Dynamic Wrapping and Recursion with Rcpp

April 8, 2013
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Dynamic Wrapping and Recursion with Rcpp

We can leverage small parts of the R’s C API in order to infer the type of objects directly at the run-time of a function call, and use this information to dynamically wrap objects as needed. We’ll also present an example of recursing through a list. To get a basic familiarity with the main functions exported from R API, I...

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Next Kölner R User Meeting: 12 April 2013

April 8, 2013
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Next Kölner R User Meeting: 12 April 2013

Quick reminder: The next Cologne R user group meeting is scheduled for this Friday, 12 April 2013. We will discuss cluster analysis and shiny. Further details and the agenda are available on our KölnRUG Meetup site. Please sign up if you would like to come along. Notes from the last Cologne R user group meeting are...

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analyze the pesquisa nacional por amostra de domicilios (pnad) with r

April 7, 2013
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think of the pesquisa nacional por amostra de domicilios (pnad) as the brazilian census for off-years - the ones that don't end in zero.  the principal household survey for the nation of brazil, pnad measures general education, labor, income, and ...

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Dirichlet Process, Infinite Mixture Models, and Clustering

April 7, 2013
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Dirichlet Process, Infinite Mixture Models, and Clustering

The Dirichlet process provides a very interesting approach to understand group assignments and models for clustering effects.   Often time we encounter the k-means approach.  However, it is necessary to have a fixed number of clusters.  Often we encounter situations where we don’t know how many fixed clusters we need.  Suppose we’re trying to identify

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A quick guide to non-transitive Grime Dice

April 7, 2013
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A quick guide to non-transitive Grime Dice

A very special package that I am rather excited about arrived in the mail recently. The package contained a set of 6-sided dice. These dice, however, don’t have the standard numbers one to six on their faces. Instead, they have assorted numbers between zero and nine. Here’s the exact configuration: Aside from maybe making for

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Venue Recommendation – A Simple Use Case Connecting R and Neo4j

April 7, 2013
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Venue Recommendation – A Simple Use Case Connecting R and Neo4j

Last month I attended the CeBIT trade fair in Hannover. Besides the so called “shareconomy” there was also another main topic across all expedition halls - Big Data. This subject is not completely new and I think that a lot of you also have experiences with some of the tools associated with Big Data. But due to the great...

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Mastering Matrices

April 7, 2013
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Mastering Matrices

R has many ways to store information.  Most of the time, our data comes in the form of a dataset, which we bring into R as a data.frame object. However, there are times when we want to use matrices as well. This post will show you how matrices can...

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Sync

April 7, 2013
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Sync

I am listening to the audiobook Sync: How Order Emerges from Chaos in the Universe, Nature, and Daily Lifeby Steven Strogatz which I got from Audible. Obviously a mathematical book is not ideal to listen to, but lacking illustrations I can ma...

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Travis CI for R?

April 7, 2013
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Travis CI for R?

I'm always worried about CRAN: a system maintained by FTP and emails from real humans (basically one of Uwe, Kurt or Prof Ripley). I'm worried for two reasons: the number of R packages is growing exponentially; time and time again I see frustrations ...

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Guide to accessing MS SQL Server and MySQL server on Mac OS X

April 6, 2013
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Native GUI client access to MS-SQL and MySQL We can use Oracle SQL Developer with the jTDS driver to access Microsoft SQL Server. Note: jTDS version 1.3.0 did not work for me; I had to use version 1.2.6. Detailed instructions can be found here. We can use MySQL Workbench to access MySQL server. Setup is... Read more »

Mortality after paediatric heart surgery using public domain data

April 6, 2013
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Mortality after paediatric heart surgery using public domain data

This post comes with some big health warnings. The recent events in Leeds highlight the difficulties faced in judging the results of surgery by individual hospital. A clear requirement is timely access to data in a form easily digestible by the public. Here I’ve scraped the publically available data from the central cardiac audit database

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Retirement : simulating wealth with random returns, inflation and withdrawals – Shiny web application

April 6, 2013
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Retirement : simulating wealth with random returns, inflation and withdrawals – Shiny web application

Today, I want to share the Retirement : simulating wealth with random returns, inflation and withdrawals – Shiny web application (code at GitHub). This application was developed and contributed by Pierre Chretien, I only made minor updates. This is application is a great example of how easy it is to convert your R script into

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Worry about correctness and repeatability, not p-values

April 5, 2013
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Worry about correctness and repeatability, not p-values

In data science work you often run into cryptic sentences like the following: Age adjusted death rates per 10,000 person years across incremental thirds of muscular strength were 38.9, 25.9, and 26.6 for all causes; 12.1, 7.6, and 6.6 for cardiovascular disease; and 6.1, 4.9, and 4.2 for cancer (all P < 0.01 for linear Related posts:

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Reconstructing Principal Component Analysis Matrix

April 5, 2013
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Reconstructing Principal Component Analysis Matrix

PCA is widely used method for finding patterns in high-dimensional data. Whether you use it to compress large matrix or to remove one of the principal components in biological datasets, you’ll end up with the task of performing series of … Continue reading →

