Variogram fit with RPanel

September 21, 2011
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Variogram fit with RPanel

During the UseR 2011 conference I saw lots of examples of the use of RPanel to create a GUI in R. Yesterday, because I was a bit bored of the work I was doing I started thinking about this and I decided to try this package.My objective was to create a new panel with all the main setting for...

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A Note on Antoniak’s Approximation for Dirichlet Processes

September 21, 2011
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A Note on Antoniak’s Approximation for Dirichlet Processes

Antoniak's 1974 article titled Mixtures of Dirichlet Processes with Applications to Bayesian Nonparametric Problems (Annals of Statistics 2(6):1152-1174) is a fundamental work for most modern developments in this area. The article gives two expressions for the expected number of distinct values in a sample of size n, drawn from a Dirichlet process-distributed probability distribution with

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Solvency 2 WordCloud

September 21, 2011
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Slow day at PSY headquarters: Click see wordleWe grabbed the Solvency II directive text from the EC website (© European Union, http://eur-lex.europa.eu/) and ran it through a couple of lines of R code to draw up wordcount frequencies. Then we plotted the text in Wordlehttp://www.wordle.net/show/wrdl/4111834/Solvency_2We're not convinced about the utility of WordClouds, but they look cool....

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Example 9.6: Model comparison plots (Completed)

September 21, 2011
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Example 9.6: Model comparison plots (Completed)

We often work in settings where the data set has a lot of missing data-- some missingness in the (many) covariates, some in the main exposure of interest, and still more in the outcome. (Nick describes this as "job security for statisticians").Some ana...

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Density exploration and Wang-Landau algorithms [with R package]

September 21, 2011
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Density exploration and Wang-Landau algorithms [with R package]

Hey, Since a new paper that I’ve co-written has appeared on arXiv, here is a quick post summarizing it. The paper is named: An Adaptive Interacting Wang-Landau Algorithm for Automatic Density Exploration and describes improvements over the Wang-Landau algorithm described … Continue reading →

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Climate Reference Network: package crn 1.0

September 20, 2011
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Climate Reference Network:  package crn 1.0

I’ve just finished and uploaded another climate data package for R. This one focuses on  CRN the climate Reference Network Here is their home page   The package for now is really simple, but all of the packages  I’m building are getting simpler. In the end ( whenever that is ) I think I’ll end

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Children height and blood pressure z-scores

September 20, 2011
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Children height and blood pressure z-scores

Following on from some of my earlier posts, this is purely about, hopefully, saving some other people some time in putting this together. Height z-scores are required to then calculate the blood pressure z-scores. The CDC (Center for Disease Control … Continue reading →

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Facebook like button in Graph Gallery

September 20, 2011
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Facebook like button in Graph Gallery

I've added facebook like button in the home page of the R Graph Gallery and on each image page, i.e. this one which I "like".

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Recession forecasting III: A Better Naive Forecast

September 20, 2011
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Recession forecasting III: A Better Naive Forecast

In Recession Forecasting Part II, I compared the accuracy of Hussman's recession forecasts to the accuracy of a naive forecast that assumed the current state of the recession variable would continue next month. An anonymous comment...

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Package ‘intergraph’ (1.1-0) released!

September 20, 2011
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I just released the first official version of the ‘intergraph’ R package. With the functions provided in the current version (1.1-0) you can convert network data objects between classes ‘igraph’ and ‘network’. The package supports directed and undirected networks, and handles the node, tie, and network (graph) attributes. Mutliplex networks (i.e., with possibly multiple ties

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StackExchange and CrossValidated: An Epidemiologist’s Review

September 20, 2011
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StackExchange and CrossValidated: An Epidemiologist’s Review

This seems like as good a day as any to review CrossValidated, and the whole StackExchange constellation of websites. It’s been a month since I joined, exactly, and today I also crossed the 1,000 reputation threshold on the site. So why not give my impressions of it? First, how I got there in the first

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Use of Classification Trees to Investigate Traits of Invasive Species

September 20, 2011
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Use of Classification Trees to Investigate Traits of Invasive Species

Which traits make an alien species invasive?Due to what traits an alien species becomes established in a foreign flora?This kind of questions could be analysed by the use of recursive partitioning and classification trees..(the below example also inclu...

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Cricket All Round Performances

September 19, 2011
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In cricket a player who can perform well with both the bat and bowl is a great asset for any team and across the history of international cricket there have been a number of cricketers that hall into this bracket. It is difficult to specify a set of criteria to determine whether a player can

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About commercial publishers

September 19, 2011
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About commercial publishers

Julien Cornebise has pointed out a recent Guardian article. It is about commercial publishers of academic journals, mainly Elsevier, Springer, and Wiley, with a clear stand from its title: “Academic publishers make Murdoch look like a socialist“! The valuable argument therein is that academic publishers make hefty profits (a 40% margin for Elsevier!)

