May 11, 2020
Software 📦
CRAN:
GitHub:
New Versions
- A new version (
v1.1.1
) ofdbparser
is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.4.0
) ofMODIStsp
is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.4.4
) ofRNeXML
is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.1.1
) ofcolocr
is on CRAN - conduct co-localization analysis of fluorescence microscopy images. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.3.2
) ofcRegulome
is on CRAN - access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.3.6
) ofeia
is on CRAN - API wrapper for US Energy Information Administration open data. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.3.6
) ofbeautier
is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. - A new version (
v2.1
) oftracerer
is on CRAN - parse and analyze BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.3
) ofwritexl
is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the README to get started. - A new version (
v0.27.1
) ofgit2r
is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the README to get started. - A new version (
v0.6.0
) ofstplanr
is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. - A new version (
v1.0.0
) ofbold
is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the docs to get started. - A new version (
v0.3.4
) 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. - A new version (
v0.9.95
) oftaxize
is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.
Software Review ✔
In the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review. Please check back at our software review repository for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent. Other rOpenSci community activities continue. We express our continued great appreciation for the work of our authors and reviewers.
On the blog
Maëlle Salmon has two blog posts in the past two weeks:
- Highlights of Hugo Code Highlighting - related to work on the rOpenSci website
- A Roundup of R Tools for Handling BibTeX - including discussion of rOpenSci packages RefManageR, bib2df, and handlr
Use Cases
The following 23 works use/cite rOpenSci software:
- Adil et al. used pdftools in their paper Identifying Trends in Data Science Articles using Text Mining 1
- Finoshin et al. used rotl in their paper Iron metabolic pathways in the processes of sponge plasticity 2
- Pimiento & Benton used paleobioDB and rfishbase in their paper The impact of the Pull of the Recent on extant elasmobranchs 3
- Benhadi‐Marín et al. used rgbif in their paper Distribution of Bactrocera oleae (Rossi, 1790) throughout the Iberian Peninsula based on a maximum entropy modeling approach 4
- Ahrenfeldt et al. used treeio in their paper Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering 5
- Cinelli used hunspell in their paper Generalized rich-club ordering in networks 6
- Alfaro-Ramírez et al. used CoordinateCleaner in their paper Potential reduction of Hartweg ́s Pine (Pinus hartwegii Lindl.) geographic distribution 7
- Martinez-Feria & Basso used FedData in their paper Unstable crop yields reveal opportunities for site-specific adaptations to climate variability 8
- Rego et al. used rnaturalearth in their paper Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica 9
- Cederwall et al. used taxize in their paper Life under an oil slick: response of a freshwater food web to simulated spills of diluted bitumen in field mesocosms 10
- Mossion et al. used taxize in their paper A reference transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure 11
- Funk et al. used hunspell in their paper A Framework for Applying Natural Language Processing in Digital Health Interventions 12
- Correia et al. used skimr in their paper RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus 13
- Verde Arregoitia et al. used taxize and pdftools in their paper Patterns in research and data sharing for the study of form and function in caviomorph rodents 14
- Shivambu et al. used rgbif in their paper Impact assessment of seven alien invasive bird species already introduced to South Africa 15
- Jhwueng & O’Meara used rotl in their paper On the Matrix Condition of Phylogenetic Tree 16
- Cooke et al. used rredlist in their paper Ecological distinctiveness of birds and mammals at the global scale 17
- Palanisamy used pdftools in their paper An analysis on hidden markov model prediction factors using California wildfire and meteorological records 18
- Panayiotou used rdflib in their paper An Ontological Analysis and Natural Language Processing of Figures of Speech 19
- Ji et al. used rredlist in their paper Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA 20
- Li & Guo used rgbif in their paper Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies 21
- Silva et al. used NLMR and landscapetools in their paper Revisiting reptile home ranges: moving beyond traditional estimators with dynamic Brownian Bridge Movement Models 22
- Schwalb‐Willmann et al. used magick in their paper moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in R 23
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.
A few new use cases were shared in the forum recently:
- Rami Krispin shared: Visualize covid19 cases using rnaturalearth package; it leveraged rnaturalearth, an rOpenSci package maintained by Andy South
- Miles McBain shared: {drake} at Queensland Fire and Emergency Services; it leveraged drake, an rOpenSci package maintained by Will Landau
- Alberto Cairo shared a use case for the rOpenSci package tradestatistics maintained by Mauricio Vargas
In The News
testing
: Why You Should Document Your Tests- Should you document your tests? I for one, only sometimes include comments in my tests, but perhaps they should be documented better? Do you comment or document your tests? This blog post is about Python, but the ideas apply to any language.
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 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
- rdpla: now maintained by Alyssa Columbus
- webchem: now maintained by Erik Sapper
- mregions: in process of moving to maintenance by VLIZ
- rWBclimate: now maintained by Sergio Ibarra-Espinosa and Amanda Rehbein
We’ve got one package in need of a new maintainer:
- rinat: The current maintainer is looking for a new maintainer. Email Scott if you’re interested.
