Publications by rOpenSci - open tools for open science
tidync: scientific array data from NetCDF in R
In May 2019 version 0.2.0 of tidync was approved by rOpenSci and accepted to CRAN. Here we provide a quick overview of the typical workflow with some pseudo-code for the main functions in tidync. This overview is enough to read if you just want to try out the package on your own data. The tidync package is focussed on efficient data extraction f...
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rOpenSci Announces a New Award From The Gordon and Betty Moore Foundation to Improve the Scientific Package Ecosystem for R
Today we are pleased to announce that we have received new funding from the Gordon and Betty Moore Foundation. The $894k grant will help us improve infrastructure for R packages and enable us to move towards a science first package ecosystem for the R community. You may have already noticed some developments on this front when we announced our au...
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Community Call – Last Night, Testing Saved my Life
To the uninitiated, software testing may seem variously boring, daunting or bogged down in obscure terminology. However, it has the potential to be enormously useful for people developing software at any level of expertise, and can often be put into practice with relatively little effort. Our 1-hour Call will include two speakers and at least 20 ...
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workloopR: Analysis of work loops and other data from muscle physiology experiments in R
Studies of muscle physiology often rely on closed-source, proprietary software for not only recording data but also for data wrangling and analyses. Although specialized software might be necessary to record data from highly-specialized equipment, data wrangling and analyses should be free from this constraint. It’s becoming more common for res...
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NumFOCUS recognizes Melina Vidoni and Will Landau for their contributions to rOpenSci
rOpenSci thrives because of volunteer contributions from community members – submitting and reviewing R packages, serving as editors for software peer review, writing blog posts, sharing information about packages and resources, contributing code and documentation and answering others’ questions. Recently our fiscal sponsor, NumFOCUS, gave us...
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rnassqs: accessing USDA agricultural data via API
The United States Deparment of Agriculture National Agricultural Statistics Service (USDA-NASS) provides a wide range of agricultural data that includes animal, crop, demographic, economic, and environmental measures across a number of geographies and time periods. This data is available by direct download or queriable via the Quick Stats interfa...
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Introducing Mark Padgham, rOpenSci’s new Software Research Scientist
We’re thrilled to be introducing a new member of our team. Mark Padgham has joined rOpenSci as a Software Research Scientist working full-time from Münster, Germany. Mark will play a key role in research and development of statistical software standards and expanding our efforts in software peer review, enabled by new funding from the Sloan Fo...
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How to precompute package vignettes or pkgdown articles
As of earlier this year, we are now automatically building binaries and pkgdown documentation for all rOpenSci packages. One issue we encountered is that some packages include vignettes that require some special tools/data/credentials, which are unavailable on generic build servers. This post explains how to include such vignettes and articles in...
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HTTP testing in R: overview of tools and new features
Testing is a crucial component to any software package. Testing makes sure that your code does what you expect it to do; and importantly, makes it safer to make changes moving forward because a good test suite will tell you if a change has broken existing functionality. Our recent community call on testing is a nice place to get started with test...
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We cleaned our website URLs with R!
Last year we reported on the joy of using commonmark and xml2 to parse Markdown content, like the source of this website built with Hugo, in particular to extract links, at the time merely to count them. How about we go a bit further and use the same approach to find links to be fixed? In this tech note we shall report our experience using R to f...
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