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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-omics in 2013

June 24, 2013
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-omics in 2013

Just how many (bad) -omics are there anyway? Let’s find out. 1. Get the raw data It would be nice if we could search PubMed for titles containing all -omics: However, we cannot since leading wildcards don’t work in PubMed search. So let’s just grab all articles from 2013: and save them in a format

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Visualising Crime Hotspots in England and Wales using {ggmap}

June 24, 2013
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Visualising Crime Hotspots in England and Wales using {ggmap}

Two weeks ago, I was looking for ways to make pretty maps for my own research project. A quick search led me to some very informative blog posts by Kim Gilbert, David Smith and Max Marchi. Eventually, I Google'd the excellent crime weather map exa...

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Comparing the speed of pqR with R-2.15.0 and R-3.0.1

June 24, 2013
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Comparing the speed of pqR with R-2.15.0 and R-3.0.1

As part of developing pqR, I wrote a suite of speed tests for R. Some of these tests were used to show how pqR speeds up simple real programs in my post announcing pqR, and to show the speed-up obtained with helper threads in pqR on systems with multiple processor cores. However, most tests in

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Exploratory Data Analysis: Conceptual Foundations of Empirical Cumulative Distribution Functions

Exploratory Data Analysis: Conceptual Foundations of Empirical Cumulative Distribution Functions

Introduction Continuing my recent series on exploratory data analysis (EDA), this post focuses on the conceptual foundations of empirical cumulative distribution functions (CDFs); in a separate post, I will show how to plot them in R.  (Previous posts in this series include descriptive statistics, box plots, kernel density estimation, and violin plots.) To give you

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Merging Data — SAS, R, and Python

June 24, 2013
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Merging Data — SAS, R, and Python

On analyticbridge, the question was posed about moving an inner join from Excel (which was taking many minutes via VLOOKUP()) to some other package.  The question asked what types of performance can be expected in other systems.  Of the list ...

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Rcpp 0.10.4

June 24, 2013
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A new version of Rcpp is now on the CRAN network for GNU R; binaries for Debian have been uploaded as well. This release brings a fairly large number of fixes and improvements across a number of Rcpp features, see below for the detailed list. We a...

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A beer recommendation system made with R

June 24, 2013
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A beer recommendation system made with R

If you know a beer you like and want some recommendations for a style of beer to try, check out the yhat Beer Recommender: This neat little app is the product of a recommendation system built using the R language by the folks behind the yhat blog. It's based on about 1.5 million beer reviews from the Beer Advocate....

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My Stat Bytes talk, with slides and code

June 24, 2013
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On Thursday of last week I gave a short informal talk to Stat Bytes, the CMU Statistics department's twice a month computing seminar. Quick tricks for faster R code: Profiling to Parallelism Abstract: I will present a grab bag of tricks to speed up your R code. Topics will include: installing an optimized BLAS, how

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My Stat Bytes talk, with slides and code

June 24, 2013
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On Thursday of last week I gave a short informal talk to Stat Bytes, the CMU Statistics department‘s twice a month computing seminar. Quick tricks for faster R code: Profiling to Parallelism Abstract: I will present a grab bag of … Continue reading →

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Opel Corsa Diesel Usage

June 24, 2013
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Opel Corsa Diesel Usage

I wanted to extend my car weight distribution calculation of June 16 from only 2000 to years 2000 to 2013. Unfortunately, come Sunday afternoon the code seemed too slow and not even the beginning of a post. So, I went on to another calculation I w...

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Streamline Your Mechanical Turk Workflow with MTurkR

June 24, 2013
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Streamline Your Mechanical Turk Workflow with MTurkR

I’ve been using Thomas Leeper‘s MTurkR package to administer my most recent Mechanical Turk study—an extension of work on representative-constituent communication claiming credit for pork benefits, with Justin Grimmer and Sean Westwood.  MTurkR is excellent, making it quick and easy to: test … Continue reading →

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Creating a BI Dashboard: Part 1

June 23, 2013
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Creating a BI Dashboard: Part 1

Introduction A few first posts of this blog will demonstrate how to build each report hosted by the business intelligence (BI) application dashboard shown below (see Fig. 1). This application uses the following tools and technologies R – a free software environment for statistical computing and graphics, ASP.NET MVC4 – a free framework for building

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Revisualizing the best cities in the US in 2012- Shiny + googleVis = Incredibly powerful

June 23, 2013
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Revisualizing the best cities in the US in 2012- Shiny + googleVis = Incredibly powerful

This is the last time I will talk about visualizing the best cities of 2012 based on Bloomberg Businessweek's rankings. In an earlier post on this topic, interactive applications to plot bar graphs and histograms for different characteristics...

