R/compMS-package.R

In ColtoCaro/compMS: Bayesian Compositional Proteomics Modeling via Stan

# File for creating compMS documentation with roxygen

#' Bayesian Compositional Proteomics Modeling via Stan
#'
#' @docType package
#' @name compMS-package
#' @aliases compMS
#' @useDynLib compMS, .registration = TRUE
#'
#' @import methods
#' @importFrom rstan optimizing sampling vb constrain_pars extract extract_sparse_parts get_posterior_mean stanc
#' @import stats
#' @import Rcpp
#' @import bayesplot
#' @import rstantools
#'
#' @description
#' The \pkg{compMS} package enables users to fit compostional proteomics
#' models for isobaric tag mass spectrometry experiments.  The package is
#' designed to make these models accesible to people without a background
#' in Bayesian statistics or compositional data analysis.  This is done by
#' requiring users to follow a very specific format for data entry.  Once
#' the data is formatted properly everything else is handled internally.
#' The required fields and headers are explained in the documentation for the
#' sample data \code{\link{sampleDat}}.
#'
#' Once data has been correctly formatted and loaded into your workspace, you can
#' create a Stan model with the function \code{\link{compBayes}}.
#'
#' @section Model Details:
#' This is where I will explain the model and the options for use:
#' \describe{
#' No description yet.  For now see the supplement from the manuscript
#' https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00699
#' }
#'
#'
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