Monthly Archives: November 2010

Advanced Markov Chain Monte Carlo Methods (AMCMC)

November 27, 2010
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Advanced Markov Chain Monte Carlo Methods (AMCMC)

I’ve just received my copy of Advanced Markov Chain Monte Carlo Methods, by Liang, Liu, & Carroll. Although my PhD didn’t really involve any Bayesian methodology (and my undergrad was devoid of any Bayesian influence), I’ve found that the sort of problems I’m now tackling in systems biology demand a Bayesian/MCMC approach. There are a

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RcppArmadillo 0.2.10

November 26, 2010
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Conrad Sanderson released version 1.0.0 of Armadillo, his templated C++ library for linear algebra, earlier this week. So congratulations to Conrad on reaching 1.0.0! I folded his version 1.0.0 into a new release 0.2.10 of RcppArmadillo, our Rcpp-base...

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Yet another inferno

November 26, 2010
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Yet another inferno

Many from the R world will know The R Inferno. Abstract: If you are using R and you think you’re in hell, this is a map for you. A newly minted inferno is The 9 circles of scientific hell. Most amusing to me is Circle 4: p-value fishing, the punishment of which is brilliant. As … Continue reading...

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Computational tools for Bayesian analysis

November 26, 2010
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The increasing number of R-oriented Bayesian computational tools such as MCMCpack, MCMCglmm, DPpackage, R-INLA, spBayes, have made BUGS less and less crucial for day to day Bayesian computation. Honestly, I cannot figure out a single analysis that BUGS...

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Computational tools for Bayesian analysis

November 26, 2010
By

The increasing number of R-oriented Bayesian computational tools such as MCMCpack, MCMCglmm, DPpackage, R-INLA, spBayes, have made BUGS less and less crucial for day to day Bayesian computation. Honestly, I cannot figure out a single analysis that BUGS...

Read more »

Sweave Tutorial 1: Using Sweave, R, and Make to Generate a PDF of Multiple Choice Questions

November 26, 2010
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In this post I present an example of using Sweave to prepare a PDF of formatted multiple choice questions. More broadly the example shows how to use Sweave to incorporate elements of a database into a formatted LaTeX document. It aims to be useful to anyone wanting to learn more about the almost magical powers of make, Sweave,...

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Sweave Tutorial 1: Using Sweave, R, and Make to Generate a PDF of Multiple Choice Questions

November 26, 2010
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Sweave Tutorial 1: Using Sweave, R, and Make to Generate a PDF of Multiple Choice Questions

In this post I present an example of using Sweave to prepare a PDF of formatted multiple choice questions.More broadly the example shows how to use Sweave to incorporate elements of a databaseinto a formatted LaTeX document.It aims to be useful to any...

Read more »

Hierarchical Cluster Analysis

November 25, 2010
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Hierarchical Cluster Analysis

With the distance matrix found in previous tutorial, we can use various techniques of cluster analysis for relationship discovery. For example, in the data set mtcars, we can run the distance matrix with hclust, and plot a dendrogram that displays a ...

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Hierarchical Cluster Analysis

November 25, 2010
By
Hierarchical Cluster Analysis

With the distance matrix found in previous tutorial, we can use various techniques of cluster analysis for relationship discovery. For example, in the data set mtcars, we can run the distance matrix with hclust, and plot a dendrogram that displays a ...

Read more »

Happy Thanksgiving!

November 25, 2010
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It's holiday time here in the US, so we're taking a break at Revolutions. We'll be back with more R goodness on Monday, but in the meantime, think of the turkeys. R-chart: Don't be a Turkey

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