Category Archives: R

Metabarcoding for every body, every habitat, every time

The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. … Continue reading

Posted in bioinformatics, community, community ecology, DNA barcoding, fieldwork, metagenomics, next generation sequencing, phylogenetics, R | Tagged , , , , , , | Leave a comment

Phylogenetic trees in R using ggtree

Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 package. With ggtree, plotting trees in R has … Continue reading

Posted in bioinformatics, howto, phylogenetics, R | Tagged , , , | 2 Comments

Video Tutorial: editing R plots in Adobe Illustrator

Adobe Illustrator is a powerful tool for creating and editing figures; unfortunately, it’s also really intimidating. So today at The Molecular Ecologist we’re trying something a little different: a screen-capture video tutorial about using Adobe Illustrator to enhance and edit plots … Continue reading

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Making Maps in R, volume 2: ggplots

The open-source statisical programming environment R is truly a Swiss Army knife for molecular ecology. With the right code, R can processes genetic data and trait measurements, analyze how genetic variants relate to traits, reconstruct phylogenetic trees, and illustrate the … Continue reading

Posted in howto, R, software | Tagged , | 6 Comments

Geographical Heat Maps in R

I go crazy for fancy data visualizations in R, and a figure in a recent publication has had me wondering if there is an easy way to incorporate density distributions (or as in their case, a distribution of f4 statistics, … Continue reading

Posted in bioinformatics, howto, R, software | Tagged , | 2 Comments

Quick and dirty tree building in R

One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading

Posted in howto, methods, phylogenetics, R, software | Tagged , , , , , , , | 3 Comments

Genomics of Hybridization – Part II, Top three of 2015

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population … Continue reading

Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged , , , , | Leave a comment

2D Posterior Density Plots in R

I have been grappling with visualizing two dimensional histograms of posterior density distributions of parameters, as estimated by one of your favorite programs – IMa2, MIGRATE-n, MSVAR, etc. All these programs print out distributions of estimated parameters, and here’s a … Continue reading

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | 1 Comment

Models matter when linking genetic diversity to niche model predictions

Ecological niche models and the methods to create them continue to evolve. These techniques provide a tidy way to relate the distributions of taxa to environmental variables from the present, past, or future. Oh, and they are pretty too: Those pretty … Continue reading

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PCA of multilocus genotypes in R

An earlier post from Mark Christie showed up on my feed on calculating allele frequencies from genotypic data in R, and I wanted to put together a quick tutorial on making PCA (Principal Components Analysis) plots using genotypes. I used … Continue reading

Posted in bioinformatics, genomics, howto, population genetics, R, software | Tagged , , | 6 Comments