C. C., Howell, H. J., & Searcy, C. A. (2020). Habitat suitability models for the imperiled wood turtle (Glyptemys insculpta) raise concerns for the species’ persistence under future climate change. Global Ecology and Conservation, 24, e01247. https://doi.org/10.1016/j.gecco.2020.e01247 ↩
Scott, A. 2020. Spatial variation in PM2. 5 concentrations across Timaru. Report, Environment Canterbury Regional Council https://bit.ly/3icvorg ↩
Tonnis, B., Wang, M. L., Li, X., Wang, J., Puppala, N., Tallury, S., & Yu, J. (2020). Peanut FAD2 Genotype and Growing Location Interactions Significantly Affect the Level of Oleic Acid in Seeds. Journal of the American Oil Chemists’ Society, 97(9), 1001–1010. https://doi.org/10.1002/aocs.12401 ↩
Da Silva Abel, E. L., Delgado, R. C., Vilanova, R. S., Teodoro, P. E., da Silva Junior, C. A., Abreu, M. C., & Silva, G. F. C. (2020). Environmental dynamics of the Juruá watershed in the Amazon. Environment, Development and Sustainability. https://doi.org/10.1007/s10668-020-00890-z ↩
Vantas, K., Sidiropoulos, E., & Evangelides, C. (2020). Estimating Rainfall Erosivity from Daily Precipitation Using Generalized Additive Models. Environmental Sciences Proceedings, 2(1), 21. https://doi.org/10.3390/environsciproc2020002021 ↩
Weber, A. (2020). Digital elevation models of German waterway and navigation. Report. http://doi.bafg.de/BfG/2020/BfG-2011.pdf ↩
Nania, D., Flecks, M., & Rödder, D. (2020). Continuous expansion of the geographic range linked to realized niche expansion in the invasive Mourning gecko Lepidodactylus lugubris (Duméril & Bibron, 1836). PLOS ONE, 15(7), e0235060. https://doi.org/10.1371/journal.pone.0235060 ↩
Keppeler, F. W., Montaña, C. G., & Winemiller, K. O. (2020). The relationship between trophic level and body size in fishes depends on functional traits. Ecological Monographs. https://doi.org/10.1002/ecm.1415 ↩
Doyle, M. A., Schurer, S., & Silburn, S. (2020). Unintended Consequences of Welfare Reform: Evidence from Birth Outcomes of Aboriginal Australians. SSRN. http://ftp.iza.org/dp13543.pdf ↩
Sass, C. A. B., Pimentel, T. C., Aleixo, M. G. B., Dantas, T. M., Cyrino Oliveira, F. L., Freitas, M. Q., … Esmerino, E. A. (2020). Exploring social media data to understand consumers’ perception of eggs: A multilingual study using Twitter. Journal of Sensory Studies. https://doi.org/10.1111/joss.12607 ↩
Allerton, T. A. P. (2020). Functional Attributes of Post-Disturbance Regeneration in Puerto Rican Tropical Dry Forest. Dissertation Thesis. https://bit.ly/2R9upwT ↩
Davies, A. D., Lewis, Z., & Dougherty, L. R. (2020). A meta-analysis of factors influencing the strength of mate-choice copying in animals. Behavioral Ecology. https://doi.org/10.1093/beheco/araa064 ↩
Becker, D. J., & Han, B. A. (2020). The macroecology and evolution of avian competence for Borrelia burgdorferi. bioRxiv https://doi.org/10.1101/2020.04.15.040352 ↩
Greenville, A. C., Newsome, T. M., Wardle, G. M., Dickman, C. R., Ripple, W. J., & Murray, B. R. (2020). Simultaneously operating threats cannot predict extinction risk. Conservation Letters. https://doi.org/10.1111/conl.12758 ↩