A Graphical Explanation of how to Interpret a Dendrogram

March 15, 2012
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A Graphical Explanation of how to Interpret a Dendrogram

Dendrograms are a convenient way of depicting pair-wise dissimilarity between objects, commonly associated with the topic of cluster analysis. This is a complex subject that is best left to experts and textbooks, so I won't even attempt to cover it her...

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New R User Group in Montreal

March 15, 2012
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New R User Group in Montreal

The Montreal R User Group is now official. You can join the group by visiting the meetup site. The group has existed since 2010 in a narrower incarnation as the BGSA R/Stats Workshop Series. Previous workshops have featured invited facilitators on topics such as Causal Analysis, GLMs, GAMs, Multi-model inference, Phylogenetic analysis, Bayesian modeling, Meta-analysis,

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Project Euler: Problem 16

March 15, 2012
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215 = 32768 and the sum of its digits is 3 + 2 + 7 + 6 + 8 = 26.What is the sum of the digits of the number 21000?Handling large numbers or rather, very large numbers, can be a pain at times. But have no fear, for GMP is here.GMP  makes the s...

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Call for chapters: Data Mining Applications with R

March 15, 2012
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Call for chapters: Data Mining Applications with R

Data Mining Applications with R A book to be published by Elsevier http://www.RDataMining.com/books/book2 Proposal Submission Deadline: April 30, 2012 Introduction R is one of the most widely used data mining tools in scientific and business applications, among dozens of commercial … Continue reading →

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Ideas on A Really Fast Statistics Journal

March 15, 2012
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I was writing comments on the blog post A proposal for a really fast statistics journal, and I realized the comment box was too small to write down my ideas. I like the proposal a lot, and I feel really bad about the current model of submitting and rev...

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R and Hadoop: Step-by-step tutorials

March 14, 2012
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R and Hadoop: Step-by-step tutorials

At the recent Big Data Workshop held by the Boston Predictive Analytics group, airline analyst and R user Jeffrey Breen gave a step-by-step guide to setting up an R and Hadoop infrastructure. Firstly, as a local virtual instance of Hadoop with R, using VMWare and Cloudera's Hadoop Demo VM. (This is a great way to get familiar with Hadoop.)...

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AQP / soilDB Demo: Dueling Dendrograms

March 14, 2012
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AQP / soilDB Demo: Dueling Dendrograms

Previously, soil profile comparison methods from the aqp package only took into account horizon-level attributes. As of last week the profile_compare() function can now accommodate horizon and site-level attributes. In other words, it is now possible t...

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Plotting individual growth charts

March 14, 2012
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Plotting individual growth charts

This R code draws individual growth plots as shown in “Applied Longitudinal Data Analysis: Modeling Change and Event Occurrence” by Judith D. Singer and John B. Willett, an excellent book on multilevel modeling and survival analysis. This code recreates figure … Continue reading →

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R code for p curves

March 14, 2012
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I have finally got around to posting the R code for my p curve simulation. Those familiar with R will realize how crude it is (I've been caught up with other urgent stuff and had no time to explore further).You are welcome to play with (and improve!) t...

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Portfolio Optimization: Specify constraints with GNU MathProg language

March 14, 2012
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Portfolio Optimization: Specify constraints with GNU MathProg language

I have previously described a few examples of portfolio construction: Introduction to Asset Allocation Maximum Loss and Mean-Absolute Deviation risk measures 130/30 Portfolio Construction Minimum Investment and Number of Assets Portfolio Cardinality Constraints Multiple Factor Model – Building 130/30 Index (Update) I created a number of helper functions to simplify process of making the constraints(

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Scales and transformations in ggplot2 0.9.0

March 14, 2012
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Scales and transformations in ggplot2 0.9.0

Some R code designed for ggplot2 0.8.9 is not compatible with ggplot2 0.9.0, and today the ggplot2 web site has outdated documentation which gives this broken example: Dennis Murphy points to the ggplot2 0.9.0 transition guide from where I derived … Continue reading →

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NIT: Fatty acids study in R – Part 007

March 14, 2012
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NIT: Fatty acids study in R – Part 007

Once we have chosen the model, we can continue acquiring spectra of new samples. Spectra is exported to a txt or csv file and we imported in R to be reprocessed.We use the function “predict” from the PLS package. I have done this with 20 new sample...

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Creating a Stratified Random Sample of a Dataframe

March 14, 2012
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Creating a Stratified Random Sample of a Dataframe

Expanding on a question on Stack Overflow I'll show how to make a stratified random sample of a certain size: d <- expand.grid(id = 1:35000, stratum = letters)p = 0.1dsample <- data.frame()system.time(for(i in levels(d$stratum)) { dsub <...

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Video Tip: Convert Gene IDs with Biomart

March 14, 2012
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I get asked frequently how to convert from one gene identifier to another. This can be tricky, especially when relying on gene symbols, as Will pointed out in a previous post a few years ago. There are several tools that can do this, including DAVID an...

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March Madness! Wanna Win?

March 14, 2012
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March Madness! Wanna Win?

