How does this work? What sort of markdown is this?

Well, according to This Rblogger post about the R Markdown feature, it supports GitHub Flavored Markdown (GFM) and therefore the source code blocks within GFM. Does this mean if I make a source code block in Rmd, it automatically knows that it is R code? Does it also compile the R code? Will it perform nice text-highlighting on the code? I hope so.

Let's find out. First, let's load the phyloseq package, which can be installed using these instructions, and has other examples and descriptions in the phyloseq wiki

library("phyloseq")
library("ggplot2")

For a small, trivially-simple example, use the 3-sample, ~100-species esophagus dataset

data(esophagus)

Now load the ape package, and retrieve the patristic distances between taxa using cophenetic.phylo. Will need to convert output from cophenetic into a "dist" class object using the dist function.

library("ape")
eso.dist <- dist(cophenetic(tre(esophagus)))

What is the range of distance values for eso.dist?

range(eso.dist)

## [1] 0.156 1.055

Now provide this custom "dist"ance object to make_network to create an igraph network object. Note that we need to select a value for a distance threshold that seems useful for a cophenetic distance (we will repeat later on with a co-occurrence distance, Jaccard).

eg <- make_network(esophagus, "species", eso.dist, 0.3)

Now create a plot of this species network using plot_network.

p <- plot_network(eg, esophagus, "species")
print(p)