The climate change debate focuses mainly around the assumption that the annual global mean temperatures of the past few decades have been the highest in the past millenium. How do we know what the annual global mean temperature was in the year, say, 1351 AD? The answer is: Through temperature proxies. ... [Read more...]

With more than 5,000 R packages now available (from the CRAN and BioConductor repositories), for any statistical or data analysis procedure you can confidently say, "there's a package for that". To make it easier for SAS and SPSS users to find what they need in R, Bob Muenchen has updated his ... [Read more...]

Michael Kellen, Director of Technology at Sage Bionetworks, is trying to build a GitHub for science. It's called Synapse and Kellen described it in a talk at the Sage Bionetworks Commons Congress 2012, this past weekend: 'Synapse' Pilot for Building an... [Read more...]

R-Bloggers has recently been buzzing about Julia, the new kid on the statistical programming block. Julia, however, is hardly the sole contender for the market of R defectors, with Clojure-fork Incanter generating buzz as well. Even with these two making noise, I think there’s a huge point that everyone ... [Read more...]

The R language has passed another milestone, a paper aimed at the academic programming language community (or at least one section of this community) has been written about it, Evaluating the Design of the R Language by Morandat, Hill, Osvald and Vitek. Hardly earth shattering news, but it may have ... [Read more...]

Monday, April 30, 2012  14h-16h. Stewart Biology Rm w6/12 (Montreal) guRu: Denis Haine (Université de Montréal) Topics Reproducible research was first coined by Pr. Jon Claerbout, professor of geophysics at Stanford University, to describe that the results from researches can be replicated by other scientists by making available data, procedures, ... [Read more...]

Yesterday I wrote an article that looked at the top 20 Cognitive Behavior Therapy journals with the most publications; today I will explain how I did it with R. [Read more...]

What the title of this post is supposed to mean is: "Estimating a simple aggregate consumption function using Bayesian regression analysis".In a recent post I mentioned my long-standing interest in Bayesian Econometrics. When I teach this material I usually include a simple application that involves estimating a consumption function ... [Read more...]

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Cohort analysis is super important if you want to know if your service is in fact a leaky bucket despite nice growth of absolute numbers. There’s a good write up on that subject “Cohorts, Retention, Churn, ARPU” by Matt Johnson. So how to do it using R and how ... [Read more...]

A year ago I wrote a post on speeding up R computations. Some of the tips that I mentioned then have since been made redundant by a single package: compiler. Forget about worrying about curly brackets and whether to write 3*3 or 3^2 - compile... [Read more...]

The following function matrix.poly allows for the addition of polygons to a plot based on a matrix and defined matrix positions. I have used this function on occasion to highlight specific matrix locations (e.g. in the above figure). You can do the same by overlaying another image (left ... [Read more...]

Dear R Programmers,There is new package "colbycol" on CRAN, which makes our jobs easier when we have large files i.e. more than a GB to be read in R. Especially, when we don't need all of the columns/variables for our analysis. Kudos for author, Carlos... [Read more...]

Following up on John Mount’s post on remembering symbol parameters in ggplot2, I decided to give it a try and included symbols, line types, and colors (based upon Earl Glynn’s wonderful color chart).  Code follows below. require(ggplot2) ... [Read more...]

Le Grand Casino of Monte CarloOn Monday I’m going to be leading a little stats workshop on randomization tests and null models. In preparation for this I wrote up code for null model examples I wanted to write a post that introduced the basics of these models (Null models, ... [Read more...]

Mapping near Paloma, CA This image has nothing to do with the following content. A quick example of how to use the USDA-NRCS soil data access query facility (SDA), via the soilDB package for R. The following code describes how to get component-level so... [Read more...]

Collaborative development of phyloseq on GitHub. Official stable release of phyloseq on Bioconductor. Advances in DNA sequencing technology have dramatically improved the scope and scale of culture-independent investigations into microbial communities. There are effective software tools available to process raw DNA … Continue reading → [Read more...]

In my previous post about rewriting my code to run in parallel part one I mentioned that we will make a small change to adfTest() function as well. In this post we will perform this small but performance-dramatic change. When you take a closer look at the source code of ... [Read more...]

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Multiple Sclerosis (MS) is a debilitating and complex disease with an unknown cause — and for which there is currently no cure. The SUNY Buffalo is home to one of the leading multiple sclerosis (MS) research centers in the world, and as reported in Healthcare IT News, the research team is ... [Read more...]