Posts Tagged 'r' 6

R Phone Home: Notifications with pushoverr

R Phone Home: Notifications with pushoverr

November 23, 2016

There are a lot of times when it would be great if your computer talked to you. pushoverr allows you to send yourself or your group notifications from R. Instead of compulsively checking the status of a running job, you can just have R tell you when it’s done, if it failed, or what the results are.

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Connecting R to Everything with IFTTT

Connecting R to Everything with IFTTT

June 18, 2015

IFTTT (“if this then that”) is one of my favorite tools. I use it to keep and share articles, turn on my home’s lights at sundown, alert me when certain keywords are mentioned on Twitter/Reddit/etc., and many other things. Recently, the great people at IFTTT announced the Maker Channel, which allows recipes to make and receive web requests. This second option caught my interest as a nice way to do all kinds of things from R. For example, you could set the temperature with a Nest Thermostat, blink your hue lightbulbs, write some data to a Google Drive document, or do a whole lot of other things.

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Creating Reproducible Software Environments with Packrat

July 15, 2014

Open science has grown tremendously in the past few years. While there’s still a long way to go, the availability of data, software, and other materials is making it possible to re-use these products to expand upon previous work and apply them to new areas. Through responsible conduct of research (RCR) training, journal requirements, changing individual and institutional principles, and open access evangelism, it’s now much more common for researchers to package their work with the intention of sharing it with others. What exactly this entails depends on a lot of things, including the field of research, the type of data, and how the data were processed and analyzed. At a minimum, one would hope for all of the appropriate data, a description of the software used for analysis or the software itself, and some metadata describing the data and how it was processed.

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Plotting Microtiter Plate Maps

Plotting Microtiter Plate Maps

May 1, 2014

I recently wrote about my workflow for Analyzing Microbial Growth with R. Perhaps the most important part of that process is the plate map, which describes the different experimental variables and where they occur. In the example case, the plate map described which strain was growing and in which environment for each of the wells used in a 96-well microtiter plate. Until recently, I’ve always created two plate maps. The first one is hand-drawn using pens and markers and sat on the bench with me when I started an experiment. By marking the wells with different colors, line types, and whatever other hieroglyphics I decide on, I can keep track of where everything is and how to inoculate the wells.

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Analyzing Microbial Growth with R

Analyzing Microbial Growth with R

April 9, 2014

In experimental evolution research, few things are more important than growth. Both the rate of growth and the resulting yield can provide direct insights into a strain or species’ fitness. Whether one strain with a trait of interest can outgrow (and outcompete) another that possesses a variation of that trait often depends primarily on the fitnesses of the two strains.

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Creating Colorblind-Friendly Figures

Creating Colorblind-Friendly Figures

October 16, 2013

Color is often used to display an extra dimension in plots of scientific data. Unfortunately, everyone does not decode color in exactly the same way. This is especially true for those with color vision deficiency, which affects up to 8 percent of the population in its two most common forms. As a result, it has been estimated that the odds of a given plot reaching a reviewer with some form of color vision deficiency in a group of three males is approximately 22%. Hopefully, when we are creating figures, this number alone is compelling enough to always keep these viewers in mind. The truth, however, is that your figures aren‘t only seen by reviewers: they are seen by a much wider group that includes readers of your paper, members of the audience when you present your work, viewers of your lab‘s website, and potentially many others. As your audience grows, your choices in color become more and more important for effectively communicating your work.

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