R/pfExtract.R

In paleofire/paleofire: Analysis of Charcoal Records from the Global Charcoal Database

#' Extract charcoal data for a list of sites
#'
#' Extract charcoal data from an object returned by \code{\link{pfSiteSel}}
#'
#'
#' @param ID An object returned by \code{\link{pfSiteSel}}.
#' @return
#'
#' \item{out}{A matrix of charcoal data with the following structure:
#' out[,1]=Site identifiers, out[,2]=Depths, out[,3]=Estimated ages,
#' out[,4]=Charcoal data.}
#' @author O. Blarquez
#' @examples
#' \dontrun{
#' ## Retrieve a site
#' ID=pfSiteSel(site_name=="Pas-de-Fond")
#' ## Or a group of sites (Western North America)
#' ID=pfSiteSel(continent=="North America", long<(-100))
#'
#' ## Extract data
#' A=pfExtract(ID)
#'
#' # Plot the first site raw charcoal data
#' plot(A[A[,1]==ID$id_site[1],3],A[A[,1]==ID$id_site[1],4],type="l",main=ID$site_name[1],
#'      xlab="Age",ylab="raw Char")
#' }
pfExtract <- function(ID) {
  ## Avoid no visible binding for global variable
  paleofiredata <- NULL
  rm(paleofiredata)

  # Extract data for sites
  data(paleofiredata, envir = environment())
  if (is.numeric(ID)) {
    Ext <- paleofiredata[paleofiredata[, 1] %in% ID, ]
  } else {
    Ext <- paleofiredata[paleofiredata[, 1] %in% ID$id_site, ]
  }
  return(Ext)
}