Rcpp class in Sat 9 Mar in NYC

February 24, 2013
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Join Dirk Eddelbuettel for six hours of detailed and hands-on instructions and discussions around Rcpp, RInside, RcppArmadillo, RcppGSL and other packages . . . Rcpp has become the most widely-used language extension for R. Currently deployed by 103 CRAN packages and a further 10 BioConductor packages, it permits users and developers to pass “whole R The post Rcpp...

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Ten Things the Emacs Social Science Starter Kit gives you

February 24, 2013
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I recently made some updates to the Emacs Social Science Starter Kit. I maintain the SSSK for my own convenience, but other people have found it useful as well. By now there are a lot of little bits and pieces in the kit, so I thought it might be usefu...

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Ten Things the Emacs Social Science Starter Kit gives you

February 24, 2013
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I recently made some updates to the Emacs Social Science Starter Kit. I maintain the SSSK for my own convenience, but other people have found it useful as well. By now there are a lot of little bits and pieces in the kit, so I thought it might be usefu...

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Ten Things the Emacs Social Science Starter Kit gives you

February 24, 2013
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I recently made some updates to the Emacs Social Science Starter Kit. I maintain the SSSK for my own convenience, but other people have found it useful as well. By now there are a lot of little bits and pieces in the kit, so I thought it might be usefu...

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the BUGS Book [guest post]

February 24, 2013
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the BUGS Book [guest post]

(My colleague Jean-Louis Fouley, now at I3M, Montpellier, kindly agreed to write a review on the BUGS book for CHANCE. Here is the review, en avant-première! Watch out, it is fairly long and exhaustive! References will be available in the published version. The additions of book covers with BUGS in the title and of the corresponding

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Dynamic community occupancy modeling with R and JAGS

February 24, 2013
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Dynamic community occupancy modeling with R and JAGS

This post is intended to provide a simple example of how to construct and make inferences on a multi-species multi-year occupancy model using R, JAGS, and the ‘rjags’ package. This is not intended to be a standalone tutorial on dynamic community occupancy modeling. Useful primary literature references include MacKenzie et al. (2002), Kery and Royle (2007), Royle and Kery...

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Workflow w/ reports package

February 24, 2013
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Workflow w/ reports package

NOTE: THIS IS NOW A PACKAGE SEE THIS LINK FOR DETAILS Let me start with a video for people who just want to see what I’m demo-ing first: I’ve been interested in speeding up workflow lately and spending a lot … Continue reading →

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Simple Count Probability

February 24, 2013
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Simple Count Probability

Data can take the form of counts: Compliments or complaints received Items returned Number of E. coli cases Data can also be expressed in rates: Percent of web traffic from a user permissions type Percent of businesses in a region passing a safety audit A random variable X has the Poisson distribution with parameter lambda

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Major update to the R-package geomorph

February 24, 2013
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Hi Folks,We have just completed a major update to the R-package geomorph:software for geometric morphometric analyses in R.  Included are several new functions to  carry out additional GM analyses, as well as enhancements of existing function...

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Copying Data from Excel to R and Back

February 24, 2013
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Copying Data from Excel to R and Back

A lot of times we are given a data set in Excel format and we want to run a quick analysis using R's functionality to look at advanced statistics or make better visualizations. There are packages for importing/exporting data from/to Excel, but I have f...

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Large correlation in parallel

February 24, 2013
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Large correlation in parallel

A little improvement to the bigcor function proposed on Rmazing to compute huge correlation matrix in R, I made the function work in parallel using all the CPU cores available on the machine. The code is here.Here is a benchmark of the 2 func...

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The Wisdom of Crowds – Clustering Using Evidence Accumulation Clustering (EAC)

February 24, 2013
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The Wisdom of Crowds – Clustering Using Evidence Accumulation Clustering (EAC)

Today’s blog post is about a problem known by most of the people using cluster algorithms on datasets without given true labels (unsupervised learning). The challenge here is the “freedom of choice” over a broad range of different cluster algorithms and how to determine the right parameter values. The difficulty is the following: Every clustering algorithm and even...

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Earthquakes in Netherlands

February 24, 2013
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Earthquakes in Netherlands

In the Netherlands we have Natural Gas. Unfortunately winning this gas seems to cause some quakes. As quakes go, they are not strong. However, our buildings are not made to resist quakes, before 1986 they were unheard of, so there is some damage. It is now predicted they could get stronger and more frequent. This caused a bit of a...

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Simplify your R workflow with functions #rstats

February 24, 2013
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Simplify your R workflow with functions #rstats

Update/ Thanks to Bernd I could improve the function of how to import the data, so here’s the updated script! /Update In R, you often may have scripts or code snippets that will be reused. In such cases, you can … Weiterlesen →

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Multi-species dynamic occupancy model with R and JAGS

February 24, 2013
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Multi-species dynamic occupancy model with R and JAGS

This post is intended to provide a simple example of how to construct and make inferences on a multi-species multi-year occupancy model using R, JAGS, and the ‘rjags’ package. This is not intended to be a standalone tutorial on dynamic community occupancy modeling. Useful primary literature references include MacKenzie et al. (2002), Kery and Royle (2007), Royle and Kery...

