Plotting contours

March 18, 2008
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Plotting contours

Plenty of packages allow you to plot contours of a "z" value; however, I wanted to be able to plot a specific density contour of a sample from a bivariate distribution over a plot that was a function of the x and y parameters. The example only plots th...

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Plotting contours

March 18, 2008
By
Plotting contours

Plenty of packages allow you to plot contours of a "z" value; however, I wanted to be able to plot a specific density contour of a sample from a bivariate distribution over a plot that was a function of the x and y parameters. The example only plots th...

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An Example for Just Another Gibbs Sampler (JAGS)

March 4, 2008
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JAGS is a cross platform BUGS. Because it runs in a command mode, it is somewhat faster than other BUGS. However, I found it is a bit tacky to use it as a Windows/PC user. I found the manual very useful but some of the language is a bit uncommon to regular users. For instance, compile [,nthins( < n...

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An Example for Just Another Gibbs Sampler (JAGS)

March 4, 2008
By

JAGS is a cross platform BUGS. Because it runs in a command mode, it is somewhat faster than other BUGS. However, I found it is a bit tacky to use it as a Windows/PC user. I found the manual very useful but some of the language is a bit uncommon to regular users. For instance, compile [,nthins( < n...

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Writing Rd files in Vim

March 3, 2008
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Writing Rd files in Vim

I have made a small “translation” of a portion of “Writing R Extensions” manual about the Rd files to a vimhelp format. You can find it on vim.org, under this link http://www.vim.org/scripts/script.php?script_id=2177. If that does not work just search for a script “rd” there. The script itself is called “rdhelp.txt”.

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Ordered logistic model with varying intercepts (random effects)

March 2, 2008
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I coauthor a paper with Ozan, a friend who I know when I was TAing Bayesian Methods in ICPSR. The paper tries to see if the 9/11 has any effect on American's attitudes on Muslim. We have dataset from different years: 2 from pre-9/11 periods and 2 from ...

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Ordered logistic model with varying intercepts (random effects)

March 2, 2008
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I coauthor a paper with Ozan, a friend who I know when I was TAing Bayesian Methods in ICPSR. The paper tries to see if the 9/11 has any effect on American's attitudes on Muslim. We have dataset from different years: 2 from pre-9/11 periods and 2 from ...

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Find type of variables in a data frame

February 20, 2008
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sapply(a,class) gives type of field (character, numeric, or factor) for each variable in the data frame a.

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A wraper function to convert coda files into a BUGS object

February 11, 2008
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I used to fit Bayesian model using WinBUGS via R a lot. But now I am more and more prone to run models on OpenBUGS directly. I have document the reason why I like OpenBUGS and wrote a auto OpenBUGS function here. In short, I like to be able to know wha...

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A wraper function to convert coda files into a BUGS object

February 11, 2008
By

I used to fit Bayesian model using WinBUGS via R a lot. But now I am more and more prone to run models on OpenBUGS directly. I have document the reason why I like OpenBUGS and wrote a auto OpenBUGS function here. In short, I like to be able to know wha...

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R graph with two y-axes

February 4, 2008
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R graph with two y-axes

I’ve been asked how to do this several times, so I thought it might help to put an example online. x <- 1:5 y1 <- rnorm(5) y2 <- rnorm(5,20) par(mar=c(5,4,4,5)+.1) plot(x,y1,type="l",col="red") par(new=TRUE) plot(x, y2,,type="l",col="blue",xaxt="n",yaxt="n",xlab="",ylab="") axis(4) mtext("y2",side=4,line=3) legend("topleft",col=c("red","blue"),lty=1,legend=c("y1","y2"))

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R graph with two y-axes

February 4, 2008
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R graph with two y-axes

I’ve been asked how to do this several times, so I thought it might help to put an example online. x <- 1:5 y1 <- rnorm(5) y2 <- rnorm(5,20) par(mar=c(5,4,4,5)+.1) plot(x,y1,type="l",col="red") par(new=TRUE) plot(x, y2,,t...

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Drop unused factor levels

February 4, 2008
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When creating a subset of a dataframe, I often exclude rows based on the level of a factor. However, the "levels" of the factor remain intact. This is the intended behavior of R, but it can cause problems in some cases. I finally discovered how to clean up levels in this post to R-Help. Here is an example:>...

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Drop unused factor levels

February 4, 2008
By

When creating a subset of a dataframe, I often exclude rows based on the level of a factor. However, the "levels" of the factor remain intact. This is the intended behavior of R, but it can cause problems in some cases. I finally discovered how to clean up levels in this post to R-Help. Here is an example: >...

