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Vignettes
Vignettes are a standard in R for documenting package-level tools and intended uses. They are often more useful than the function-level documentation because they provide examples of the interactions of multiple functions and/or "complete" analysis tasks. Vignettes should be enjoyed as a mixed-language PDF that includes both R code and English text that has been "weaved" together using the Sweave package/engine. The goal of a vignette is to combine the motivation and interpretation of analyses along with code that can reproduce the same results and be re-used for other analysis and new problems.
Vignette of basic importing, filtering, storing, and working with phylogenetic sequencing data in phyloseq:
More vignettes in preparation. Return soon and/or write encouraging messages