2018-11-12

rOpenSci HQ

OzUnconf https://ozunconf18.ropensci.org/ is running for the third year. The unconference is 22-23 November in Melbourne, Australia. OzUnconf is based on our main unconference in the US (http://unconf18.ropensci.org/) but more accessible to folks in Australia/Asia.
We have an upcoming community call this week on Working with images in R. Don’t miss it!

Software 📦

CRAN: GitHub:

New packages

The first version (v0.1.0) of zbank is on CRAN - an interface to the ZooBank API (http://zoobank.org/Api); ZooBank (http://zoobank.org/) is the official registry of zoological nomenclature. Checkout the README to get started.

New versions

A new version (v0.2.0) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started.

fixes to select_indicators, deprivation_decile, fingertips_data and indicators fxns
A new version (v3.0.0) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started.

Major change: now uses static data; requests return all data in one go now
A new version (v1.3) of antiword is on CRAN - Extract text from Microsoft Word documents. See the release notes for changes. Checkout the README to get started.

fix for sys 2.0
A new version (v1.3) of unrtf is on CRAN - Extract text from Rich Text Format (RTF) documents. See the release notes for changes. Checkout the README to get started.

fix for sys 2.0; fix for Solaris
A new version (v1.0.2) of available is on CRAN - check if the title of a package is available. See the release notes for changes. Checkout the README to get started.

add dialog when run interactively; now use BiocManager
A new version (v0.3.0) of worrms is on CRAN - client for World Register of Marine Species. See the release notes for changes. Checkout the vignette to get started.

plural versions of fxns now only warn where they used to stop on error
A new version (v0.2.9) 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.

fix for use case of using only webmockr without vcr; update docs
A new version (v4.0) of tesseract is on CRAN - bindings to Tesseract, an OCR engine https://opensource.google.com/projects/tesseract. See the release notes for changes. Checkout the vignette to get started.

upgrade to Tesseract 4.0 for windows/macos users; drop hard dep on tibble
A new version (v2.2.0) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the vignettes to get started.

various fixes; drops phylobase dep.
A new version (v1.5.0) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started.

allow ZIP compression; fix to write_txt_img
A new version (v0.0.5) of arkdb is on CRAN - archive and unarchive databases as flat text files. See the release notes for changes. Checkout the docs to get started.

fix to ark() fxn when accessing Postgres connections

Software Review ✔

We accept community contributed packages via our onboarding 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.

On the blog

Technotes

Jeroen Ooms wrote about a new version of his package tesseract: Tesseract 4 is here! State of the art OCR in R!. Check out the package at ropensci/tesseract.

rOpenSci HQ

Stefanie Butland wrote up detailed notes on how to do a good unconference ice breaker: Sharing the Recipe for rOpenSci’s Unconf Ice Breaker.

Use cases

The following 13 works use/cite rOpenSci software:

Milà et al. used in rtimicropem in their paper When, Where, and What? Characterizing Personal PM2.5 Exposure in Periurban India by Integrating GPS, Wearable Camera, and Ambient and Personal Monitoring Data ¹
Barra et al. used plotly in their paper Stroke incidence in the young: evidence from a Norwegian register study ²
Ornstein used FedData in their dissertation The Political Economy of Urban Growth ³
Clegg et al. used worrms in their paper The impact of intraspecific variation on food web structure ⁴
Guerra-Grenier used plotly in their dissertation Resisting the Pied Piper: Colorful Defense Mechanisms in Insect Eggs, with a Focus on Stink Bugs (Heteroptera: Pentatomidae) ⁵
Orwoll et al. used plotly in their paper The relationships between physical performance, activity levels and falls in older men ⁶
Kandlikar et al. used taxize in their paper ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations ⁷
Smith et al. used rgbif in their paper A global test of ecoregions ⁸
Collins et al. used rgbif and rentrez in their paper Persistence of environmental DNA in marine systems ⁹
Mendez et al. used magick in their paper Imaging natural history museum collections from the bottom up: 3D print technology facilitates imaging of fluid-stored arthropods with flatbed scanners ¹⁰
Bentz et al. used rgbif in their paper The evolution of language families is shaped by the environment beyond neutral drift ¹¹
Chatzos used plotly in their thesis Project for the development of a higher education management dashboard in R ¹²
Menegotto & Rangel used rgbif in their paper Mapping knowledge gaps in marine diversity reveals a latitudinal gradient of missing species richness ¹³

