Summary of community detection algorithms in igraph 0.6

June 17, 2012
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  Based on Launchpad traffic and mailing list responses, Gabor and Tamas will soon be releasing igraph 0.6.  In celebration, I’ll be publishing a number of helpful lists and tables I’ve put together to organize information about igraph.   In…Read more ›

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An exercise in R using local open data

June 17, 2012
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An exercise in R using local open data

Last week I went to the “Government Open Data Hack Day” (godhd on twitter) in Birmingham (UK), organised by Gavin Broughton and James Catell. The idea was to get hold of local open data and try and make use of … Continue reading →

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3D Maps in R

June 16, 2012
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3D Maps in R

Talking about elevation, one can also plot a wire frame 3D view of an area using the persp function. Using the same data source from my previous post, 3D view of Marinduque, Philippines was produced using the following code below: ################...

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Why You Shouldn’t Conclude "No Effect" from Statistically Insignificant Slopes

June 16, 2012
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It is quite common in political science for researchers to run statistical models, find that a coefficient for a variable is not statistically significant, and then claim that the variable "has no effect." This is equivalent to proposing a research &#8...

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integrating R with other systems

June 16, 2012
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I just returned from the useR! 2012 conference for developers and users of R. One of the common themes to many of the presentations was integration of R-based statistical systems with other systems, be they other programming languages, web systems, or enterprise data systems. Some highlights for me were an update to Rserve that includes

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Euro2012 Viz: Second Group Games

June 16, 2012
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Euro2012 Viz: Second Group Games

The second round of group games ended last night (sadly with Sweden’s elimination). Here is what the last number of days has done to the plots.

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Name popularity

June 15, 2012
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Name popularity

This dynamic representation of the popularity of names over the years is a favorite. It’s not new, but I still find new things to appreciate, like names that used to apply to both sexes and now only one (Ellie), or vice versa (Harley). It seems l...

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Carnon [and Core, end]

June 15, 2012
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Carnon [and Core, end]

Yet another full day working on Bayesian Core with Jean-Michel in Carnon… This morning, I ran along the canal for about an hour and at last saw some pink flamingos close enough to take pictures (if only to convince my daughter that there were flamingos in the area!). Then I worked full-time on the spatial

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Cubism Horizon Charts in R

June 15, 2012
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Cubism Horizon Charts in R

Like many, I have been in awe of the d3.js and cubism.js visualization packages created by Mike Bostock. Mike Bostock @ Square talks about Time Series Visualization from Librato on Vimeo. The charts are beautiful and extraordinarily functional, so I th...

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about boxplot

June 15, 2012
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From Wiki:"... the bottom and top of the box are always the 25th and 75th percentile (the lower and upper quartiles, respectively), and the band near the middle of the box is always the 50th percentile (the median). But th...

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Project Euler — problem 10

June 15, 2012
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Just finish my last assignment for this week. IT’S WEEKEND, officially. Let me take a break to have a look at the tenth problem, another prime problem. It’s no doubt that prime is the center of the number theory and fundamental … Continue reading →

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Using R in/for Governments

June 15, 2012
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Using R in/for Governments

Recently British government (by Office  of National Statistics: ONS) just published their version of R manual for analysis of the government survey. The links to PDF and MS word versions of the manual including the R syntax are as below. Note: The R syntax link is not working now. I am contacting the ONS, hope

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How long does it take to get pregnant?

June 15, 2012
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How long does it take to get pregnant?

My girlfriend’s biological clock is ticking, and so we’ve started trying to spawn. Since I’m impatient, that has naturally lead to questions like “how long will it take?”. If I were to believe everything on TV, the answer would be easy: have unprotected sex once and pregnancy is guaranteed. A more cynical me suggests that

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Rounding in R

June 15, 2012
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Forgive me if you are already aware of this, but I found it quite alarming. I know that most code is interpreted by the computer in binary and we input in decimal, so problems can arise in conversion and with floating point. But the example I have below is so simple that it really surprised me.I was converting...

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More on birthday probabilities

June 15, 2012
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More on birthday probabilities

Last week, Joe Rickert used R and four years of US Census data to create an image plot of the relative probabilities of being born on a given day of the year: Chris Mulligan also tackled this problem with R, but this time using 20 years of Census data from 1969 to 1988. Chris extracted the birthday frequencies using...

