Mar 2, 2020
rOpenSci HQ
- Join us for our next Community Call - Maintaining an R package - on March 18, 2020, with Julia Silge, Leonardo Collado Torres, Erin Grand, Elin Waring, and Scott Chamberlain.
Software š¦
CRAN: GitHub:
New Packages
- The first version (
v0.2.8
) ofosfr
is on CRAN - interface to the Open Science Framework (OSF). See the release notes for changes. Checkout the docs to get started. - The first version (
v0.1.0
) oftaxadb
is on CRAN - a local taxonomic database interface. Checkout the docs to get started. - The first version (
v0.1.0
) ofoutsider.base
is on CRAN - base package for outsider. Checkout the docs to get started.
New Versions
- A new version (
v1.0.3
) ofcyphr
is on CRAN - high level encryption wrappers. See the release notes for changes. Checkout the docs to get started.fix test for stringsAsFactors change for R v4
- A new version (
v0.2.1
) ofgit2rdata
is on CRAN - store and retrieve data.frames in a Git repository. See the release notes for changes. Checkout the docs to get started.fix examples and tests for stringsAsFactors change for R v4
- A new version (
v0.5.0
) ofwebchem
is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started.new data sources; many bug fixes
- A new version (
v0.6.0
) ofwebmockr
is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started.improved function reference in docs site; fixes for JSON encoded body requests; many other fixes
- A new version (
v7.11.0
) ofdrake
is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.allow dynamic files; many improvements and bug fixes
- A new version (
v1.1.2
) oflingtypology
is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started.many parameter name changes across functions; fixes for stringsAsFactors change for R v4
- A new version (
v2.4.3
) ofRNeXML
is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the docs to get started.fix tests for stringsAsFactors change for R v4
- A new version (
v0.5.1
) ofstplanr
is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.fixes for stringsAsFactors change for R v4
- A new version (
v1.3.0
) ofUCSCXenaTools
is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started.added two new data hubs; improved a function
- A new version (
v2.3.5
) ofbeautier
is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started.gains 4 new functions, renames a few functions
- A new version (
v0.0.11
) ofpiggyback
is on CRAN - Managing larger data on a GitHub repository. See the release notes for changes. Checkout the docs to get started.guess_repo()
now infers a remote when there are multiple remotes; fixes torelease_info()
andpb_info()
- A new version (
v0.3.3
) oftaxa
is on CRAN - taxonomic classes for groupings of taxonomic names without data, and those with data. See the release notes for changes. Checkout the docs to get started.numeric column names in tables in taxmap are now supported; bug fixes
- A new version (
v3.1.2
) ofqualtRics
is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started.5 functions deprecated; now using updated version of Qualtrics API
- A new version (
v1.1.0
) ofdbparser
is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started.complete overhaul of exported function names
- A new version (
v0.4.0
) ofisdparser
is on CRAN - parse NOAA Integrated Surface data files. See the release notes for changes. Checkout the docs to get started.new function
isd_parse_csv()
to work with ISD csv files - A new version (
v0.0.6
) ofplotdap
is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started.fixed problem when no time coordinate in dataset;
add_tabledap()
overlays on gridded maps now work for ggplot2
Software Review ā
We accept community contributed packages via our software review system - an open software review system, sorta like scholarly paper review, but way better. Weāll 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 weāll ping you when thereās a submission that fits in your area of expertise.
The following package was recently submitted:
- treedata.table > A Wrapper For data.table For Fast Manipulation Of Phylogenetic Trees Matched To Data
- Author: Josef Uyeda
- Issue: ropensci/onboarding#367
- Reviewers: not yet assigned
The following package recently went through our software-review process and has been approved:
- parzer > Parse Coordinates
- Author: Scott Chamberlain
- Issue: ropensci/onboarding#341
- Reviewers:
On the blog
Itās time for another installment of ā¦ 2 Months in 2 Minutes - rOpenSci News, February 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)
Julia Stewart Lowndes cross-posted a blog post on our blog: rOpenSciās Leadership in #rstats Culture. In it she reflects on her experience at the 2020 RStudio conference as well as her experience at the 2015 rOpenSci Unconference.
