Waste Not, Want Not Supplemental Files

This repo hosts the supplemental source/output files corresponding to Protocol 1 of the following article.

McMurdie and Holmes (2014) Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible. PLoS Computational Biology

(in press)

Please make sure to cite the above article if you make use of these supplemental files.

Source Code Index

Quick Links to Output

• Source Code Index
• Minimal Rarefy Example
• Simulations Design
• Dispersion Survey
• Cluster Accuracy Simulation
• Differential Abundance Simulation

The R Markdown Source Code

For more advanced users interested in seeing and/or modifying the R markdown source code from which these reproducible, web browser-friendly output files were created.

dispersion-survey/dispersion.Rmd

minimal-rarefy-example/minimal-rarefy-example.Rmd

simulation-cluster-accuracy/simulation-cluster-accuracy-server.Rmd

simulation-design/simulation-design-figure-ex-matrix.Rmd

simulation-differential-abundance/simulation-differential-abundance-server.Rmd

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Phyloseq Extensions

For brief reproducible examples of related extensions for the phyloseq package, see the phyloseq extensions front page.