Category Archives: R

To Sweave, or not to Sweave, that is the question

Posted on December 16, 2011 by

I am about to start writing up the manuscript of my recent biomath seminar (Act 3: Pineda-Krch. 2011. Cycles at the edge of existence: Emergence of quasi-cycles in strongly destabilized ecosystems.). While the slides for the talk were put together using … Continue reading →

Posted in manuscript, R, Sweave, writing | 9 Comments

The Joy of R: A Feline Guide

Posted on November 5, 2011 by

Just because it’s caturday Images by Mario Pineda-Krch (CC BY-NC-SA 3.0) This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.

Posted in cats, computing, humour, R, Sweave | 3 Comments

Cycles in finite populations: A reproducible seminar in three acts

Posted on November 1, 2011 by

For this years Halloween I presented the mathematical biology seminar at the Centre for Mathematical Biology. Here is the title and the abstract… Cycles in finite populations: a reproducible seminar in three acts Many natural populations exhibit cyclic fluctuations. Explaining the underlying … Continue reading →

Posted in LaTeX, Open Notebook science, open science, predator-prey model, presentation, programing, R, Sweave | 11 Comments

Vanilla C code for the Stochastic Simulation Algorithm

Posted on October 24, 2011 by

The Gillespie stochastic simulation algorithm (SSA) is the gold standard for simulating state-based stochastic models. If you are a R buff, a SSA novice and want to get quickly up and running stochastic models (in particular ecological models) that are not … Continue reading →

Posted in computer simulations, computing, cookbook, Daniel Gillespie, Gillespie algorithm, GillespieSSA, R | 1 Comment

What is R, really?

Posted on March 31, 2011 by

On CRAN, the official web home of all things R it says, R is a free software environment for statistical computing and graphics. Well, that sounds all hunky dory. But let’s take a close look at what this statement really … Continue reading →

Posted in computing, open science, R | 7 Comments

The Joy of Sweave – A Beginner’s Guide to Reproducible Research with Sweave

Posted on January 17, 2011 by

Just wrapped up the slides for the first version of the The Joy of Sweave – A Beginner’s Guide to Reproducible Research with Sweave which I presented today in our lab. I am making the slides available under a Creative Commons … Continue reading →

Posted in presentation, R, Sweave | 4 Comments

Top 10 things that suck about Sweave

Posted on December 1, 2010 by

People rave about Sweave and the literate programing paradigm and I am guilty as charged. I speak Sweave, I think Sweave, I dream Sweave. As a matter of fact my default mode of operation is Sweave and anything else is an … Continue reading →

Posted in humour, R, Sweave | 24 Comments

Computational efficiency of great-circle distance calculations in R

Posted on November 28, 2010 by

An obvious omission in my previous post on Great-circle distance calculations in R was a lack of discussion on the computational efficiency of the various methods, and in particular comparing different implementations of the same method. One of the comments … Continue reading →

Posted in cookbook, R | 4 Comments

Great-circle distance calculations in R

Posted on November 23, 2010 by

Recently I found myself needing to calculate the distance between a large number of longitude and latitude locations. As it turns out, because the earth is a three-dimensional object, you cannot simply pretend that you are in Flatland, albeit some … Continue reading →

Posted in cookbook, R | 9 Comments

Making R growl

Posted on November 18, 2010 by

Spending the day churning through large data set or doing some heavy-duty number crunching? What is one to do while the computer is running in overdrive? We’ll, for one, you could get a steaming cup of joe and write a … Continue reading →

Posted in cookbook, R | 6 Comments

GillespieSSA 0.5-4 is released

Posted on August 16, 2010 by

I just uploaded GillespieSSA 0.5-4 to CRAN. It should be  just a matter of days before it has propagated itself across all mirrors. This release consists of minor revisions with no (intended) changes in functionality. The main change (and it is … Continue reading →

Posted in computer simulations, GillespieSSA, Git, Linus Torvalds, R | Leave a comment

High-performance computing in R at useR! 2008

Posted on August 12, 2008 by

The useR! 2008 meeting is about to commence. Although I am not able to go this year I will be keeping a close eye on the talks and slides that (I assume) will be posted.  Last years useR! meeting (which … Continue reading →

Posted in computer cluster, computer simulations, computing, R, useR! | Leave a comment

Paper on GillespieSSA now published

Posted on May 2, 2008 by

My paper on the GillespieSSA package has now been published in the latest volume of Journal of Statistical Software. Check it out.

