R/metacoder-package.R

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

#===================================================================================================
#' Metacoder
#' 
#' A package for planning and analysis of amplicon metagenomics research projects.
#' 
#' The goal of the \code{metacoder} package is to provide a set of tools for:
#' 
#' \itemize{
#'   \item Standardized parsing of taxonomic information from diverse resources.
#'   \item Visualization of statistics distributed over taxonomic classifications.
#'   \item Evaluating potential metabarcoding primers for taxonomic specificity.
#'   \item Providing flexible functions for analyzing taxonomic and abundance data.
#' }
#' 
#' To accomplish these goals, \code{metacoder} leverages resources from other R packages, interfaces with
#' external programs, and provides novel functions where needed to allow for entire analyses within R.
#' 
#' @section Documentation:
#' 
#' The full documentation can be found online at \url{https://grunwaldlab.github.io/metacoder_documentation/}.
#' 
#' There is also a short vignette included for offline use that can be accessed  by the following code:
#' 
#' \code{browseVignettes(package = "metacoder")}
#' 
#' \strong{Plotting:}
#' 
#' \itemize{
#'   \item \code{\link{heat_tree}}
#'   \item \code{\link{heat_tree_matrix}}
#' }
#'
#' \strong{In silico PCR:}
#' 
#' \itemize{
#'   \item \code{\link{primersearch}}
#' }
#'
#' \strong{Analysis:}
#' 
#' \itemize{
#'   \item \code{\link{calc_taxon_abund}}
#'   \item \code{\link{calc_obs_props}}
#'   \item \code{\link{rarefy_obs}}
#'   \item \code{\link{compare_groups}}
#'   \item \code{\link{zero_low_counts}}
#'   \item \code{\link{calc_n_samples}}
#'   \item \code{\link{filter_ambiguous_taxa}}
#' }
#' 
#' \strong{Parsers:}
#' 
#' \itemize{
#'   \item \code{\link{parse_greengenes}}
#'   \item \code{\link{parse_mothur_tax_summary}}
#'   \item \code{\link{parse_mothur_taxonomy}}
#'   \item \code{\link{parse_newick}}
#'   \item \code{\link{parse_phyloseq}}
#'   \item \code{\link{parse_phylo}}
#'   \item \code{\link{parse_qiime_biom}}
#'   \item \code{\link{parse_rdp}}
#'   \item \code{\link{parse_silva_fasta}}
#'   \item \code{\link{parse_unite_general}}
#' }
#' 
#' \strong{Writers:}
#' 
#' \itemize{
#'   \item \code{\link{write_greengenes}}
#'   \item \code{\link{write_mothur_taxonomy}}
#'   \item \code{\link{write_rdp}}
#'   \item \code{\link{write_silva_fasta}}
#'   \item \code{\link{write_unite_general}}
#' }
#' 
#' \strong{Database querying:}
#' 
#' \itemize{
#'   \item \code{\link{ncbi_taxon_sample}}
#' }
#' 
#' @author Zachary Foster and Niklaus Grunwald
#' @name metacoder
#' @docType package
#' @useDynLib metacoder
#' @importFrom Rcpp sourceCpp
NULL