RStudio Beta 3 (v0.94)

June 14, 2011
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RStudio Beta 3 (v0.94)

RStudio Beta 3 (v0.94) is available for download today. The goal for this release was to refine and improve our core features based on the feedback we’ve gotten on our first two betas. Highlights of the new release include: Source editor enhancements — New editor features include brace/paren/quote matching, more intelligent cursor placement after newlines, function

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Boxplots without boxes

June 14, 2011
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Let’s say you have several categories with multiple data points each that you would like to plot as individual points. Even if you have only a single point, the R graphics package will plot a line (without a box for … Continue reading →

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No lake is an island: PhD Opportunity

June 14, 2011
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No lake is an island: PhD Opportunity

NERC recently funded the formation of the UK Lake Ecological Observation Network (UKLEON) as part of the its Networks of Sensors programme. UKLEON is lead by Ian Jones at CEH Lancaster. A fully-funded PhD project is associated with the UKLEON … Continue reading →

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Multiple Comparisons for GLMMs using glmer() & glht()

June 14, 2011
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Multiple Comparisons for GLMMs using glmer() & glht()

...that's an example of how to apply multiple comparisons to a generalised linear mixed model using the function glmer from package lme4 & glht() from package multcomp. By the way you see a nice example for visualizing data from a nested sampli...

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Embedding a time series with time delay in R — Part II

June 14, 2011
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Some months ago, I posted a function that extended the base R function embed() to allow for time delay embedding. Today, David Gonzales alerted me to an inconsistency between embed() and Embed().

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Dependence and Correlation

June 13, 2011
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Dependence and Correlation

In everyday life I hear the word "correlation" thrown around far more often than "dependence." What's the difference? Correlation, in its most common form, is a measure of linear dependence; the catch is that not all dependencies are linear. The set...

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Asians Love Their Bandwidth

June 13, 2011
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Asians Love Their Bandwidth

I recently ran across some data from comScore networks. The data contains results from surveys from a number of households across the US with demographic information (ethnicity, household income, household size, state, zipcode, etc.) along with whether...

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Sweave source for poll report

June 13, 2011
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Sweave source for the poll report for those who expressed some interest. You’ll also need this file of R function definitions, utilities.R. I also wrote a little shell script that calls Sweave and xelatex etc, hacking the Sweave.sh script that ships with R.

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Donor analysis in R – Smith for Congress

June 13, 2011
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Donor analysis in R – Smith for Congress

In a previous post I introduced the Smith for Congress data set. The data is 49k contributions made by individuals to a congressional campaign for the 2006-2010 electoral cycles. Smith for Congress is not the name of the actual campaign. Individual contributions are not required to be disclosed by a campaign unless the individual donates

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Example 8.40: Side-by-side histograms

June 13, 2011
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Example 8.40: Side-by-side histograms

It's often useful to compare histograms for some key variable, stratified by levels of some other variable. There are several ways to display something like this. The simplest may be to plot the two histograms in separate panels.SASIn SAS, the most d...

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Using simulation to demonstrate theory: Hardy-Weinberg Equilibrium

June 13, 2011
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Using simulation to demonstrate theory: Hardy-Weinberg Equilibrium

One of my teaching roles is in an introductory Genetics course, where first year students are presented with a wide range of new ideas at a relatively fast pace.  It seems that often, students choose to take a memorization approach to learning the material, rather than taking the chance to think about how and why

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R package DOSE released

June 12, 2011
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Disease Ontology (DO) provides an open source ontology for the integration of biomedical data that is associated with human disease. DO analysis can lead to interesting discoveries that deserve further clinical investigation. DOSE was designed for semantic similarity measure and enrichment analysis. Read More: 619 Words Totally

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REITs for Everybody Might Now Mean REITs for Nobody

June 12, 2011
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REITs for Everybody Might Now Mean REITs for Nobody

THIS IS MY OPINION AND ANALYSIS AND IS NOT INVESTMENT ADVICE.  YOU ARE RESPONSIBLE FOR YOUR OWN GAINS AND LOSSES. I think REITs traditionally attract conservative dividend investors (grandparents), but due to their recent behavior, REITs also attr...

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Listing of Statistics and Machine Learning Conferences

June 12, 2011
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Occasionally, I will query Google with “statistics conferences”, “machine learning conferences” or “pattern recognition conferences” and the like. But often, it is difficult to obtain anything meaningful other than the conferences of which ...

