Generating Sankey Diagrams from rCharts

July 23, 2013
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Generating Sankey Diagrams from rCharts

A couple of weeks or so ago, I picked up an inlink from an OCLC blog post about Visualizing Network Flows: Library Inter-lending. The post made use of Sankey diagrams to represent borrowing flows, and by implication suggested that the creation of such diagrams is not as easy as it could be… Around the same

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Review: Kölner R Meeting 19 July 2013

July 23, 2013
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Review: Kölner R Meeting 19 July 2013

Despite the hot weather and the beginning of the school holiday season in North Rhine Westphalia the Cologne R user group met yet again for two fascinating talks and beer and schnitzel afterwards.Analysing Twitter data to evaluate the US Dollar / Euro exchange rates Dietmar Janetzko presented ideas to forecast US Dollar / Euro exchange rate movements...

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Vectors of S4 classes with non-trivial slots

July 22, 2013
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Vectors of S4 classes with non-trivial slots

Here’s another rabbit hole where I spent a bit of time this evening. I like OOP and I like the way R uses vectors. I’ve created a few classes and had started to code a function which would plot a set of them. It all seemed straightforward until I realized that the infrastructure for treating

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Visual debugging with RStudio

July 22, 2013
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Visual debugging with RStudio

Introduction From release 098.208 the last RStudio IDE comes with a visual debugger. Now debugging with R and RStudio becomes a simple and efficient task. This short post does not want to be a crash course: “debugging with R” nor … Continue reading →

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Bike sharing in 100 cities

July 22, 2013
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Bike sharing in 100 cities

Many cities around the world have bike sharing programs: pick up a bike at a docking station, ride it across town and drop it off at another session, and just pay for the time you use. (Even Albacete, the Spanish college down hosting last month's UseR conference, had one.) Most of these systems provide open data feeds of bike...

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More goodies from rCharts

July 22, 2013
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More goodies from rCharts

The guys developing rCharts continue to release enhancements by the day and I have taken advantage to update a couple of Shiny apps The CRAN download app now sports the new exporter feature so that any chart a user comes up with can be saved as a SVG vector, PNG or JPEG image or as

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Hierarchical Linear Model

July 22, 2013
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Hierarchical Linear Model

Linear regression probably is the most familiar technique of data analysis, but its application is often hamstrung by model assumptions. For instance, if the data has a hierarchical structure, quite often the assumptions of linear regression are feas...

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Create R package – Rstudio, github, devtools

July 22, 2013
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If you are going to create your first package in R, there is common set of tools you will probably use - Rstudio, devtools package and github. You don't have to, but it will save you a lot of time and your code wil be versioned and better understandabl...

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David vs. Goliath in Men’s Professional Tennis

July 22, 2013
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David vs. Goliath in Men’s Professional Tennis

David dances lightly from side to side, his small feet stirring up wisps of dust from the clay surface. Twirling his racket in anticipation, he peers intently at his colossal foe hoping to spot some clue where the first serve will go. Across the net is...

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Loading up your custom toolkits at startup – R

July 22, 2013
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If you are anything like me then you have dozens if not hundreds of personal functions that you have written to accomplish a number of tasks.  Many of the tasks that you would like to do are similar to previous tasks that you have already done. &n...

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Analyzing Your Data on the AWS Cloud (with R)

July 22, 2013
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Analyzing Your Data on the AWS Cloud (with R)

Guest post by Jonathan Rosenblatt Disclaimer: This post is not intended to be a comprehensive review, but more of a “getting started guide”. If I did not mention an important tool or package I apologize, and invite readers to contribute in the comments. …Read more »

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My first Bioconductor conference (2013)

July 21, 2013
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My first Bioconductor conference (2013)

The BioC 2013 conference was held from July 17 to 19. I attended this conference for my first time, mainly because I'm working at the Fred Hutchinson Cancer Research Center this summer, and the conference venue was just downstairs! No flights, no hotel...

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Read Excel files from R

July 21, 2013
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Many people still save their data into Microsoft Excel files. This is an unhappy choice for many reasons but many was already written about this topic. Furthermore, unfortunately Excel become a de facto standard in many business environment and this … Continue reading →

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Do the Simpsons characters like each other?

July 21, 2013
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Do the Simpsons characters like each other?

One day, while I was walking around Cambridge, I had a random thought -- how do the characters on the Simpsons feel about each other? It doesn't take long to figure out how Homer feels about Flanders (hint: he doesn't always like him), or how Burns feels about everyone, but how does Marge feel about Bart? How does Flanders...

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Do the Simpsons characters like each other?

July 21, 2013
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Do the Simpsons characters like each other?

One day, while I was walking around Cambridge, I had a random thought — how do the characters on the Simpsons feel about each other? It doesn’t take long to figure out how Homer feels about Flanders (hint: he doesn’t always like him), or how Burns feels about everyone, but how does Marge feel about Bart? ...

