Category Archives: R

Geophylogeny plots in R for Dummies

Posted on 27 Nov, 2014 by Arun Sethuraman

Amid basting my tofurky, here’s a follow-up to my previous post on quick-fix overlays of admixture plots on geographical maps in R. I recently discovered a wonderful R package called “phytools” from Liam Revell, which makes really neat phylogenetic trees (with … Continue reading →

Posted in howto, phylogenetics, population genetics, R, software, STRUCTURE | Tagged , | 4 Comments

Admixture maps in R for Dummies

Posted on 13 Nov, 2014 by Arun Sethuraman

Before we get started, I’d like to point everyone to an excellent tutorial here by Kim Gilbert on making maps in R. I have been grappling with overlaying admixture plots, and migration routes on top of maps recently, and thought I’d put … Continue reading →

Posted in howto, population genetics, R, software, STRUCTURE | Tagged , | 14 Comments

Calculating genetic differentiation with R

Posted on 20 May, 2014 by Mark Christie

As molecular ecologists, it is often necessary and useful to calculate some measure of genetic differentiation. This is often accomplished with metrics such as Wright’s Fst an or an unbiased analog (e.g., Weir & Cockerham’s Fst; G’st etc.). In addition … Continue reading →

Posted in population genetics, R, software | 13 Comments

Using GitHub with R and RStudio

Posted on 12 Nov, 2013 by Mark Christie

A few weeks back, The Molecular Ecologist released an article about GitHub and also created an organization where you can fork or simply download code shared by the Molecular Ecology community. A few of you out there may still be … Continue reading →

Posted in bioinformatics, howto, R, software | 29 Comments

Random drift and phenotypic evolution

Posted on 15 Oct, 2013 by peterfields

This week we have a guest post from Markku Karhunen. Markku’s research at the University of Helsinki included the development and implementation of a number of very interesting and useful population genetics methods. In his guest post Markku discusses these … Continue reading →

Posted in adaptation, methods, population genetics, quantitative genetics, R, software, Uncategorized | 2 Comments

Using R to run parallel analyses of population genetic data in STRUCTURE: ParallelStructure

Posted on 3 Sep, 2013 by Jeremy Yoder

In this guest post, Francois Besnier explains how to use ParallelStructure, his new R package for running STRUCTURE analyses in parallel computing environments. To start with, thanks to The Molecular Ecologist blog team (Tim and Jeremy) for the invitation to … Continue reading →

Posted in howto, population genetics, R, software, STRUCTURE | 5 Comments

Want to share your code?

Posted on 27 Aug, 2013 by kimgilbert

In this line of work, we have all encountered tasks that are tedious, time consuming, and repetitive.  (Or if not, maybe give it a bit more time.) When confronted with these situations, people tend to fall into one of two … Continue reading →

Posted in bioinformatics, community, genomics, howto, methods, next generation sequencing, phylogenetics, population genetics, quantitative genetics, R, software, theory | 14 Comments

Making heatmaps with R for microbiome analysis

Posted on 20 Aug, 2013 by Jeremy Yoder

Arianne Albert is the Biostatistician for the Women’s Health Research Institute at the British Columbia Women’s Hospital and Health Centre. She earned a PhD from the University of British Columbia under the tutelage of Dolph Schluter before branching off into … Continue reading →

Posted in howto, microbiology, R, software | Tagged , , | 71 Comments

Species distribution models in R

Posted on 23 Apr, 2013 by Jeremy Yoder

Update, 20 August 2013: Many readers have requested a copy of the Joshua tree data set used as an example in this post, and I’ve finally secured permission from the coauthors of the original study to post it to Dryad. … Continue reading →

Posted in howto, R, software | Tagged , | 27 Comments

Making Maps with R

Posted on 18 Sep, 2012 by kimgilbert

First off, thanks to Tim and Jeremy for the invitation to write a guest post here on using R to make maps! As a brief introduction, my name is Kim Gilbert, and I am a Ph.D. student at the University … Continue reading →

Posted in howto, R, software | Tagged , , | 122 Comments