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Two Castles Run 2011

June 12, 2011
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Two Castles Run 2011

I did the Two Castles Run today; it’s a 10km race between Warwick and Kenilworth castles. The organizers were very quick to put the results online and even went the extra mile of offering them as a CSV file. It … Continue reading →

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Additive modelling and the HadCRUT3v global mean temperature series

June 12, 2011
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Additive modelling and the HadCRUT3v global mean temperature series

Earlier, I looked at the HadCRUT3vgl data set using generalized least squares to investigate whether the trend in temperature since 1995 was statistically significant. Here I want to follow-up one of the points from the earlier posting; namely using a … Continue reading →

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Can You Beat the Market with Modern Portfolio Theory? (Part 2)

June 12, 2011
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Can You Beat the Market with Modern Portfolio Theory? (Part 2)

(Obligatory Warning: This post should not be considered investment advice. The author(s) of this blog are not certified financial analysts. Any analysis presented here is meant only as an opinion. Following our opinion could end up losing you a lot of ...

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Animated Plots with R

June 12, 2011
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Animated Plots with R

Using ImageMagick it's pretty easy to make an animated gif from a set of plots. Essentially the way to do it is to save a plot for each frame of the animation and then convert them into a .gif. Here's a simple example that plots binomial density's for ...

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On Crows

June 12, 2011
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On Crows

Today I made the mistake of clicking on the "Next Blog" button, which took me to a rather inane post complaining that crows are (obviously) stupid (because they are sometimes hit by cars). I was reminded that crows are actually quite smart.

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Additive modelling and the HadCRUT3v global mean temperature series

June 12, 2011
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Additive modelling and the HadCRUT3v global mean temperature series

Earlier, I looked at the HadCRUT3vgl data set using generalized least squares to investigate whether the trend in temperature since 1995 was statistically significant. Here I want to follow-up one of the points from the earlier posting; namely using a statistical technique that fits a local, and not global, model to the...

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A Little R Counter

June 11, 2011
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A Little R Counter

I recently read a great post about environments in R, which featured this little bit of code:> createCounter <- function(value) { function(i) { value <<- value+i} }> counter <- createCounter(0)> counter(1)> a <- counter(0)&gt...

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The importance of being unoriginal (and befriending google)

June 11, 2011
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In search of bin countsI look at histograms and density functions of my data in R on a regular basis. I have some idea of the algorithms behind these, but I've never had any reason to go under the hood until now. Lately, I've been looking using the b...

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Global warming since 1995 ‘now significant’

June 11, 2011
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Global warming since 1995 ‘now significant’

Yesterday (June 11, 2011) the BBC reported on comments by Prof. Phil Jones, of the Climatic Research Unit (CRU), University of East Anglia (UEA), that the warming experienced by the planet since 1995 was statistically significant. That the trend in … Continue reading →

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Identifying and characterizing droughts with R

June 11, 2011
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Identifying and characterizing droughts with R

Recently, I’ve been playing with patterns of drought in paleo records of streamflow. One of the earliest and most helpful tools I’ve developed, identifies and characterizes droughts in extremely long time series using R. I’m still hacking my way through it, but this is what has been cooking thus far… For this example I’ll be

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Maximum Entropy Now Supported for Windows

After several weeks trying to find the source of a bug in the maximum entropy library when compiling on Windows, Dirk Eddelbuttel pointed me in the right direction to resolve the issue. Although it required a re-write of the library using the new Rcpp API, maximum ent

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Can You Beat the Market with Modern Portfolio Theory? (Part 1)

June 11, 2011
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Can You Beat the Market with Modern Portfolio Theory? (Part 1)

For an integer programming class, Andrew and I were interested in seeing if some ideas from modern portfolio theory could be used to "beat the market."In particular, our goals were the following:For a particular time period, compute the covariance...

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Global warming since 1995 ‘now significant’

June 11, 2011
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Global warming since 1995 ‘now significant’

Yesterday (June 11, 2011) the BBC reported on comments by Prof. Phil Jones, of the Climatic Research Unit (CRU), University of East Anglia (UEA), that the warming experienced by the planet since 1995 was statistically significant....

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OpenStates from R via API: watch your elected representatives

June 10, 2011
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OpenStates from R via API: watch your elected representatives

I am writing some functions to acquire data from the OpenStates project, via their API. They have a great support community at Google Groups as well.On its face this post is not obviously about ecology or evolution, but well, our elected represent...

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REITs for Everybody

June 10, 2011
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REITs for Everybody

THIS IS NOT INVESTMENT ADVICE.  IT IS SIMPLY MY OPINION.  LISTENING TO MY OPINION MIGHT LOSE LOTS OF MONEY. I contend that REITs now have two buyers: dividend pickers and beta chasers.  The beta chasers’ demand has driven prices to sig...

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