Software Review:
Malcom Morgan wrote about his recently rOpenSci reviewed package opentripplanner: opentripplanner: Fast and Easy Multimodal Trip Planning in R with OpenTripPlanner. Malcom discusses the design of the package, and how to use opentripplanner.
Use Cases
The following 15 works use/cite rOpenSci software:
- Godfrey et al. used rotl in their paper Ray fractions and carbohydrate dynamics of tree species along a 2750 m elevation gradient indicate climate response, not spatial storage limitation 1
- Zhong used rnoaa in their paper Towards Developing a Double Cropping System Between Winter Barley and Soybean in the Upper Midwest 2
- Betts et al. used NLMR and landscapetools in their paper Extinction filters mediate the global effects of habitat fragmentation on animals 3
- Kim et al. used iheatmapr in their paper Higher frequency of vertebrateāinfecting viruses in the gut of infants born to mothers with type 1 diabetes 4
- Atalah & Forrest used clifro in their paper Forecasting mussel settlement using historical data and boosted regression trees 5
- KarakĆ¼lah et al. used biomartr in their paper TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model 6
- Yusri et al. used rgbif in their paper Distribution Modelling of Porites (Poritidae) in Indonesia 7
- Clark & Luis used rotl in their paper Nonlinear population dynamics are ubiquitous in animals 8
- Ekroos et al. used rgbif in their paper High land-use intensity in grasslands constrains wild bee species richness in Europe 9
- Lysne used visdat in their paper Biomarkers of one-carbon metabolism and B-vitamin status: Targeted metabolomics in rats and humans exploring the effects of PPARĪ±-activation and dietary composition 10
- Vitale et al. used rentrez and fulltext in their paper A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information 11
- Wcisel et al. used rentrez in their paper NULL 12
- Sansone et al. used rtweet in their paper The Sentiment Analysis of Tweets as a New Tool to Measure Public Perception of Male Erectile and Ejaculatory Dysfunctions 13
- Finnegan et al. used rdhs in their paper Using a Chord Diagram to Visualize Dynamics in Contraceptive Use: Bringing Data Into Practice 14
- Kim et al. used chlorpromazineR in their paper Neuroanatomical profiles of treatment-resistance in patients with schizophrenia spectrum disorders 15
From the Forum
We have a discussion forum (using Discourse) for the rOpenSci community. Itās a really nice way to have conversations on the internet. From time to time weāll highlight recent discussions of interest.
Peter Desmet asked a good question that many R package maintainers run in to: What if raw data in package is too large?
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.
Weāve 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 RĆ¼eger
- rdpla: now maintained by Alyssa Columbus
- webchem: now maintained by Erik Sapper
- mregions: in process of moving to maintenance by VLIZ
We donāt 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
- Mailing list: Sign up with an email address to get this newsletter sent to your inbox -> ropensci.org/#subscribe
- Alternatively, you can subscribe to this newsletter via our XML feed at https://news.ropensci.org/feed.xml or our JSON feed at https://news.ropensci.org/feed.json
- rOpenSci on Twitter: @ropensci
- The rOpenSci blog at ropensci.org/blog - you can subscribe in any RSS aggregator, or manually via https://ropensci.org/feed.xml. We also announce new blog posts on our Twitter account.