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R package: codetools

February 4, 2008
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Since the release of R_2.6.0, R package developers were advised to use the ``codetools" package to check potential bugs. However, as I am not familiar with computer language, I found the warning messages a bit confusing. For example:> checkUsage(glm.fit): no visible binding for global variable ‘n’I don't understand what it really means. Apparently, `n' was not globally defined but...

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Paper on the Gillespie Stochastic Simulation Algorithm in press

February 1, 2008
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Paper on the Gillespie Stochastic Simulation Algorithm in press

Just got news that my revisions to the reviewer’s comments on my paper GillespieSSA: Implementing the Gillespie Stochastic Simulation Algorithm in R were accepted. Hence, this paper is not officially in press in the Journal of Statistical Software. Here’s the … Continue reading →

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New material on the GGobi book web page

January 30, 2008
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The GGobi book is now available from Springer and Amazon, after quite a delay. Getting the figures printed correctly was difficult. Solutions to the exercises in the back of each chapter are available for instructors by emailing Springer.The movies on ...

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New material on the GGobi book web page

January 30, 2008
By

The GGobi book is now available from Springer and Amazon, after quite a delay. Getting the figures printed correctly was difficult. Solutions to the exercises in the back of each chapter are available for instructors by emailing Springer.The movies on ...

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The hammer, or the sledgehammer? A small study in simulation

January 29, 2008
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RKN over at Epidemiology blog had a small problem he solved using simulation:I have been interested in the following question: if there are, let's say, 5 genes involved in the liability of fx risk, and each gene has two alleles with one of them conferr...

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Shading overlapping area of curves in R

January 28, 2008
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I was trying to plot figure in R like the one below, which is basically the veto player model of Tsebelis. Based on my knowledge of R now, I encountered 2 major problems:I don't know if there is a function that can draw archs, or at least partial curves from circles.I don't know if there is a good way...

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Heuristics for statistics

January 28, 2008
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Heuristics for statistics

SIMPLE WAYS TO DETECT AND COMMUNICATE STATISTICAL EFFECTS Decision Science News is fond of heuristics and the Simonian view that for many problems organisms face, optimization is a fiction and satisficing makes us smart. Statistics is an area in which it is easy to see precision that isn’t there and find “optima” in problems that

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Hack-at-it 2007

January 28, 2008
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Hack-at-it 2007

The GGobi Hack-at-it 2007 was held just before useR! 2007 in Ames Iowa.The main focus this year was on the data pipeline again, and on pipelines in other software.Several projects were discussed: the geometric shapes, high-dimensional games, local neig...

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Hack-at-it 2007

January 28, 2008
By
Hack-at-it 2007

The GGobi Hack-at-it 2007 was held just before useR! 2007 in Ames Iowa.The main focus this year was on the data pipeline again, and on pipelines in other software.Several projects were discussed: the geometric shapes, high-dimensional games, local neig...

Read more »

ERGMs in R

January 23, 2008
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ERGMs in R

Developers of statnet, a collection of packages for R for fitting Exponential Random Graph Models (ERGM), issued a major update. First change is that the main package is now called ergm. Secondly, a set of additional packages has been made available. Apart from package network, that provides a class system for relational data on which

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Resources for S4 classes and methods

January 23, 2008
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Resources for S4 classes and methods

Learning the programming in the new S4 system of classes and methods in R can be quite cumbersome, even though the methods package is very well documented. That is why I collected some of the info and materials that I am aware of on a separate page here. I warmly welcome any suggestions for extending

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GillespieSSA 0.5-1 is released

January 15, 2008
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GillespieSSA 0.5-1 is released

I just uploaded GillespieSSA 0.5-1 to CRAN. Now it’s just a matter of days before it has propagated itself across all CRAN mirrors. This version consists primarily of revisions I made in response to the reviewer comments on the paper … Continue reading →

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Moving average/median

January 7, 2008
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?rollmean (package=zoo)?rollmedian (package=zoo)?runmed (package=stats)

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Quantile regression in R

January 5, 2008
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Quantile regression in R

Roger Koenker, a quantile regression crusader, has an R package that implements the procedure. It is called quantreg, and it is documented here. This package has apparently been around for quite some time, but I was only recently turned on to quantile ...

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Christmas presents…

December 21, 2007
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Our Christmas tree has not been decorated yet, but the presents are there: the BMC Bioinformatics paper on userscripts in life sciences, Bioclipse 1.2.0, a long list of blogs to rate, and a very nice overview from Wendy Warr on workflow environments, d...

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