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Principal Components Analysis Shiny App

June 23, 2013
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Principal Components Analysis Shiny App

I’ve recently started experimenting with making Shiny apps, and today I wanted to make a basic app for calculating and visualizing principal components analysis (PCA). Here is the basic interface I came up with. Test drive the app for yourself using the code below or  check out the the R code HERE. Above is an example of the

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Parallel computation with helper threads in pqR

June 23, 2013
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Parallel computation with helper threads in pqR

One innovative feature of pqR (my new, faster, version of R), is that it can perform some numeric computations in “helper” threads, in parallel with other such numeric computations, and with interpretive operations performed in the “master” thread. This can potentially speed up your computations by a factor as large as the number of processor cores

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Time Is on My Side – A Small Example for Text Analytics on a Stream

June 23, 2013
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Time Is on My Side – A Small Example for Text Analytics on a Stream

Introduction and Background While my last posting was about recommendation in the context of Location Based Social Networks there are also other interesting topics regarding the analysis of unstructured data. The most established one is probably Text Analytics/Mining focusing on all sorts of text data.For me, coming from spatial analysis, these topic is relatively new but I couldn’t help noticing...

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Got Bootstrap?

June 23, 2013
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Got Bootstrap?

This week I read the book by Michael Chernick and Robert LaBudde, An Introduction to Bootstrap Methods with Applications to R. It’s an interesting oeuvre for useRs of all stripes. I strongly recommend check it out. The book brings lots of examples of bootstrapping applications, such as standard errors, confidence intervals, hypothesis testing, and even

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GRNN and PNN

June 23, 2013
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GRNN and PNN

From the technical prospective, people usually would choose GRNN (general regression neural network) to do the function approximation for the continuous response variable and use PNN (probabilistic neural network) for pattern recognition / classification problems with categorical outcomes. However, from the practical standpoint, it is often not necessary to draw a fine line between GRNN

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Generating Alerts From Guardian University Tables Data

June 23, 2013
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Generating Alerts From Guardian University Tables Data

One of the things I’ve been pondering with respect to the whole data journalism process is how journalists without a lot of statistical training can quickly get a feel for whether there may be interesting story leads in a dataset, or how they might be able to fashion “alerts” that bring attention to data elements

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FuzzyNumbers-0.3-1 released

June 23, 2013
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A new version of the FuzzyNumbers package for R has just been submitted to the CRAN archive. Check out our step-by-step tutorial. ** FuzzyNumbers Package CHANGELOG ** ********************************************************************* 0.3-1 /2013-06-23/ * piecewiseLinearApproximation() - general case (any knot.n) for method="NearestEuclidean" now…Read more ›

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Prototyping A General Regression Neural Network with SAS

June 22, 2013
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Prototyping A General Regression Neural Network with SAS

Last time when I read the paper “A General Regression Neural Network” by Donald Specht, it was exactly 10 years ago when I was in the graduate school. After reading again this week, I decided to code it out with SAS macros and make this excellent idea available for the SAS community. The prototype of

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Advanced Graphics I

June 22, 2013
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Advanced Graphics I

Polygon is a such handy function in R for drawing beautiful charts where we can select regions (polygons) of the surface. It’s quite useful for indicating confidence regions of parameters, predictions for time-series, or areas under distributions:

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Calling C++ from R using Rcpp

June 22, 2013
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Why call C/C++ from R? I really like programming in R. The fact that it is open source immediately wins my favour over Matlab. It can, however, be quite slow especially if you “speak” R with a strong C/C++ accent. This sluggishness, especially when writing unavoidable for loops, has led me to consider other programming The post Calling...

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What is “Practical Data Science with R”?

June 22, 2013
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What is “Practical Data Science with R”?

A bit about our upcoming book “Practical Data Science with R”. Nina and I share our current draft of the front matter from the book, which is a description which will help you decide if this is the book for you (we hope that it is). Or this could be the book that helps explain Related posts:

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