Simulating Sudden Oak Death Dynamics

November 16, 2012
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Simulating Sudden Oak Death Dynamics

I am working on a project with the Rizzo Lab examining the dynamics of Sudden Oak Death (SOD). I really have to write more about this, but today I’m just going to post the results of an initial exercise. Here I attempt to replicate model results from Cobb et al. (2012). The model in that paper simulates...

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Revolution Newsletter: November 2012

November 16, 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 November edition (with highlights from this blog and community events) online. You can subscribe to the Revolution Newsletter to get it monthly via email. Now Available: Revolution R Enterprise 6.1 The latest release of Revolution Analytics' enterprise-ready data...

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Excel + Cytoscape + R = ExCytR

November 16, 2012
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Excel + Cytoscape + R = ExCytR

My new project is coming along nicely and should be released early 2013. It builds on the structures developed in imDEV to link Excel, Cytoscape and R using RExcel,  RCytoscape, and CytoscapeRPC . This trio can be used to rapidly generate beautiful and  informative network representations of data. Here is an example of a  undirected Gaussian graphical

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Logo Contest Winner

November 16, 2012
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Logo Contest Winner

Congratulations to Bradley Saul, the winner of the Simply Statistics Logo contest! We had some great entries which made it difficult to choose between them. You can see the new logo to the right of our home page or the … Continue reading →

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Hjust and Vjust

November 16, 2012
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Hjust and Vjust

So, when you’re setting the position of text in ggplot, you may have to use the hjust and vjust commands. Depending on your demands, and if you don’t understand what they’re doing, they might seem hard to use. I found one script that...

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Exit PEBOS – Enter exit polls

November 16, 2012
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Exit PEBOS – Enter exit polls

PEBOS is over. Time to look at the details of the Election. The final results are not yet in, but the exit polls are there, and up for grabs. Just to get warm: here's a tiny example.Obviously Romney had an age problem. But for now I don't want to specu...

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Network vizualization and meaning shifting due to algorithm settings

November 15, 2012
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Network vizualization and meaning shifting due to algorithm settings

Data visualizations are useful for exploratory work and as an aid in communicating findings. Data visualizations also seem to be in demand these days as a kind of eye candy for capturing attention. But when we look at one engaging enough to hold our attention, we want to know what it means. In other words,

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Want to win "Guess who?" – Have an institutional neural network approach

November 15, 2012
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Want to win "Guess who?" – Have an institutional neural network approach

Have you ever played the board game "Guess who?". For those who have not experienced childhood (because it might be the only reason to ignore this board game), this is a game consisting in trying to guess who the opponent player is thinking o...

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GEE QIC update

November 15, 2012
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GEE QIC update

Here is improved code for calculating QIC from geeglm in geepack in R (original post). Let me know how it works. I haven’t tested it much, but is seems that QIC may select overparameterized models. In the code below, I … Continue reading →

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What does R do? Bring people together, of course!

November 15, 2012
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What does R do? Bring people together, of course!

Last night we had a great meet up of the Montreal R User Group. I got things started with a little presentation asking the question “What does R do?” (slides). I made the presentation using Montreal R User Group member Ramnath Vaidyanathan‘s Slidify package. Slidify allows you to generate rather handsome HTML5 slides directly using

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Bottom-up creation of data-driven capabilities: automate your work

November 15, 2012
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My previous post on how to transform an organization into a more data-driven version of itself made a pretty big assumption that often doesn’t hold true. I assumed that people in the organization wanted their company or agency to become more data-driven. I think almost everyone says they want that if asked. I even think

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Create elegant, interactive presentations from R with Slidify

November 15, 2012
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Create elegant, interactive presentations from R with Slidify

If you often find yourself cutting-and-pasting charts or tables generated in R into PowerPoint or Keynote, you might want to take a look at Slidify. Created by R user Ramnath Vaidyanathan, Slidify is an R package that allows you to use R Markdown to define the slide content and automatically embed R output. This is especially useful if the...

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Innovation in Statistical Computing

November 15, 2012
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In A Capitalist’s Dilemma, Whoever Wins on Tuesday, Clayton Christensen lays out three kinds of innovations through which an industry cycles: Empowering Innovations - those that offer products and services to a new customer base. The classic empowering (or disruptive) innovation is Ford Motor Company’s introduction of the low-cost Model T coupled with the ability of Ford’s own...

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Reproducible Research: With Us or Against Us?

November 15, 2012
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Last night this article by Chris Drummond of the Canadian National Research Council (Conseil national de recherches Canada) popped up in my Google Scholar alert. The title of the article, “Reproducible Research: a Dissenting Opinion” would seem to indicate that he disagrees … Continue reading →

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Textual Healing Part II

November 15, 2012
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Textual Healing Part II

Yesterday’s post showed a number of quick coding options for changing text in a basic ggplot. Here’s another two tricks for fine-tuning faceted plots. Again, let’s load our made up data about tooth growth (a real dataset in R, ToothGr...

