---
title: "Introduction"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# Introduction

`MicrobiomeR` is a microbiome workflow package that uses [phyloseq](https://github.com/joey711/phyloseq) for 
data import, [taxa](https://github.com/ropensci/taxa) for the primary R object called a Taxmap, 
[metacoder](https://github.com/grunwaldlab/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](https://grunwaldlab.github.io/metacoder_documentation/) package by providing tools that mimic 
some of the functionalities of the [phyloseq](http://joey711.github.io/phyloseq/) package.  The key difference is
that the main data object is a [taxa::taxmap object](https://github.com/ropensci/taxa#the-taxmap-class) 
instead of a [phyloseq::phyloseq object](http://joey711.github.io/phyloseq/import-data.html#import_biom).


## 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.