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
- Mailing list: Sign up with an email address to get this newsletter sent to your inbox -> ropensci.org/#subscribe
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- 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
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Adil, S. H., Ebrahim, M., Ali, S. S. A., & Raza, K. 2019. Identifying Trends in Data Science Articles using Text Mining. In 2019 4th International Conference on Emerging Trends in Engineering, Sciences and Technology (ICEEST) (pp. 1-7). IEEE. https://ieeexplore.ieee.org/document/8981702 ↩
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Finoshin, A. D., Adameyko, K. I., Mikhailov, K. V., Kravchuk, O. I., Georgiev, A. A., Gornostaev, N. G., … Lyupina, Y. V. (2020). Iron metabolic pathways in the processes of sponge plasticity. PLOS ONE, 15(2), e0228722. https://doi.org/10.1371/journal.pone.0228722 ↩
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Pimiento, C., & Benton, M. J. (2020). The impact of the Pull of the Recent on extant elasmobranchs. Palaeontology. https://doi.org/10.1111/pala.12478 ↩
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Benhadi‐Marín, J., Santos, S. A. P., Baptista, P., & Pereira, J. A. (2020). Distribution of Bactrocera oleae (Rossi, 1790) throughout the Iberian Peninsula based on a maximum entropy modeling approach. Annals of Applied Biology. https://doi.org/10.1111/aab.12584 ↩
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Ahrenfeldt, J., Waisi, M., Loft, I. C., Clausen, P. T. L. C., Allesøe, R., Szarvas, J., … Lund, O. (2020). Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-59292-w ↩
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Cinelli, M. (2019). Generalized rich-club ordering in networks. Journal of Complex Networks, 7(5), 702–719. https://doi.org/10.1093/comnet/cnz002 ↩
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Alfaro-Ramírez, F. U., Ramírez-Albores, J. E., Vargas-Hernández, J. J., Franco-Maass, S., & Pérez-Suárez, M. (2020). Potential reduction of Hartweg´s Pine (Pinus hartwegii Lindl.) geographic distribution. PLOS ONE, 15(2), e0229178. https://doi.org/10.1371/journal.pone.0229178 ↩
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Martinez-Feria, R. A., & Basso, B. (2020). Unstable crop yields reveal opportunities for site-specific adaptations to climate variability. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-59494-2 ↩
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Rego, A., Sousa, A. G. G., Santos, J. P., Pascoal, F., Canário, J., Leão, P. N., & Magalhães, C. (2020). Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica. Microorganisms, 8(2), 279. https://doi.org/10.3390/microorganisms8020279 ↩
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Cederwall, J., Black, T. A., Blais, J. M., Hanson, M. L., Hollebone, B. P., Palace, V. P., … Orihel, D. M. (2020). Life under an oil slick: response of a freshwater food web to simulated spills of diluted bitumen in field mesocosms. Canadian Journal of Fisheries and Aquatic Sciences, 77(5), 779–788. https://doi.org/10.1139/cjfas-2019-0224 ↩
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Mossion, V., Dauphin, B., Grant, J., Zemp, N., & Croll, D. (2020). A reference transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure. https://doi.org/10.1101/2020.02.17.952283 ↩
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Funk, B., Sadeh-Sharvit, S., Fitzsimmons-Craft, E. E., Trockel, M. T., Monterubio, G. E., Goel, N. J., … Taylor, C. B. (2020). A Framework for Applying Natural Language Processing in Digital Health Interventions. Journal of Medical Internet Research, 22(2), e13855. https://doi.org/10.2196/13855 ↩
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Correia, C. N., McLoughlin, K. E., Nalpas, N. C., Magee, D. A., Browne, J. A., Rue-Albrecht, K., … MacHugh, D. E. (2018). RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus). Frontiers in Genetics, 9. https://doi.org/10.3389/fgene.2018.00278 ↩
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Verde Arregoitia, L. D., Teta, P., & D’Elía, G. (2020). Patterns in research and data sharing for the study of form and function in caviomorph rodents. Journal of Mammalogy. https://doi.org/10.1093/jmammal/gyaa002 ↩
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Shivambu, T. C., Shivambu, N., & Downs, C. T. (2020). Impact assessment of seven alien invasive bird species already introduced to South Africa. Biological Invasions. https://doi.org/10.1007/s10530-020-02221-9 ↩
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Jhwueng, D.-C., & O’Meara, B. C. (2020). On the Matrix Condition of Phylogenetic Tree. Evolutionary Bioinformatics, 16, 117693432090172. https://doi.org/10.1177/1176934320901721 ↩
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Cooke, R. S. C., Eigenbrod, F., & Bates, A. E. (2020). Ecological distinctiveness of birds and mammals at the global scale. Global Ecology and Conservation, 22, e00970. https://doi.org/10.1016/j.gecco.2020.e00970 ↩
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Palanisamy, S. (2019). An analysis on hidden markov model prediction factors using California wildfire and meteorological records (Doctoral dissertation, California State University, Sacramento). https://bit.ly/2yCWk2M ↩
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Panayiotou, C. (2020). An Ontological Analysis and Natural Language Processing of Figures of Speech. International Journal of Artificial Intelligence & Applications, 11(1), 17–30. https://doi.org/10.5121/ijaia.2020.11102 ↩
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Ji, Y., Baker, C. C., Li, Y., Popescu, V. D., Wang, Z., Wang, J., … Yu, D. W. (2020). Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA. https://doi.org/10.1101/2020.02.10.941336 ↩
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Li, X., & Guo, B. (2020). Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies. Proceedings of the Royal Society B: Biological Sciences, 287(1920), 20193008. https://doi.org/10.1098/rspb.2019.3008 ↩
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Silva, I., Crane, M., Marshall, B. M., & Strine, C. T. (2020). Revisiting reptile home ranges: moving beyond traditional estimators with dynamic Brownian Bridge Movement Models. https://doi.org/10.1101/2020.02.10.941278 ↩
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Schwalb‐Willmann, J., Remelgado, R., Safi, K., & Wegmann, M. (2020). moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in R. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13374 ↩