title: r creating documentation from multiple R files
body: <p>I have a project with multiple .R files. They need to be run in order (output from one is input into the next, etc.). Each is standalone, expecting that the input it needs has been generated previously. I have an R file I call <code>automate.R</code> that sources each .R file in the correct order. Each .R file starts with some text with rmarkdown code like the following.</p>
  
  <pre><code>#' @title calculate nutrient requirements for SSP age group categories
  #' @author Gerald C. Nelson, \email{nelson.gerald.c@@gmail.com}
  #' @keywords utilities, IMPACT data, gdx
  # Intro -------------------------------------------------------------------
  
  # Copyright (C) 2015 - 2018 Gerald C. Nelson, except where noted
  #' @description - This script calculates nutrient requirements for SSP age group categories
  #' The source of the requirements is
  #' @source \url{http://www.nal.usda.gov/fnic/DRI/DRI_Tables/recommended_intakes_individuals.pdf}
  #' @include nutrientModFunctions.R
  </code></pre>
  
  <p>Eventually I might want to convert some of this to a package, but for now, how do I have lines with markdown tags from each script be combined into one documentation file? The entire project is available at <a href="https://github.com/GeraldCNelson/nutmod" rel="nofollow noreferrer">https://github.com/GeraldCNelson/nutmod</a>, in case anyone wants some specific R code.</p>