\name{export_env_file}
\alias{export_env_file}
\title{Export environment (ENV) file for UniFrac Server.}
\usage{
  export_env_file(physeq, file = "", writeTree = TRUE,
  return = FALSE)
}
\arguments{
  \item{physeq}{(Required). Experiment-level
  (\code{\link{phyloseq-class}}) object. Ideally this also
  contains the phylogenetic tree, which is also exported by
  default.}

  \item{file}{(Optional). The file path for export. If
  not-provided, the expectation is that you will want to
  set \code{return} to \code{TRUE}, and manipulate the ENV
  table on your own. Default is \code{""}, skipping the ENV
  file from being written to a file.}

  \item{writeTree}{(Optional). Write the phylogenetic tree
  as well as the the ENV table. Default is \code{TRUE}.}

  \item{return}{(Optional). Should the ENV table be
  returned to the R workspace? Default is \code{FALSE}.}
}
\description{
  Creates the environment table that is needed for the
  original UniFrac algorithm. Useful for cross-checking, or
  if want to use UniFrac server. Optionally the
  ENV-formatted table can be returned to the \code{R}
  workspace, and the tree component can be exported as
  Nexus format (Recommended).
}
\examples{
# # Load example data
# data(esophagus)
# export_env_file(esophagus, "~/Desktop/esophagus.txt")
}