Vignettes

Vignettes

Vignettes are a standard in R for documenting package-level tools and intended uses (vignette definition). 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:

Basics Vignette

Vignette showing many analysis and plotting examples, using datasets already included in phyloseq:

Analysis Vignette