Monthly Archives: August 2014

Simpler R coding with pipes > the present and future of the magrittr package

August 5, 2014
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Simpler R coding with pipes > the present and future of the magrittr package

This is a guest post by Stefan Milton, the author of the magrittr package which introduces the %__% operator to R programming. Preface (by Tal Galili) I was first introduced to the %__% (a.k.a: pipe) operator in R, thanks to Hadley Wickham’s (fascinating) dplyr tutorial (link to the workshop’s material) at useR!2014. After several discussions during the conference (including one very

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Clarifying difference between Ratio and Interval Scale of Measurement

August 5, 2014
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Clarifying difference between Ratio and Interval Scale of Measurement Clarifying difference between Ratio and Interval Scale of Measurement Introduction Recently while preparing lecture on scales of measurements and types of statistical data, I came across two scales of measurement when numbers are used to denote a quantitative variable. I took some time to clarify the difference between “Interval...

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GRAN and switchr can’t send you back in time, but they can send R (sort of)

August 5, 2014
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GRAN and switchr can’t send you back in time, but they can send R (sort of)

Using package repositories to recreate the past, distribute the present, and protect against the future by Gabriel Becker (@groundwalkergmb) Bioinformatics and Computational Biology Genentech Research and Early Developmen 1. Have you ever needed to reach into the distant past … to recreate a years old result? Take - as an arbitrary example - Anders and Huber's paper on Differential...

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Parameterized SQL queries

August 5, 2014
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Mateusz Żółtak asked me to spread the word about his new R package for parameterized SQL queries. Below you can find the copy of package vignette. If you work with SQL in R you may find it useful. Mateusz Żółtak The package RODBCext is an extension of the RODBC database connectivity package. It provides support

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ESA 2014: Don’t Know Much About History…

August 5, 2014
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ESA 2014: Don’t Know Much About History…

After my last post text-mining ESA Annual Meeting abstracts, Nash Turley was interested in the presence of the term “natural history” in ESA abstracts. I decided to collect a little more data by including programs back to 2010, giving a five-year data set. Thankfully the program back to 2010 remains in mostly the same format, so it’s...

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Rotated axis labels in R plots

August 5, 2014
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Rotated axis labels in R plots

It's somehow amazing to me that the option for slanted or rotated axes labels is not an option within the basic plot() or axis() functions in R.  The advantage is mainly in saving plot area space when long labels are needed (rather than as a means...

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Social Media Mining and Bioinformatics (with R)

August 5, 2014
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Social Media Mining and Bioinformatics (with R)

In June and July, I receive copies of two books, Social Media Mining with R, by Nathan Danneman and Richard Heimann Bioinformatics with R Cookbook, by Paurush Praveen Sinha For the first one, two recent interesting books deal with the same topic. Reza Zafarani, Mohammad Ali Abbasi and Huan Liu published last year Social Media Mining: An Introduction. Actually, the book can...

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Thanks to R Markdown: Perhaps Word is an option after all?

August 5, 2014
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Thanks to R Markdown: Perhaps Word is an option after all?

In many cases Word is still the preferred file format for collaboration in the office. Yet, it is often a challenge to work with it, not so much because of the software, but how it is used and abused. Thanks to Markdown it is no longer painful to inclu...

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Dodged bar charts, why not a line graph?

August 4, 2014
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Dodged bar charts, why not a line graph?

I often see graphs that are poorly implemented in that they do not achieve their goal. One such type of graph that I see are dodged bar charts. Here is an example of a dodged bar chart summarizing the number of all star players by team (focusing spec...

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BH release 1.54.0-3

August 4, 2014
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BH release 1.54.0-3

A new release of our BH package providing Boost headers for use by R is now on the CRAN mirrors. This release is the third based on Boost 1.54.0. At the request of the maintainer of the recent added RcppMLPACK package, it adds the Boost.Heap l...

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