Nov 11, 2019
rOpenSci HQ
rOpenSci Announces a New $896k Award From The Gordon and Betty Moore Foundation to Improve the Scientific Package Ecosystem for R. Read the blog post by Karthik Ram
Software 📦
CRAN: GitHub:
New Versions
- A new version (
v2.3
) ofpdftools
is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started.pdf_text() improvements; new fxns pdf_ocr_text/pdf_ocr_data wrap tesseract
- A new version (
v0.5.3
) ofgender
is on CRAN - Predict gender from names using historical data. See the release notes for changes. Checkout the vignette to get started.docs improvements, testing fixes
- A new version (
v2.4.0
) ofRNeXML
is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the vignettes to get started.use Additional_repositories for taxadb
- A new version (
v0.2.0
) ofcitecorp
is on CRAN - client for the Open Citations Corpus. See the release notes for changes. Checkout the docs to get started.oc_doi2ids/oc_pmid2ids/oc_pmcid2ids functions now vectorized; bug fixes
- A new version (
v0.9.4
) ofrnoaa
is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started.new gefs fxns gefs_dimensions/gefs_ensembles; gefs fxn fixes; argo family fxns no longer work as API is gone - but FTP fxns still work (
argo_guoy_files()
/argo()
) - A new version (
v0.2.3
) oftidync
is on CRAN - a tidy approach to NetCDF data exploration and extraction. See the release notes for changes. Checkout the docs to get started.test fixes
- A new version (
v0.9.0
) ofcrul
is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started.HttpResponse object gains methods for checking response content type; head verb now uses auth correctly
- A new version (
v1.0.4
) ofessurvey
is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.1.4
) ofsolrium
is on CRAN - general purpose R interface to Solr. See the release notes for changes. Checkout the vignettes to get started.fix
delete_by_query()
/$delete_by_query()
method - A new version (
v1.0.2
) ofspocc
is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started.fix failing tests on cran
- A new version (
v1.4.0
) ofrgbif
is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started.new fxn
mvt_fetch()
for GBIF’s Map Vector Tiles; overhaul ofocc_issues
/name_issues
fxns; many fixes - A new version (
v0.8.0
) ofgeojsonio
is on CRAN - Convert Data from and to GeoJSON or TopoJSON. See the release notes for changes. Checkout the vignettes to get started.geojson_read()
gains method for PostGIS;geojson_read()
now uses sf instead of sp;geojson_list()
gains precision param; bug fixes - A new version (
v0.8.0
) ofritis
is on CRAN - an R client for ITIS (Integrated Taxonomic Information Service). See the release notes for changes. Checkout the docs to get started.improve
itis_search()
examples; bug fix foritis_group()
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:
- dbparser > DrugBank Database XML Parser
- Author: Mohammed Ali
- Issue: ropensci/onboarding#347
- Reviewers: not yet assigned
The following packages recently went through our software review process and have been approved:
- workloopR > Analysis of Work Loops and Other Data from Muscle Physiology Experiments
- Author: Vikram Baliga
- Issue: ropensci/onboarding#326
- Reviewers:
- eia > API Wrapper for ‘US Energy Information Administration’ Open Data
- Author: Matthew Leonawicz
- Issue: ropensci/onboarding#342
- Reviewers:
- photosearcher > Searches Flickr for photographs and metadata
- Author: Nathan Fox
- Issue: ropensci/onboarding#325
- Reviewers:
On the blog
Michael Quinn and Elin Waring wrote about a new version (v2) of their package skimr - (Re)introducing skimr v2 - A year in the life of an open source R project
Michael Sumner wrote about his package tidync that was recently approved in rOpenSci software review - tidync: scientific array data from NetCDF in R
Use Cases
The following 15 works use/cite rOpenSci software:
- Palstrøm et al. used writexl in their paper Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets 1
- Cinelli et al. used hunspell in their paper The interconnectedness of the economic content in the speeches of the US Presidents 2
- Umlauf et al. used [rnaturalearth][] in their paper bamlss: A Lego Toolbox for Flexible Bayesian Regression 3
- Bager Olsen et al. used rredlist in their paper Thirty-six years of legal and illegal wildlife trade entering the USA 4
- Vidal et al. used brranching in their paper Geography is more important than host plant use for the population genetic structure of a generalist insect herbivore 5
- De Luca et al. used rgbif in their paper Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies 6
- Ondra used [camsRad][] in their paper Reliability based design approach to stochastic supply planning 7
- Wang et al. used neotoma in their paper Bayesian ages for pollen records since the last glaciation in North America 8
- Nalborczyk et al. used skimr in their paper Can we decode phonetic features in inner speech using surface electromyography? 9
- Stanstrup et al. used webchem in their paper The metaRbolomics Toolbox in Bioconductor and beyond 10
- Feng et al. used CoordinateCleaner in their paper A checklist for maximizing reproducibility of ecological niche models 11
