Monthly Archives: February 2011

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 … Continue reading →

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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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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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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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