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rOpenSci - open tools for open science

rOpenSci - open tools for open science
Open Tools and R Packages for Open Science
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Published
Author Jeroen Ooms

Last week, version 1.0 of the magick package appeared on CRAN: an ambitious effort to modernize and simplify high quality image processing in R. This R package builds upon the Magick++ STL which exposes a powerful C++ API to the famous ImageMagick library. The best place to start learning about magick is the vignette which gives a brief overview of the overwhelming amount of functionality in this package.

Published
Author Noam Ross

Since June, we have been highlighting the many projects that emerged from this year’s rOpenSci Unconf. These projects start many weeks before unconf participants gather in-person. Each year, we ask participants to propose and discuss project ideas ahead of time in a GitHub repo. This serves to get creative juices flowing as well as help people get to know each other a bit through discussion.

Published
Author Scott Chamberlain

What is Taxonomy? Taxonomy in its most general sense is the practice and science of classification. It can refer to many things. You may have heard or used the word taxonomy used to indicate any sort of classification of things, whether it be companies or widgets. Here, we’re talking about biological taxonomy, the science of defining and naming groups of biological organisms.

Published
Authors Eduardo Arino de la Rubia, Shannon E. Ellis, Julia Stewart Lowndes, Hope McLeod, Amelia McNamara, Michael Quinn, Elin Waring, Hao Zhu

Like every R user who uses summary statistics (so, everyone), our team has to rely on some combination of summary functions beyond summary() and str(). But we found them all lacking in some way because they can be generic, they don’t always provide easy-to-operate-on data structures, and they are not pipeable. What we wanted was a frictionless approach for quickly skimming useful and tidy summary statistics as part of a pipeline.

Published
Authors Alicia Schep, Miles McBain

We, Alicia Schep and MilesMcBain, drove the webrockets projectat #runconf17.To make progress we solicited code, advice, and entertaining anecdotesfrom a host of other attendees, whom we humbly thank for helping to makeour project possible. This post is divided into two sections: First up we’ll relate ourexperiences, prompted by some questions we wrote forone another.

Published
Authors Becca Krouse, Erin Grand, Hannah Frick, Lori Shepherd, Sam Firke, William Ampeh

Before everybody made their way to the unconf via LAX and Lyft, attendees discussed potential project ideas online. The packagemetrics package was our answer to two related issues. The first proposal centered on creating and formatting tables in a reproducible workflow.

Published
Authors Noam Ross, Alice Daish, Laura DeCicco, Molly Lewis, Nistara Randhawa, Jennifer Thompson, Nicholas Tierney

Two years ago at #runconf15, there was a great discussion about best practices for organizing R-based analysis projects that yielded a nice guidance document describing research compendia . Compendia, as we described them, were minimal products of reproducible research, using parts of R package structure to organize the inputs, analyses, and outputs of research projects.

Published
Authors Scott Chamberlain, Noam Ross

randgeo generates random points and shapes in GeoJSON and WKT formats foruse in examples, teaching, or statistical applications. Points and shapes are generated in the long/lat coordinate system and withappropriate spherical geometry; random points are distributed evenly acrossthe globe, and random shapes are sized according to a maximum great-circledistance from the center of the shape.

Published
Author Thomas J. Leeper

There is no problem in science quite as frustrating as other peoples’ data . Whether it’s malformed spreadsheets, disorganized documents, proprietary file formats, data without metadata, or any other data scenario created by someone else, scientists have taken to Twitter to complain about it. As a political scientist who regularly encounters so-called “open data” in PDFs, this problem is particularly irritating.