- Duffany used hunspell in their paper Developing CyberSecurity Skills with Intermediate Programming Courses 12
- Maherali used rotl in their paper Mutualism as a plant functional trait: linking variation in the mycorrhizal symbiosis to climatic tolerance, geographic range and population dynamics 13
- Havinga et al. used rgbif in their paper Spatial quantification to examine the effectiveness of payments for ecosystem services: A case study of Costa Rica’s Pago de Servicios Ambientales 14
- Jin et al. used tokenizers in their paper Mining consumer complaints to identify unsuccessful interactions with advanced driver assistance systems 15
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. 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
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Palstrøm N.B., Matthiesen R., Beck H.C. (2020) Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets. In: Matthiesen R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 2051. Humana, New York, NY https://doi.org/10.1007/978-1-4939-9744-2_13 ↩
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Cinelli, M., Ficcadenti, V., & Riccioni, J. (2019). The interconnectedness of the economic content in the speeches of the US Presidents. Annals of Operations Research. https://doi.org/10.1007/s10479-019-03372-2 ↩
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Umlauf, N., Klein, N., Simon, T., & Zeileis, A. (2019). bamlss: A Lego Toolbox for Flexible Bayesian Regression (and Beyond). arXiv preprint arXiv:1909.11784. https://arxiv.org/abs/1909.11784 ↩
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Bager Olsen, M. T., Geldmann, J., Harfoot, M., Tittensor, D. P., Price, B., Sinovas, P., … Burgess, N. D. (2019). Thirty-six years of legal and illegal wildlife trade entering the USA. Oryx, 1–10. https://doi.org/10.1017/s0030605319000541 ↩
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Vidal, M. C., Quinn, T. W., Stireman, J. O., Tinghitella, R. M., & Murphy, S. M. (2019). Geography is more important than host plant use for the population genetic structure of a generalist insect herbivore. Molecular Ecology. https://doi.org/10.1111/mec.15218 ↩
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De Luca, D., Kooistra, W. H. C. F., Sarno, D., Gaonkar, C. C., & Piredda, R. (2019). Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies. PeerJ, 7, e7410. https://doi.org/10.7717/peerj.7410 ↩
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Ondra, M. 2019. Reliability based design approach to stochastic supply planning. https://iaee2019ljubljana.oyco.eu/download/contribution/fullpaper/345/345_fullpaper_20190608_130510.pdf ↩
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Wang, Y., Goring, S. J., & McGuire, J. L. (2019). Bayesian ages for pollen records since the last glaciation in North America. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0182-7 ↩
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Nalborczyk, L., Grandchamp, R., Koster, E. H. W., Perrone-Bertolotti, M., & Loevenbruck, H. (2019). Can we decode phonetic features in inner speech using surface electromyography? https://doi.org/10.31234/osf.io/8v5yd ↩
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Stanstrup, J., Broeckling, C., Helmus, R., Hoffmann, N., Mathé, E., Naake, T., … Neumann, S. (2019). The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites, 9(10), 200. https://doi.org/10.3390/metabo9100200 ↩
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Feng, X., Park, D. S., Walker, C., Peterson, A. T., Merow, C., & Papeş, M. (2019). A checklist for maximizing reproducibility of ecological niche models. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-019-0972-5 ↩
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Duffany, J. (2019). Developing CyberSecurity Skills with Intermediate Programming Courses. Proceedings of the 17th LACCEI International Multi-Conference for Engineering, Education, and Technology: “Industry, Innovation, and Infrastructure for Sustainable Cities and Communities.” https://doi.org/10.18687/laccei2019.1.1.414 ↩
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Maherali, H. (2019). Mutualism as a plant functional trait: linking variation in the mycorrhizal symbiosis to climatic tolerance, geographic range and population dynamics. International Journal of Plant Sciences. https://doi.org/10.1086/706187 ↩
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Havinga, I., Hein, L., Vega-Araya, M., & Languillaume, A. (2020). Spatial quantification to examine the effectiveness of payments for ecosystem services: A case study of Costa Rica’s Pago de Servicios Ambientales. Ecological Indicators, 108, 105766. https://doi.org/10.1016/j.ecolind.2019.105766 ↩
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Jin, L., Tefft, B. C., & Horrey, W. J. (2019). Mining consumer complaints to identify unsuccessful interactions with advanced driver assistance systems. Proceedings of the 11th International Conference on Automotive User Interfaces and Interactive Vehicular Applications Adjunct Proceedings - AutomotiveUI ’19. https://doi.org/10.1145/3349263.3351313 ↩