Posted in GillespieSSA, manuscript, R | Tagged | Leave a comment

Paper on the Gillespie Stochastic Simulation Algorithm in press

Posted on February 1, 2008 by

Just got news that my revisions to the reviewer’s comments on my paper GillespieSSA: Implementing the Gillespie Stochastic Simulation Algorithm in R were accepted. Hence, this paper is not officially in press in the Journal of Statistical Software. Here’s the … Continue reading →

Posted in computer simulations, Gillespie algorithm, GillespieSSA, R | 5 Comments

GillespieSSA 0.5-1 is released

Posted on January 15, 2008 by

I just uploaded GillespieSSA 0.5-1 to CRAN. Now it’s just a matter of days before it has propagated itself across all CRAN mirrors. This version consists primarily of revisions I made in response to the reviewer comments on the paper … Continue reading →

Posted in computer simulations, GillespieSSA, programing, R | Leave a comment

GillespieSSA 0.3-1 released

Posted on October 4, 2007 by

I recently rolled up the new version of the GillespieSSA package, version 0.3-1. The tar ball of the new version is posted on its web page (here). I also submitted it to CRAN so in (due time) it should appear … Continue reading →

Posted in computer simulations, GillespieSSA, R | Leave a comment

Special Volume of JSS on Ecology and Ecological Modelling in R

Posted on October 3, 2007 by

The latest issue Journal of Statistical Software is a special volume on Ecology and Ecological Modelling in R. This has been in the woodwork for quite some time now and it is nice to finally to see this out “in … Continue reading →

Posted in ecology, programing, R | Leave a comment

GillespieSSA on CRAN

Posted on September 21, 2007 by

So it’s official – my R package GillespieSSA has been posted to the official list of packages on CRAN (The Comprehensive R Archive Network). Check it out. Now back to my manuscript. Over the last few days I have been … Continue reading →

Posted in Gillespie algorithm, GillespieSSA, manuscript, R | Leave a comment

GillespieSSA 0.2-0 is released

Posted on September 19, 2007 by

Just finished the new version of the GillespieSSA package. The tar ball of the new version is posted on its web page (here). I also submitted it to CRAN so in (due time) it should appear on the official R … Continue reading →

Posted in Gillespie algorithm, GillespieSSA, R | Leave a comment

Implementing the stochastic simulation algorithm in R

Posted on September 9, 2007 by

Dear blog, no I have not forgot you or the rest of the world. Sequestered in my humble cubicle I have been hammering away day and night for the last several weeks – hammering out a manuscript. Finally after what … Continue reading →

Posted in manuscript, metapopulation, predator-prey model, programing, R, theory, writing | Leave a comment

119 days of number crunching…

Posted on August 23, 2007 by

Just checked on the 70000+ simulations I submitted to the Cow last night. The purpose of these runs is to explore a given system (the logistic growth model in this case) using different implementations of the stochastic simulation algorithm (aka … Continue reading →

Posted in computer cluster, computer simulations, Gillespie algorithm, GillespieSSA, R | Leave a comment

Cow chewing on GillespieSSA

Posted on August 23, 2007 by

Sorry blog for the long silence. Lately I have been juggling several time critical projects and there hardly seems to be time for such mundane activities such as sleeping, eating, never mind shaving (someone pointed out that I am starting … Continue reading →

Posted in computer simulations, computing, GillespieSSA, R | 1 Comment

GillespieSSA 0.1-0 is released

Posted on August 19, 2007 by

I just submitted the first release of the GillespieSSA package to CRAN. After much debating I finally decided to adhere to the unwritten R version numbering policy of starting really really low (and asymptotically approaching 1.0-0) . Thus, the first … Continue reading →

Posted in GillespieSSA, R | Leave a comment

Open Source/Science – drilling down to unknown depths in unexpected places

Posted on August 12, 2007 by

Yet another point John Chambers addressed in his key note speech (see previous post Programing as a higher craft) was the virtue of Open Source software. According to John there are two principles for programing (with R) Enable effective and … Continue reading →

Posted in meeting, open science, R, useR 2007, useR! | Leave a comment

Programing as a higher craft

Posted on August 11, 2007 by

In his keynote speech at the useR! meeting John Chambers of Statistics research at Bell Labs (one of the founders of the S System, which subsequently gave rise to the R project) asked the question what is programing? As it … Continue reading →

Posted in meeting, programing, R, useR 2007, useR! | 1 Comment