R/pfResolution.R

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

#' Calculates age resolution indicators for charcoal records
#'
#' Calculates age resolution indicators for charcoal records selected using
#' \code{\link{pfSiteSel}} or \code{\link{pfInteractive}} functions.
#'
#'
#' @param ID An object of the class "pfSiteSel"
#' @param AgeLim Numeric, defines age limits for age resolution calculations
#' (e.g. AgeLim=c(-50,6000))
#' @return
#'
#' \item{data.frame}{A data frame with the following informations: ID_SITE,
#' SITE_NAME, Median Resolution of the record, Mean Resolution and Standard
#' deviation}
#' @author O. Blarquez
#' @examples
#' \dontrun{
#' ID=pfSiteSel(lat>40, lat<90, long>-100, long<=-50)
#' Res=pfResolution(ID,AgeLim=c(-50,8000))
#' head(Res)
#' }
pfResolution <- function(ID, AgeLim=NULL) {

  # Temporal resolution of records

  paleofiredata <- NULL
  rm(paleofiredata)
  paleofiresites <- NULL
  rm(paleofiresites)

  data(paleofiredata, envir = environment())
  data(paleofiresites, envir = environment())

  IDs <- ID # Save for output

  ID <- ID$id_site
  # Use only paleofiredata corresponding to ID
  if (is.null(AgeLim)) {
    paleofiredata <- paleofiredata[paleofiredata[, 1] %in% ID, ]
  } else {
    paleofiredata <- paleofiredata[paleofiredata[, 1] %in% ID, ]
    paleofiredata <- paleofiredata[paleofiredata$EST_AGE > AgeLim[1] & paleofiredata$EST_AGE < AgeLim[2], ]
  }

  meanres <- c()
  medianres <- c()
  sdres <- c()

  for (i in 1:length(ID)) {
    pref <- paleofiresites[paleofiresites$id_site == ID[i], ]$pref_units
    meanres[i] <- mean(diff(paleofiredata[paleofiredata$ID_SITE %in% ID[i] & paleofiredata$UNIT %in% pref, ]$EST_AGE))
    medianres[i] <- median(diff(paleofiredata[paleofiredata$ID_SITE %in% ID[i] & paleofiredata$UNIT %in% pref, ]$EST_AGE))
    sdres[i] <- sd(diff(paleofiredata[paleofiredata$ID_SITE %in% ID[i] & paleofiredata$UNIT %in% pref, ]$EST_AGE))
  }

  res <- data.frame(
    ID_SITE = as.numeric(IDs$id_site),
    SITE_NAME = IDs$site_name,
    MeanRes = as.numeric(meanres),
    MedianRes = as.numeric(medianres),
    SdRes = as.numeric(sdres)
  )
  return(res)
}