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Fun with R graphics: A raptor and a cake

November 15, 2012
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Fun with R graphics: A raptor and a cake

I like to explore the graphics features of R.  Base graphics, ggplot2 are my favourites. On  other graphics packages, I haven’t used plotrix much. I am currently exploring grid package. Raptor First one is using ggplot2. (you could also do … Continue reading →The post Fun with R graphics: A raptor and a cake appeared first on...

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Regime Detection Pitfalls

November 14, 2012
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Regime Detection Pitfalls

Today, I want to address some questions that I was getting regarding the Regime Detection post. In the Regime Detection post I showed an example based on the simulated data, and some of you tried to apply this example to actual stocks. There is one big problem that you have to be aware in designing

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Rcpp and the new R:: namespace for Rmath.h

November 14, 2012
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We released Rcpp 0.10.0 earlier today. This post will just provide a simple example for one of the smaller new features -- the new namespace for functions from Rmath.h -- and illustrate one of the key features (Rcpp attributes) in passing. R, as a statistical language and environment, has very well written and tested statistical distribution functions providing probability density, cumulative...

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Webinar Tomorrow: Big Data Trees and Hadoop Connection in Revolution R Enterprise 6.1

November 14, 2012
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Tomorrow at 9AM Pacific, Revolution Analytics VP of Product Development Sue Ranney will introduce two key Big Data features of the new Revolution R Enterprise 6.1. Now you can train classification and regression trees on data sets of unlimited size, quickly and using the resources of multiple processors and clusters. (This white paper describes our implementation of tree models...

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VIDEO: Looking to the loadings in R

November 14, 2012
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VIDEO: Looking to the loadings in R

(This article was first published on NIR-Quimiometria, and kindly contributed to R-bloggers) To leave a comment for the author, please follow the link and comment on their blog: NIR-Quimiometria. R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL,...

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Have my old job!

November 14, 2012
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Have my old job!

My old job at the Health & Safety Laboratory is being advertised, and at a higher pay grade to boot.  (Though it is still civil service pay, and thus not going to make you rich.) You’ll need to have solid mathematical modelling skills, particularly solving systems of ODEs, and be proficient at writing scientific code,

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How the Democrats may have won the House, but lost the seats

November 14, 2012
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How the Democrats may have won the House, but lost the seats

  The 2012 election is over and in the books. A few very close races remain to be officially decided, but for the most part everything has settled down over the last week. By all accounts it was a very good night for the Democrats, with wins in the presidency, senate and state houses. They also performed

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Rcpp 0.10.0

November 14, 2012
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Rcpp release 0.10.0 is now on CRAN and being uploaded to Debian. This is a new feature release, and we are very exciting about the changes, notably Rcpp attributes which make using C++ from R even easier than inline (see below as well as the new vignette for details and first examples), the extensions to Rcpp modules (see below) and more as...

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How to choose your next holidays destination – Uniform distribution on a sphere

November 14, 2012
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How to choose your next holidays destination – Uniform distribution on a sphere

If you want to choose randomly your next holidays destination, you are likely to process in a way which is certainly biased. Especially if you choose randomly the latitude and the longitude. A bit like they do in this lovely advertising (For those of y...

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Big Data ETL and Big Data Analysis

November 14, 2012
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Big Data ETL and Big Data Analysis

I was at Strata New York 2012 last month. Great conference! Thanks O'Reilly media for assembling the industry leaders and running it well.I understand it was too crowded for some of my out-of-town friends. Stepping out to the streets of mid-town Manhat...

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Textual Healing

November 14, 2012
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Textual Healing

While I know there are several awesome guides for how to make fine-tuning adjustments to plot labels/axes/ticks/text in ggplot, this is still the most common question I get from people new to ggplot: how do I change the size/font/color/position of (som...

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Expand delimited columns in R

November 14, 2012
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A postdoctoral researcher asked me the other day to help him expand a vector of comma delimited values so he could do computations in R with it. I wrote an R function to solve the problem. Here is the before...

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Timeline Maps with googleVis & Twitter Bootstrap Carousel (& updated Slidify)

November 14, 2012
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I've wanted to create timeline maps with interactive googleVis Geomaps for a while. These would be a nice way to quickly show the spatial distribution of some data over time. It turns out that it's pretty easy to do with a plugin for Twitter Bootstra...

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Building a Simple Web App using R

November 13, 2012
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Building a Simple Web App using R

I’ve been interested in building a web app using R for a while, but never put any time into it until I was informed of the Shiny package.  It looked too easy, so I absolutely had to try it out. First you need to install the package from the command line . options(repos=c(RStudio="http://rstudio.org/_packages", getOption("repos"))) install.packages("shiny")

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