Monthly Archives: June 2013

Split violin plots

June 25, 2013
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Split violin plots

(This article was first published on Ecology in silico, and kindly contributed to R-bloggers) Violin plots are useful for comparing distributions. When data are grouped by a factor with two levels (e.g. males and females), you can split the violins in half to see the difference between groups. Consider a 2 x 2 factorial experiment: treatments A and B...

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Sample size calculations equivalent to Stata functions

June 25, 2013
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A comprehensive guide to time series plotting in R

June 25, 2013
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A comprehensive guide to time series plotting in R

As R has evolved over the past 20 years its capabilities have improved in every area. The visual display of time series is no exception: as the folks from Timely Portfolio note that: Through both quiet iteration and significant revolutions, the volunteers of R have made analyzing and charting time series pleasant. R began with the basics, a simple...

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Natural Language Processing Tutorial

June 25, 2013
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Natural Language Processing Tutorial

Introduction This will serve as an introduction to natural language processing. I adapted it from slides for a recent talk at Boston Python. We will go from tokenization to feature extraction to creating a model using a machine learning algorithm. The goal is to provide a reasonable baseline on top of which more complex natural language processing can be done, and...

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My Talk at Boston Python

June 25, 2013
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I just gave a talk at Boston Python about natural language processing in general, and edX ease and discern in specific. You can find the presentation source here, and the web version of it here. There is a video of it here. Nelle Varoquaux and Michael ...

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Getting started with R

June 25, 2013
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Getting started with R

I wanted to avoid advanced topics in this post and focus on some “blocking and tackling” with R in an effort to get novices started.  This is some of the basic code I found useful when I began using R just over 6 weeks ago. Reading in data from a .csv file is a breeze with this command. > data =...

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The Dream 8 Challenges

June 25, 2013
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The Dream 8 Challenges

The 8th iteration of the DREAM Challenges are underway. DREAM is something like the Kaggle of computational biology with an open science bent. Participating teams apply machine learning and statistical modeling methods to biological problems, competing to achieve the best predictive accuracy. This year's three challenges focus on reverse engineering cancer, toxicology and the kinetics of...

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Three Ways to Run Bayesian Models in R

June 25, 2013
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Three Ways to Run Bayesian Models in R

There are different ways of specifying and running Bayesian models from within R. Here I will compare three different methods, two that relies on an external program and one that only relies on R. I won’t go into much detail about the differences in syntax, the idea is more to give a gist about how the different modeling languages...

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Exploratory Data Analysis: 2 Ways of Plotting Empirical Cumulative Distribution Functions in R

Exploratory Data Analysis: 2 Ways of Plotting Empirical Cumulative Distribution Functions in R

Introduction Continuing my recent series on exploratory data analysis (EDA), and following up on the last post on the conceptual foundations of empirical cumulative distribution functions (CDFs), this post shows how to plot them in R.  (Previous posts in this series on EDA include descriptive statistics, box plots, kernel density estimation, and violin plots.) I

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Predicting spatial locations using point processes

June 25, 2013
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Predicting spatial locations using point processes

I’ve uploaded a draft tutorial on some aspects of prediction using point processes. I wrote it using R-Markdown, so there’s bits of R code for readers to play with. It’s hosted on Rpubs, which turns out to be a great deal more convenient than WordPress for that sort of thing.

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