Access all UCSC wiggle tracks from R and your terminal

February 21, 2011
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rtracklayer package allows you to access most of the UCSC wiggle tracks from R. However, there is another way which might more practical in situations where you need to summarize the wig track scores over a given set of genomic coordinates. Although yo...

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Choropleth tutorial and regression coefficient plots

February 21, 2011
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Choropleth tutorial and regression coefficient plots

About two weeks ago, I gave short talk at Duke, wherein I presented a brief tutorial on creating choropleth maps in R using ggplot2. Since the code is already written, and the data and shapefiles already hosted online, I thought I would share the tutorial more widely. A .ZIP file containing all the files necessary … Read more

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R Tutorial Series: Two-Way Repeated Measures ANOVA

February 21, 2011
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R Tutorial Series: Two-Way Repeated Measures ANOVA

Repeated measures data require a different analysis procedure than our typical two-way ANOVA and subsequently follow a different R process. This tutorial will demonstrate how to conduct two-way repeated measures ANOVA in R using the Anova() function fr...

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R Tutorial Series: Two-Way Repeated Measures ANOVA

February 21, 2011
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R Tutorial Series: Two-Way Repeated Measures ANOVA

Repeated measures data require a different analysis procedure than our typical two-way ANOVA and subsequently follow a different R process. This tutorial will demonstrate how to conduct two-way repeated measures ANOVA in R using the Anova() function fr...

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Presentation on Building R Packages

February 21, 2011
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Last week I gave a presentation to the Melbourne R User Group on Building R Packages. The talk covered a simple package example, and an example of interfacing R with native code. The slides are here: RPackages.pdf. The R community in Melbourne (and Aus...

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Tracking the Frequency of Twitter Hashtags with R

February 21, 2011
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Tracking the Frequency of Twitter Hashtags with R

 I’ve posted three examples of Twitter hashtags datasets in the last week: one on China, one on Iran, and one on Algeria.  In order to build these datasets, I needed to obtain older tweets; this is slightly more difficult than … Continue reading →

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Child health metrics

February 20, 2011
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Child health metrics

In analysis of Child Health data, generally z-scores or percentile groupings are used as children do not growth is not linear. The CDC (Center for Disease Control and Prevention) have released tables of data for calculating these z-scores and percentiles, and here are some scripts for R to calculate these in your sample. CLICK HERE

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R Optimisation Tips using Optim and Maximum Likelihood

February 20, 2011
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This post summarises some R modelling tips I picked up at AMPC2011. I got some tips from a tutorial on parameter estimation put on by Scott Brownfrom the Newcastle Cognition Lab. The R code used in the tutorial is available directly hereor from the ...

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R Optimisation Tips using Optim and Maximum Likelihood

February 20, 2011
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R Optimisation Tips using Optim and Maximum Likelihood

This post summarises some R modelling tips I picked up atAMPC2011.I got some tips from a tutorial on parameter estimationput on by Scott Brownfrom the Newcastle Cognition Lab.The R code used in the tutorial is available directly hereor from the confer...

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Does the Student based confidence interval have any interest in practice ?

February 20, 2011
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Does the Student based confidence interval have any interest in practice ?

Friday in the course of statistics, we started the section on confidence interval, and like always, I got a bit confused with the degrees of freedom of the Student (should it be or ?) and which empirical variance (should we consider the one wher...

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R versus Matlab in Mathematical Psychology

February 20, 2011
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I recently attended the 2011 Australasian Mathematical Psychology Conference. This post summarises a few thoughts I had on the use of R, Matlab and other tools in mathematical psychology flowing from discussions with researchers at the conference. I w...

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R versus Matlab in Mathematical Psychology

February 20, 2011
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R versus Matlab in Mathematical Psychology

I recently attended the 2011 Australasian Mathematical Psychology Conference.This post summarises a few thoughts I had on the use of R, Matlab and othertools in mathematical psychology flowing from discussions with researchers atthe conference.I wanted...

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Converting MATLAB and R date and time values

February 20, 2011
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For some unknown reason, MATLAB codes its date/time values as the number of elapsed days starting from January 1 in the year 0000. R uses the equally arbitrary, but much more widespread POSIX/Unix epoch as a reference for time keeping, so that R’...

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Vectorize!

February 20, 2011
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Vectorize!