Read more »

Copying Data from Excel to R and Back

February 23, 2013
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Copying Data from Excel to R and Back

A lot of times we are given a data set in Excel format and we want to run a quick analysis using R's functionality to look at advanced statistics or make better visualizations. There are packages for importing/exporting data from/to Excel, but I have found them to be hard to work with or only work with old versions of...

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Pareto plot with ggplot2

February 23, 2013
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A Pareto chart, named after Vilfredo Pareto, is a type of chart that contains both bars and a line graph, where individual values are represented in descending order by bars, and the cumulative total is represented by the line (quoted from Wikipedia). ...

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Two papers about RcppEigen and RcppArmadillo published

February 23, 2013
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Two papers got published recently. The first one is Bates and Eddelbuettel (2013). It is titled Fast and Elegant Numerical Linear Algebra Using the RcppEigen Package, and provides a pretty thorough introduction to our RcppEigen package which uses Rcpp to provide access to the Eigen C++ template library from GNU R. The paper is out as Volume 50, Issue 5 at the (all...

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The Financial Crisis on Tape Part I

February 23, 2013
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The Financial Crisis on Tape Part I

Hello and welcome to Joe's Data Diner's first ever post!Today, I will touch on both R and Finance, but I'll try and make it accesible for those with an interest in either and not just Quants like myself!Almost everyone is now aware that asset correlati...

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Getting Help with R Programming: Useful Survival Skills

Getting Help with R Programming: Useful Survival Skills

Useful Resources to Learn about R on the Internet When I program in R and struggle with something, the first thing that I usually turn to is Google.  I search the relevant function or the desired outcome, and I often find the solutions within the first few hits.  They likely show up in the documentation,

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Simulating Population Growth in Cities Using R

February 23, 2013
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Simulating Population Growth in Cities Using R

R is great for anyone who wants to get started on learning Simulation. (Both Discrete Event or Agent-based, with stochastic elements in the process.) This post is inspired by Matt Asher's "quick-and-dirty" R simulation work on Population Growth. Matt u...

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from OTU table to HEATMAP!

February 23, 2013
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from OTU table to HEATMAP!

In this tutorial you will learn: what is a heatmap how to create a clean, highly customizable heatmap using heatmap.2 in the gplots package in R how to remove samples with poor output (not very many sequences) how to rearrange your samples by a metadata category how to make a color coded bar above the heatmap

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Free e-book on Data Science with R

February 22, 2013
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Free e-book on Data Science with R

A new book by Jeffrey Stanton from Syracuse Iniversity School of Information Studies, An Introduction to Data Science, is now available for free download. The book, developed for Syracuse's Certificate for Data Science, is available under a Creative Commons License as a PDF (20Mb) or as an interactive eBook from iTunes. The book begins with the following clear definition...

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Shiny 0.4.0 now available

February 22, 2013
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Shiny 0.4.0 now available

Shiny version 0.4.0 is now available on CRAN. The most visible change is that the API has been slightly simplified. Your existing code will continue to work, although Shiny will print messages about how to migrate your code. Migration should be straightforward, as described below. It will take a bit of work to switch to

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Video: IBM Opinionated Infrastructure Hangout

February 22, 2013
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Had a great time earlier this week on a Google Hangout as part of the IBM Opinionated Infrastructure series. Moderator James Governor (analyst from RedMonk) kept the conversation lively, with topics ranging from to the value of information to the benefits of predictive analytics and evolution of Hadoop. R gets a mention at several points in the conversation, which...

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Migrating from SPSS to R #rstats

February 22, 2013
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Migrating from SPSS to R #rstats

Preface I will every now and then post my experience with R, a package for statistical analyses. I try to show some solutions for common types of analyses or problems you are facing when you start working with R. These … Weiterlesen →

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Don’t use correlation to track prediction performance

February 22, 2013
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Don’t use correlation to track prediction performance

Using correlation to track model performance is “a mistake that nobody would ever make” combined with a vague “what would be wrong if I did do that” feeling. I hope after reading this feel a least a small urge to double check your work and presentations to make sure you have not reported correlation where Related posts:

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What’s my daughter listening to? HTML chart gen in R

February 22, 2013
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  My daughter, who turns 10 in April, has discovered pop music. She’s been listing to Virgin Radio 99.9, one of our local stations. Virgin provides an online playlist that goes back four days, so I scraped the data and brought it into R. The chart shown at top shows all of the songs played

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bigcor: Large correlation matrices in R

February 22, 2013
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bigcor: Large correlation matrices in R

As I am working with large gene expression matrices (microarray data) in my job, it is sometimes important to look at the correlation in gene expression of different genes. It has been shown that by calculating the Pearson correlation between genes, one can identify (by high values, i.e. > 0.9) genes that share a common

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