R/MicrobiomeR-package.R

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

#' MicrobiomeR
#'
#' A microbiome workflow package using phyloseq for data import, metacoder for data analysis,
#' and ggplot2 for data visualization.
#'
#' The goal of this package is to enhance the use of the \code{\link[metacoder:metacoder]{metacoder}} package by
#' providing tools that mimic the \code{\link[phyloseq:phyloseq-package]{phyloseq}} package.  The only difference being that
#' the main data object is a \code{\link[taxa:taxmap]{taxmap object}} instead of a \code{\link[phyloseq:phyloseq-class]{phyloseq object}}.
#'
#' @section Other Documentation:
#' Below are some links to helpful R package used, while developing this package.
#'
#' \describe{
#'   \item{metacoder}{\url{https://grunwaldlab.github.io/metacoder_documentation/}}
#'   \item{taxa}{\url{https://github.com/ropensci/taxa}}
#'   \item{phyloseq}{\url{http://joey711.github.io/phyloseq/}}
#'   \item{microbiome}{\url{http://microbiome.github.io/microbiome/}}
#'   \item{MicrobiomeR}{\url{https://github.com/vallenderlab/MicrobiomeR}
#' }}
#' The [MicrobiomeR_Workflow] and [MicrobiomeR_Formats] help sections are also useful for understanding the
#' package.
#'
#'
#' @author Rob Gilmore and Shaurita Hutchins
#' @name MicrobiomeR
#' @docType package
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