Here is an email sent by one of my students a few days ago: Do you know how to integrate a function with an  “if”? For instance: >X=rnorm(100) >Femp=function(x){ +   return(sum(X<x)) +} >integrate(Femp,0,1)$value does not work. My reply was that the fundamental reason it does not work is that integrate (or curve for instance)

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Dataset: Tweets from the Chinese Protests #cn220

February 20, 2011
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Dataset: Tweets from the Chinese Protests #cn220

  Earlier this week, I posted a ~100k tweet dataset on the #25bahman protests in Iran.  The corresponding figure of frequencies showed a strong presence on Twitter, with over 500 tweets per 5 minute period at peak.  You can download the … Continue reading →

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New R features in Bio7 1.5

February 20, 2011
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New R features in Bio7 1.5

Bio7 1.5 has been released and comes with new functionalities for R. For all who don’t know Bio7 here is a short description: Bio7 is a integrated development environment for ecological modelling based on the Rich-Client-Platform concept of the Java IDE Eclipse. The Bio7 platform contains several perspectives which arrange several views for a special

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UseR! 2011 in Warwick

February 20, 2011
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UseR! 2011 in Warwick

This year useR! conference will take place in Warwick, on August 16-18.  It is being organised by the department of Statistics and funded by CRiSM and Revolution Analytics (providers of the R tee-shirt!). I wish I could attend but mid-August is usually associated with genuine (post-JSM) family vacations. Filed under: R, Statistics, University life Tagged:

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Talking R through Java

February 20, 2011
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Talking R through Java

Today I played a bit with JRI as part of rJava, a Java-R-interface. Here you can learn how to setup for Debian/Ubuntu/akins.

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Open-sourcing some of my automation code

February 19, 2011
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Open-sourcing some of my automation code

To automate my trading I use a mix of scripts. Everything goes – R, Python, shell, C++, etc. For some time now I have been satisfied with the tools I have created. They run once a day, gather data from EODDATA, update the database, run some R magic to decide what needs to be done

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Software tools for data analysis – an overview

February 19, 2011
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Software tools for data analysis – an overview

by Szilard Pafka Discussions on various software tools (C, C++, Perl, Python, Unix shell, R, Matlab, SAS, SPSS, Excel, databases, Hadoop etc.) used in data analysis. Szilard Pafka (founder and co-organizer of the Los Angeles R users group) presents an … Continue reading →

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Parallel computation [permutations]

February 19, 2011
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Parallel computation [permutations]

François Perron is visiting me for two months from Montréal and, following a discussion about the parallel implementation of MCMC algorithms—to which he also contributed with Yves Atchadé in 2005—, he remarked that a deterministic choice of permutations with the maximal contrast should do better than random or even half-random permutations. Assuming p processors or

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Screen Scraping, Mapping in R

February 19, 2011
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by Earl F. Glynn, Kansas Watchdog The PowerPoint slides below give an overview of screen scraping and mapping in R. Details with comments about many of the R statements can be found in these articles: Simple R Screen Scraping Example R Screen Scraping:...

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Working with multiple graphs in R

February 19, 2011
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Working with multiple graphs in R

I'm trying out screencasting to help illustrate some tips and tricks with the statistics software package R, but also to hone my skills in this area.I'm including the code for this example as an attachment to this post.I'm in the proces...

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R Bloggers: The Site I Wish Existed in 2007

February 19, 2011
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R Bloggers: The Site I Wish Existed in 2007

  My first experience with R was in 2007 as a sophomore in undergrad.  As part of a larger project on pricing day-ahead electricity futures, I wanted to cluster locational marginal price (LMP) data from the ISO-NE.  Something like k-means is easy … Continue reading →

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IBM has a Natural Language Purpose

February 19, 2011
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I wanted to write a blog post about the advancements of Natural Language Processing in light of the performance of IBM's Watson on the Jeopardy challenge last week.  Natural Language Processing is the science of transforming and interpreting human...

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IBM has a Natural Language Purpose

February 19, 2011
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I wanted to write a blog post about the advancements of Natural Language Processing in light of the performance of IBM's Watson on the Jeopardy challenge last week.  Natural Language Processing is the science of transforming and interpreting human...

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RcppArmadillo 0.2.13

February 19, 2011
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Yesterday Conrad Sanderson released version 1.1.4 of his Armadillo templated C++ library for linear algebra, so hot on the heels our 0.2.12 release from a few days ago comes version 0.2.13 of RcppArmadillo, our Rcpp-based integration into R. This new...

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Readability vs speed in R

February 19, 2011
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I have bad news for those of you trying to produce lucid code!

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Analysis and Mapping of Kansas Judicial Retention Elections by County Using R

February 19, 2011
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by Earl F. Glynn, Kansas Watchdog This article describes how the data obtained from scraping 105 pages of county election data were analyzed and mapped using R. Background The Kansas Secretary of State published Nov. 2010 election results online, inclu...

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