In the news

Dominic Royé wrote a blog post on how to access OpenStreetMap data with R, that used our osmdata package from Mark Padgham and company:

New tutorial on how you can access the database of @openstreetmap from the R environment. #rstat #overpassAPI #ggplot2 #mapping #gis https://t.co/9fqq8z6lCJ pic.twitter.com/zvjeEPMDeM
— Dominic Royé (@dr_xeo) November 5, 2018

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Footnotes

Milà, C., Salmon, M., Sanchez, M., Ambrós, A., Bhogadi, S., Sreekanth, V., … Tonne, C. (2018). When, Where, and What? Characterizing Personal PM2.5 Exposure in Periurban India by Integrating GPS, Wearable Camera, and Ambient and Personal Monitoring Data. Environmental Science & Technology. https://doi.org/10.1021/acs.est.8b03075 ↩
Barra, M., Labberton, A. S., Faiz, K. W., Lindstrøm, J. C., Rønning, O. M., Viana, J., … Rand, K. (2018). Stroke incidence in the young: evidence from a Norwegian register study. Journal of Neurology. https://doi.org/10.1007/s00415-018-9102-6 ↩
Ornstein, J. (2018). The Political Economy of Urban Growth. Dissertation. https://deepblue.lib.umich.edu/bitstream/handle/2027.42/145832/ornstein_1.pdf?sequence=1&isAllowed=y ↩
Clegg, T., Ali, M., & Beckerman, A. P. (2018). The impact of intraspecific variation on food web structure. Ecology. https://doi.org./10.1002/ecy.2523 ↩
Guerra-Grenier Jr, E. (2018). Resisting the Pied Piper: Colorful Defense Mechanisms in Insect Eggs, with a Focus on Stink Bugs (Heteroptera: Pentatomidae) (Doctoral dissertation, Carleton University). https://curve.carleton.ca/system/files/etd/6c45742b-6f0e-4fb7-a131-4e7bddc3fb69/etd_pdf/cb0a257b1921794188a309b53d0d614a/guerra-grenier-resistingthepiedpipercolorfuldefensemechanisms.pdf ↩
Orwoll, E. S., Fino, N. F., Gill, T. M., Cauley, J. A., Strotmeyer, E. S., … Ensrud, K. E. (2018). The relationships between physical performance, activity levels and falls in older men. The Journals of Gerontology: Series A. https://doi.org/10.1093/gerona/gly248 ↩
Kandlikar, G. S., Gold, Z. J., Cowen, M. C., Meyer, R. S., Freise, A. C., Kraft, N. J. B., … Curd, E. E. (2018). ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. F1000Research, 7, 1734. https://doi.org/10.12688/f1000research.16680.1 ↩
Smith, J. R., Letten, A. D., Ke, P.-J., Anderson, C. B., Hendershot, J. N., Dhami, M. K., … Daily, G. C. (2018). A global test of ecoregions. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-018-0709-x ↩
Collins, R. A., Wangensteen, O. S., O’Gorman, E. J., Mariani, S., Sims, D. W., & Genner, M. J. (2018). Persistence of environmental DNA in marine systems. Communications Biology, 1(1). https://doi.org/10.1038/s42003-018-0192-6 ↩
Mendez, P. K., Lee, S., & Venter, C. E. (2018). Imaging natural history museum collections from the bottom up: 3D print technology facilitates imaging of fluid-stored arthropods with flatbed scanners. ZooKeys, 795, 49–65. https://doi.org/10.3897/zookeys.795.28416 ↩
Bentz, C., Dediu, D., Verkerk, A., & Jäger, G. (2018). The evolution of language families is shaped by the environment beyond neutral drift. Nature Human Behaviour, 2(11), 816–821. https://doi.org/10.1038/s41562-018-0457-6 ↩
Chatzos, D. (2018). Project for the development of a higher education management dashboard in R (Master’s thesis, Universitat Politècnica de Catalunya). https://upcommons.upc.edu/bitstream/handle/2117/123443/memoria.pdf ↩
Menegotto, A., & Rangel, T. F. (2018). Mapping knowledge gaps in marine diversity reveals a latitudinal gradient of missing species richness. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07217-7 ↩