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Standard, Robust, and Clustered Standard Errors Computed in R

June 15, 2012
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Standard, Robust, and Clustered Standard Errors Computed in R

Where do these come from? Since most statistical packages calculate these estimates automatically, it is not unreasonable to think that many researchers using applied econometrics are unfamiliar with the exact details of their computation. For the purposes of illustration, I am going to estimate different standard errors from a basic linear regression model: , using the

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Update to Data on Github Post: Solution to an RCurl problem

June 14, 2012
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Update to Data on Github Post: Solution to an RCurl problem

A reader of my most recent post tried the R code I had written to download the data set of electoral disproportionality from the GitHub repository. However, it didn’t work for them. After entering disproportionality.data <- getURL(url) they go...

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useR 2012: my materials

June 14, 2012
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Just a quick note that I’ve posted the slides, code, and dataset from my useR 2012 talk. I’m having a great time here in Nashville and will write up a conference review soon, with links to the many excellent packages … Continue reading →

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Pretty Correlation Map of PIMCO Funds

June 14, 2012
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Pretty Correlation Map of PIMCO Funds

As PIMCO expands beyond fixed income, I thought it might be helpful to look at correlation of PIMCO mutual funds to the S&P 500.  Unfortunately due to the large number of funds, I cannot use the chart.Correlation from PerformanceAnalytics.&nbs...

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Mindoro Digital Elevation Map

June 14, 2012
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Mindoro Digital Elevation Map

Saw a map produced by my previous student using a commercial GIS software.Using R raster package and data from diva-gis.org. I produced the same map

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#4 R: A powerful tool for the geochemist

June 14, 2012
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#4 R: A powerful tool for the geochemist

  R is an incredibly powerful programming tool used by a large community of people who require an easy to use, light weight, FREE, and fundamentally awesome statistics package! I have recently discovered that R can be used by geologists whose IT skills are often pitied by their more computer literate geophysicist colleagues. Long story short

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Revolution Newsletter: June 2012

June 14, 2012
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The most recent edition of the Revolution Newsletter is out. The news section is below, and you can read the full June edition (with highlights from this blog and community events) online. You can subscribe to the Revolution Newsletter to get it monthly via email. Revolution R Enterprise 6 Now Available! The latest release of Revolution R Enterprise brings...

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Some interesting ggplot2 tutorials for the social sciences @ Code à la Mode

June 14, 2012
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Some interesting ggplot2 tutorials for the social sciences @ Code à la Mode

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Recent R packages for ecology and evolution

June 14, 2012
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Many R packages/tools have come out recently for doing ecology and evolution. All of the below were described in Methods in Ecology and Evolution, except for spider, which came out in Molecular Ecology Resources. Here are some highlights. mvabund pap...

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Performance with foreach, doSNOW, and snowfall

June 13, 2012
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Is it just me, or does the performance of the foreach package with a doSNOW backend operating on a socket grid suck?Here at work, I am helping to setup a cluster of Windows machines for distributed R processing.  We have lots of researchers runnin...

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Making rApache load rJava

June 13, 2012
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Here at work I've been in the business of developing webapps using R as the backend computational framework.  The list of parts to get this running is pretty lightweight, just:R Apache 2rApacheI'm not going to cover how to set these things up here...

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Rook Tutorial at useR! 2012

June 13, 2012
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Rook Tutorial at useR! 2012

I had such a blast presenting my tutorial on Rook yesterday. Thanks go out to all who attended! All the slides are online here and I’ll be updating my RookTutorial github project with all the great suggestions I got from the attendees. Also, check back soon as I’m planning more postings on Rook. Cheers!

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Body Weight in the United States – Part 2, "Non Factors"

June 13, 2012
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Body Weight in the United States – Part 2, "Non Factors"

Sometimes the story isn't what is a trend, but rather what is not a trend. In this second installment about body weight in the U.S., listing what doesn't seem to be contributing factors will help narrow down what might actually be the p...

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Estimation of hydraulic conductivity and its uncertainty from grain-size data using GLUE and artificial neural networks.

June 13, 2012
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Estimation of hydraulic conductivity and its uncertainty from grain-size data using GLUE and artificial neural networks.

AbstractVarious approaches exist to relate saturated hydraulic conductivity (Ks) to grain-size data. Most methods use a single grain-size parameter and hence omit the information encompassed by the entire grain-size distribution. This study compares two data-driven modelling methods—multiple linear regression and artificial neural networks—that use the entire grain-size distribution data as input for Ks prediction. Besides the predictive capacity of the methods,...

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