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Organise your data

April 5, 2013
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Use R to specify factors, recode variables and begin by-group analyses. Video Files This file contains data on pain score after laparoscopic vs. open hernia repair. Age, gender and primary/recurrent hernia also included. The ultimate aim here is to work out which of these factors are associated with more pain after this operation. lap_hernia Script

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Properly “internationalized” regular expressions in R

April 5, 2013
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We should pay special attention to writing a truly portable code that works in the same fashion under different locales and character encodings. Currently, R has two Regex engines, ERE (via TRE) and PRE (via PCRE). What is surprising, they…Read more ›

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Security in R: RAppArmor package & paper updates

April 5, 2013
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This week version 0.8.3 of RAppArmor appeared on CRAN. RAppAmor is a package to dynamically enforce security policies and hardware restrictions in R on Linux systems. It currently supports Ubuntu 12.04+, Debian 7 and OpenSuse 12.1+. The readme page has more info, and helpful video tutorials to get you started. One important change in the ...

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Multiple pairwise comparisons for categorical predictors

April 5, 2013
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Multiple pairwise comparisons for categorical predictors

Dale Barr (@datacmdr) recently had a nice blog post about coding categorical predictors, which reminded me to share my thoughts about multiple pairwise comparisons for categorical predictors in growth curve analysis. As Dale pointed out in his post, the R default is to treat the reference level of a factor as a...

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Interview by DecisionStats

April 5, 2013
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Ajay Ohri interviewed me on his popular DecisionStats blog. Topics discussed ranged widely from Fellows Statistics, to Deducer, to statnet, to Poker A.I., to Big Data.    

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Extending RevoScaleR for Mining Big Data – Hexbins

April 5, 2013
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Extending RevoScaleR for Mining Big Data – Hexbins

by Derek McCrae Norton, Senior Sales Engineer It is my job to help potential clients see that the tasks they are used to completing can be completed on big data in Revolution R Enterprise (and that it is easy). Honestly, this is my dream job, and in my eyes it is sort of like playing and getting paid for...

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Import/Export data to and from xlsx files

April 5, 2013
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Import/Export data to and from xlsx files

As Ive already written, getting data into R from your precious xlsx files is really handy. No need to clutter up your computer with txt or csv files. The previous post I wrote about the gdata package for importing data from xlsx files and was pointed to, among others, the xlsx package. xlsx seems to

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Estimated Follower Accession Charts for Twitter

April 5, 2013
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Estimated Follower Accession Charts for Twitter

Just over a year or so ago, Mat [email protected] introduced me to a visualisation he’d been working on (How should Page Admins deal with Flame Wars?) that I started to refer to as an accession chart (Visualising Activity Around a Twitter Hashtag or Search Term Using R). The idea is that we provide each entrant

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R, D3.js and SNA Course

I took the SNA course by Lada Adamic in coursera. It's a super interesting course. In fact, I was using the networks only how a visualization tool, and that is what it make me little bit embarrassing because there are more, a lot of more. You can detec...

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d3 Lifeline from vega and clickme

April 4, 2013
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This has been an exciting week for d3.js and R with the release of vega by the data vis powerhouses at Trifacta launch of clickme and already significant rewrite to accommodate vega inception of a very promising d3 templates DexCharts described in multiple posts. I am glad to have had...

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Announcing eeptools 0.2

April 4, 2013
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My R package eeptools has reached version 0.2. As with the last release, this is still a preliminary release which means that functionality is not full, function names and code behavior may still change from version to version, and I am still looking f...

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Subtraction Is Crazy

April 4, 2013
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Subtraction Is Crazy

I was re-reading Michael Murray’s explanation of cointegration: and marvelling at the calculus. Calculus blows my mind sometimes. Like, hey guess how much we can do with subtraction. — protëa(@isomorphisms) March 28, 2013 Of course it’s not any subtraction. It’s subtracting a function from a shifted version of itself. Still doesn’t sound like a universal revolution. (But of course the...

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R, D3js and SNA Course

April 4, 2013
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R, D3js and SNA Course

Update 2015-11-09: This is migration from an old post. I took the SNA course by Lada Adamic in coursera. It’s a super interesting course. In fact, I was using the networks only how a visualization tool, and that is what it make me little bit embarrassing because there are more, a lot of more. You can detect communities,...

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Tutorial- Building Biological Networks

April 4, 2013
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Tutorial- Building Biological Networks

I love networks! Nothing is better for visualizing complex multivariate relationships be it social, virtual or biological. I recently gave a hands-on network building tutorial using R and Cytoscape to build large biological networks. In these networks Nodes represent metabolites and edges can be many things, but I specifically focused on biochemical relationships and chemical

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Demographic analysis using the `popbio` library and some other fun stuff

April 4, 2013
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Demographic analysis using the `popbio` library and some other fun stuff

This week at the Davis R Users’ Group we had a great presentation by Kara Moore O’Leary on using the popbio package to examine rare plant demographics. The following is her script run through knitr. You can download the original script and associated data here. Find out more about Kara and her work at...

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