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Using jri to connect JAVA to R

September 19, 2011
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The R package rJava allows R to be accessed in Java programs. The part of the package that allows this is jri. The notes on the rJava site about getting jri to work didn’t help me much getting it to … Continue reading →

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R 2.14 to be released on October 31; R 2.13 patch on September 13

September 19, 2011
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The next major release of R has been announced: R 2.14.0 is scheduled for October 31. Details are still coming in about the new features planned for this release, but R core member Luke Tierney has revealed some of the performance improvements expected, and R core member Brian Ripley has spoken of forthcoming low-level support for multi-threaded computing and...

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Appendable saving in R

September 19, 2011
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One of the most crucial problems in HPC is that every error you make have much greater impact than in the normal computing — there is nothing more amusing than finding out that few-day simulation broke few minutes before the end because of an unfortunate value thrown by a random generator, typo in result saving code or

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Three free books for better programming in R (and any other language)

September 19, 2011
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Like many users and producers of R packages, I have never had any formal training in computer science. I’ve come to to the conclusion that this is a serious omission in a professional researcher’s training. Computer scientists and professional hackers … Continue reading →

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rgdal + raster + RCurl = My next package

September 18, 2011
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rgdal + raster + RCurl = My next package

This package has been a long time in the making.  In the end it’s more of a data package than a functional package, but pulling all the pieces together required me to learn some really cool packages: raster ( which I already knew ) rgdal and RCurl.  I’ll provide a littel bit of an overview

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DTW: dynamic time warping 动态时间规整

September 18, 2011
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Basically, DTW (dynamic time warping) is an algorithm to output cumulative distance of two time sequences, which is widely used e.g. for classification and clustering.For example, when using k-mean for clustering, we can use DTW as distance function. Here is one of such nice instances (using R: http://www.rdatamining.com/examples/ts-mining)Relevant information from Anshul's email.  A review of DTW http://csdl.ics.hawaii.edu/techreports/08-04/08-04.pdfCode:Python code: https://mlpy.fbk.eu/R...

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Map the distribution of your sample by geolocating ip addresses or zip codes

September 18, 2011
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Map the distribution of your sample by geolocating ip addresses or zip codes

Yesterday I wanted to create a map of participants from a study on social media and partisan selective exposure that Sean Westwood and I ran recently, with participants from Amazon’s Mechanical Turk.  We recorded ip addresses for each Turker participant, so … Continue reading →

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Implementation of the CDC Growth Charts in R

September 17, 2011
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I implemented in R a function to re-create the CDC Growth Chart, according to the data provided by the CDC.In order to use this function, you need to download the .rar file available at this megaupload link.Mirror: mediafire link.Then unrar the file, a...

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Bayesian Models with Censored Data: A comparison of OLS, tobit and bayesian models

September 17, 2011
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Bayesian Models with Censored Data: A comparison of OLS, tobit and bayesian models

The following R code models a censored dependent variable (in this case academic aptitude) using a traditional least squares, tobit, and Bayesian approaches.  As depicted below, the OLS estimates (blue) for censored data are inconsistent and will ...

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The Long Tail of the Pareto Distribution

The Long Tail of the Pareto Distribution

In my last two posts, I have discussed cases where the mean is of little or no use as a data characterization.  One of the specific examples I discussed last time was the case of the Pareto type I distribution, for which the density is given by:                        p(x) = aka/xa+1defined for all x > k, where k and a...

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littler 0.1.5

September 17, 2011
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Brown-bag release time for littler. One of the minor cleanups in the 0.1.4 release from Thursday actually introduced a nasty little bug as you can't call Rf_KillAllDevices() when you do not have any graphics device. Doh. So with apologies for the l...

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UK R Courses – 2012

September 17, 2011
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UK R Courses – 2012

The School of Mathematics & Statistics at Newcastle University (UK), are again running some R courses. In January, 2012, we will run: January 16th: Introduction to R; January 17th: Programming with R; January 18th & 19th: Advanced graphics with R. The courses aren’t aimed at teaching statistics, rather they aim to go through the fundemental

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Introduction to Beamer

September 17, 2011
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Introduction to Beamer

A friend of mine, who is quite smart by the way (she is a PhD. student in Physics at Cambridge), recently asked me for some help with Beamer. Well most of my knowledge and code came from Utkarsh when I had started about a year ago. Initially, I ha...

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Elements of Bayesian Econometrics

September 16, 2011
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Elements of Bayesian Econometrics

 posterior = (likelihood x prior) / integrated likelihoodThe combination of a prior distribution and a likelihood function is utilized to produce a posterior distribution.  Incorporating information from both the prior distribution and the likelihood function leads to a reduction in variance and an improved estimator. As n→...

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ifelse function in R only returns the first element

September 16, 2011
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If you also favor to use the function, be aware of the returned value. For example:> ifelse(1>0, 3, 4) 3> ifelse(1>0, c(2, 3), c(4, 5)) # only the first element returned. 2 > ifelse(c(1:10)>5, 'on', 'off') "off" "off...

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