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title: "Introduction"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
```{r setup, include = FALSE}
collapse = TRUE,
comment = "#>"
# Introduction
`MicrobiomeR` is a microbiome workflow package that uses [phyloseq]( for
data import, [taxa]( for the primary R object called a Taxmap,
[metacoder]( for data analysis, and a combination of packages for
data visualization including `ggplot2`.
The goal of this package is to enhance the use of the
[metacoder]( package by providing tools that mimic
some of the functionalities of the [phyloseq]( package. The key difference is
that the main data object is a [taxa::taxmap object](
instead of a [phyloseq::phyloseq object](
## What makes MicrobiomeR special?
MicrobiomeR boasts a seamless and comprehensive workflow to analyze microbiome data which **(1)** emphasizes statistical rigor, **(2)** simplifies the creation of beautiful, meaningful, and easily reproducible publication-ready visualizations, and **(3)** adds versatile functions that incorporates the most widely used microbiome packages for R including vegan, microbiome, taxa, phyloseq, and metacoder.
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