Footnotes
-
Godfrey, J. M., Riggio, J., Orozco, J., GuzmĆ”nāDelgado, P., Chin, A. R. O., & Zwieniecki, M. A. (2020). Ray fractions and carbohydrate dynamics of tree species along a 2750Ā m elevation gradient indicate climate response, not spatial storage limitation. New Phytologist, 225(6), 2314ā2330. https://doi.org/10.1111/nph.16361Ā ↩
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Zhong, B. (2019). Towards Developing a Double Cropping System Between Winter Barley and Soybean in the Upper Midwest. http://bit.ly/3co35EsĀ ↩
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Betts, M. G., Wolf, C., Pfeifer, M., Banks-Leite, C., Arroyo-RodrĆguez, V., Ribeiro, D. B., ā¦ Ewers, R. M. (2019). Extinction filters mediate the global effects of habitat fragmentation on animals. Science, 366(6470), 1236ā1239. https://doi.org/10.1126/science.aax9387Ā ↩
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Kim, K. W., Allen, D. W., Briese, T., Couper, J. J., Barry, S. C., ā¦ Colman, P. G. (2020). Higher frequency of vertebrateāinfecting viruses in the gut of infants born to mothers with type 1 diabetes. Pediatric Diabetes, 21(2), 271ā279. https://doi.org/10.1111/pedi.12952Ā ↩
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Atalah, J., & Forrest, B. (2019). Forecasting mussel settlement using historical data and boosted regression trees. Aquaculture Environment Interactions, 11, 625ā638. https://doi.org/10.3354/aei00337Ā ↩
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KarakĆ¼lah, G., Arslan, N., Yandım, C., & Suner, A. (2019). TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model. PeerJ, 7, e8192. https://doi.org/10.7717/peerj.8192Ā ↩
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Yusri, S., Siregar, V. P., & Suharsono. (2019). Distribution Modelling of Porites (Poritidae) in Indonesia. IOP Conference Series: Earth and Environmental Science, 363, 012025. https://doi.org/10.1088/1755-1315/363/1/012025Ā ↩
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Clark, T. J., & Luis, A. D. (2019). Nonlinear population dynamics are ubiquitous in animals. Nature Ecology & Evolution, 4(1), 75ā81. https://doi.org/10.1038/s41559-019-1052-6Ā ↩
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Ekroos, J., Kleijn, D., BatĆ”ry, P., Albrecht, M., BĆ”ldi, A., BlĆ¼thgen, N., ā¦ Smith, H. G. (2020). High land-use intensity in grasslands constrains wild bee species richness in Europe. Biological Conservation, 241, 108255. https://doi.org/10.1016/j.biocon.2019.108255Ā ↩
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Lysne, V. (2019). Biomarkers of one-carbon metabolism and B-vitamin status: Targeted metabolomics in rats and humans exploring the effects of PPARĪ±-activation and dietary composition. http://bit.ly/3crBaneĀ ↩
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Vitale, O., Preste, R., Palmisano, D., & Attimonelli, M. (2019). A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. Molecular Genetics & Genomic Medicine, 8(2). https://doi.org/10.1002/mgg3.1085Ā ↩
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Wcisel, D. J., III, J. T. H., Yoder, J. A., & Dornburg, A. (preprint) Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly. https://doi.org/10.21203/rs.2.16269/v3Ā ↩
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Sansone, A., Cignarelli, A., Ciocca, G., Pozza, C., Giorgino, F., Romanelli, F., & Jannini, E. A. (2019). The Sentiment Analysis of Tweets as a New Tool to Measure Public Perception of Male Erectile and Ejaculatory Dysfunctions. Sexual Medicine, 7(4), 464ā471. https://doi.org/10.1016/j.esxm.2019.07.001Ā ↩
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Finnegan, A., Sao, S. S., & Huchko, M. J. (2019). Using a Chord Diagram to Visualize Dynamics in Contraceptive Use: Bringing Data Into Practice. Global Health: Science and Practice, 7(4), 598ā605. https://doi.org/10.9745/ghsp-d-19-00205Ā ↩
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Kim, J., Plitman, E., Iwata, Y., Nakajima, S., Mar, W., Patel, R., ā¦ Graff-Guerrero, A. (2020). Neuroanatomical profiles of treatment-resistance in patients with schizophrenia spectrum disorders. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 99, 109839. https://doi.org/10.1016/j.pnpbp.2019.109839Ā ↩