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Unique bytes in a sliding window as a file content signature

July 21, 2013
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Unique bytes in a sliding window as a file content signature

I was at a workshop a few months ago where a speaker pointed out a useful technique for spotting whether a file contains compressed data, e.g., a virus hidden in a script by compressing it to look like a jumble of numbers. Compressed data contains a uniform distribution of byte values (after all, compression is

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Modeling Match Results in La Liga Using a Hierarchical Bayesian Poisson Model: Part one.

July 21, 2013
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Modeling Match Results in La Liga Using a Hierarchical Bayesian Poisson Model: Part one.

This is a slightly modified version of my submission to the UseR 2013 Data Analysis Contest which I had the fortune of winning :) The purpose of the contest was to do something interesting with a dataset consisting of the match results from the last five seasons of La Liga, the premium Spanish football (aka soccer) league. In...

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Do the Simpsons characters like each other?

July 21, 2013
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Do the Simpsons characters like each other?

One day, while I was walking around Cambridge, I had a random thought -- how do the characters on the Simpsons feel about each other? It doesn't take long to figure out how Homer feels about Flanders (hint: he doesn't always like him), or how Burns feels about everyone, but how does Marge feel about Bart? How does Flanders...

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iRefR – PPI data access from R

July 21, 2013
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iRefR – PPI data access from R

I use a lot of protein-protein interaction (PPI) data as biological networks represent the systems within which our genes and proteins of interest function. There are many sources of PPI data, including BioGRID and IntAct etc. A recent effort has … Continue reading →

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Did the pattern of rain change in the last 100 years?

July 21, 2013
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Did the pattern of rain change in the last 100 years?

Last week I showed rain data from six stations in Netherlands years 1906 till now. The obvious next question is; did it change? A surprisingly difficult question. The data is not normal distributed, but it is time-correlated, location correlated.T...

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Le Monde puzzle [#825]

July 20, 2013
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Le Monde puzzle [#825]

The current puzzle is the last one before the summer break and not exciting enough to take along: Take the first ten digits, create five pairs out of those, and for each pair (x,y) derive the quantity (min(x,y)+1.5max(x,y)). What is the collection of pairs that maximises the product of those quantities? I wrote the following

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BCEs0

July 20, 2013
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BCEs0 is the new R package I've written $-$ well, nearly finished to, anyway; it should be ready in version 1.0 in the next few days. The acronym stands for Bayesian models for Cost-Effectiveness with structural 0s, and it basically implements the mode...

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A Quick and Dirty Guide to Exploratory Data Visualization

July 20, 2013
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A Quick and Dirty Guide to Exploratory Data Visualization

One of the things I've noticed teaching statistical fundamentals or working with colleagues is the lack of focus on first visually exploring the data.  Novices seem to want to jump right in with correlations and statistical tests without getting a...

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Generalized Linear Modelling in R (part 1)

July 20, 2013
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Generalized Linear Modelling in R (part 1)

In classical linear modelling we are assuming that the response variable (Y) is normally distributed, however for certain type of data like count data or presence/absence data this is not the case. There is in statistic an ensemble of technique called Generalized Linear Modelling (GLM in short) where the reponse variable follow one known distribution,

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Searching for chemical substances based on ATC codes from WHO search engine.

July 20, 2013
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The concept of how to grep search engine results with R had been one of my lingering thoughts. Because sometimes it's just feels easier if I could just grep search engine results than to find a dataset or complete database of a certain thing. So when...

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Searching for chemical substances based on ATC codes from WHO search engine.

July 20, 2013
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The concept of how to grep search engine results with R had been one of my lingering thoughts. Because sometimes it's just feels easier if I could just grep search engine results than to find a dataset or complete database of a certain thing. So when...

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Your science links for the week of July 19th

July 20, 2013
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Your science links for the week of July 19th

Howdy paleoposse! Here are this weeks sciency links for your weekend reading pleasure.  This weeks links cover gold producing neutron stars, the boredom of travelling to Mars, some words of inspiration from Richard Feynman, and Comic-Con 2013. Things that are science: The Giant Impact Model has long been the go to hypothesis for how the

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Simulation of Blackjack: the odds are not with you

July 19, 2013
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Simulation of Blackjack: the odds are not with you

I often want to simulate outcomes varying across a set of parameters. In order to accomplish this in an efficient manner I have coded up a little function that takes parameter vectors and produces results. First I will show how to set it up with some d...

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Column-Major Confusion

July 19, 2013
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As a programmer coming from a language like C I am used to understanding multidimensional arrays in the following way:int matrix = { { 1, 2, 3 }, { 4, 5, 6 }, { 7, 8, 9 }};Understandably, this is a little bit of a setback when trying to ...

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