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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:
Latest included version of Basics Vignette
Vignette showing many analysis and plotting examples, using datasets already included in phyloseq:
Latest included version of Analysis Vignette
Both vignettes are included in the package with the requisite files (.Rnw, etc.) for re-building the pdf using Sweave. Additionally, further examples and details examples will be added incrementally to this wiki in order to better show the full range of plotting and analysis options that just isn't possible under the tight space constraints of a Bioconductor software package.