Description: Winning percentage of all NCAA Men's Basketball Tournament Champions. Analysis: Down by one, the ball spins in his hand as he dribbles up the floor. With tennis shoes squeaking, he feints left, then right. Glancing up at the clock,...

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π Day Special! Estimating π using Monte Carlo

March 14, 2012
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π Day Special! Estimating π using Monte Carlo

In honour of π day (03.14 – can’t wait until 2015~) , I thought I’d share this little script I wrote a while back for an introductory lesson I gave on using Monte Carlo methods for integration. The concept is simple – we can estimate the area of an object which is inside another object

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Visualising F1 Telemetry Data and Plotting Latitude and Longitude with ggplot Map Projections in R

March 14, 2012
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Visualising F1 Telemetry Data and Plotting Latitude and Longitude with ggplot Map Projections in R

Why don’t X-Y plots of latitude and longitude data look “right” compared to traditional map views? For example, here’s an X-Y scatterplot of some of Jenson Button’s McLaren telemetry data from the 2010 Australian Formula One Grand Prix: The image was generated, from a data file hosted on Google Spreadsheets, using the following R script,

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A ridiculous proof of concept: xyz interpolation

March 14, 2012
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A ridiculous proof of concept: xyz interpolation

Ridiculous OrbThis is really the last one on this theme for a while... I had alluded to a combination of methods regarding xyz interpolation at the end of my last post and wanted to demonstrate this in a final example.The ridiculousness that you see above involved two interpolation steps. First,...

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How to convert contingency tables to data frames with R

March 14, 2012
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I wanted to write contingency tables in HTML with hwrite(). I realized that the method hwrite() does not exist for the table objects. I could use as.data.frame(), but the table produced is non-intuitive. I did a search on R-bloggers and I quickly found the solution to my problem: the as.data.frame.matrix() function. The contingency table A

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ThinkStats … in R :: Example/Chapter 2 :: Example 2.1-2.3

March 14, 2012
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ThinkStats … in R :: Example/Chapter 2 :: Example 2.1-2.3

As promised, this post is a bit more graphical, but I feel the need to stress the importance of the first few points in chapter 2 of the book (i.e. the difference between mean and average and why variance is meaningful). These are fundamental concepts for future work. The “pumpkin” example (2.1) gives us an

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Simple plots reveal interesting artifacts

March 14, 2012
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Simple plots reveal interesting artifacts

I’ve recently been working with methylation data; specifically, from the Illumina Infinium HumanMethylation450 bead chip. It’s a rather complex array which uses two types of probes to determine the methylation state of DNA at ~ 485 000 sites in the genome. The Bioconductor project has risen to the challenge with a (somewhat bewildering) variety of

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More Anthromes !

March 13, 2012
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More Anthromes !

First off let me thank folks for all the comments and suggestions. I’m just starting to explore this data so perhaps I should explain how I go about  doing this. First off, I am looking for a global bias in the record from UHI. It is well known that you can look through the data

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Japan Trade More Specifically with Korea

March 13, 2012
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Japan Trade More Specifically with Korea

Macro analysis of Japanese trade in posts Japanese Trade and the Yen and Japan Trade by Geographic Region revealed some very interesting changes.  Since the Korean Won is so undervalued versus the Japanese Yen on a Purchasing Power Parity (PPP) ba...

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Plotting forecast() objects in ggplot part 1: Extracting the Data

March 13, 2012
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Lately I've been using Rob J Hyndman's excellent forecast package. The package comes with some built in plotting functions but I found I wanted to customize and make my own plots in ggplot. In order to do that, I need a generalizable function that will...

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Plotting forecast() objects in ggplot part 1: Extracting the Data

March 13, 2012
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Lately I've been using Rob J Hyndman's excellent forecast package. The package comes with some built in plotting functions but I found I wanted to customize and make my own plots in ggplot. In order to do that, I need a generalizable function that will...

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SNA with R workshop at Sunbelt XXXII in Redondo Beach

March 13, 2012
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SNA with R workshop at Sunbelt XXXII in Redondo Beach

I am currently in Redondo Beach, CA at the Sunbelt XXXII social networks conference. The program is thick from numerous interesting talks so the event promises to be very interesting. Today in the morning I gave the workshop “Introduction to Social Network Analysis with R”. Over 50 people registered. I am grateful to all the

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Scatter Plot Matrix in R

March 13, 2012
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Stata has a large number of graphics capabilities (and I highly recommend Stata over other statistical packages for a variety of reasons), but in a few instances R is more useful. In particular, I find R useful for creating beautiful scatter plot ...

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Shapley-Shubik Power Index in R

March 13, 2012
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Shapley-Shubik Power Index in R

This spring we have Rector Elections at Warsaw School of Economics. One of my collegues Tomasz Szapiro agreed to start in the elections. This induced me to write Shapley-Shubik Power Index calculation snippet in R.Rector elections in Warsaw School...

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Video: Using R in Academic Finance

March 13, 2012
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The slides and replay for Dr Sanjiv Das's webinar, Using R for Analyzing Loans, Portfolios and Risk: From Academic Theory to Financial Practice are now available. I've embedded the slides below: they tell a great story of how Das, after being mistaken for the then-CEO of Citibank (with whom he shares a name) was then led to research (using...

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