R/readTreeMask.R

In detrendeR: A Graphical User Interface (GUI) to Visualize and Analyze Dendrochronological Data

readTreeMask <- function(rwl, stc = c(5, 2, 1)) {
  if (sum(stc) != 8) {
    stop("Site-Tree-Core mask does not sum to 8")
  }
  ids <- colnames(rwl) # series names
  #  ids = format(ids,width=8, align="l")

  test <- function(x, site.chars = stc) {
    out <- c(NA, NA, NA)
    out[1] <- substring(x, 1, stc[1])
    out[2] <- substring(x, stc[1] + 1, sum(stc[1:2]))
    out[3] <-
      substring(x, sum(stc[1:2]) + 1, sum(stc[1:2]) + stc[3])
    return(out)
  }

  out <- t(sapply(ids, test, site.chars = stc))
  out <- data.frame(out)

  tree.series <- ids
  tree.vec <- as.numeric(out[, 2])
  tree.ids <- unique(out[, 2])

  core.vec <- rep(NA, length(tree.vec))
  n.trees <- length(tree.ids)
  for (i in 1:n.trees) {
    n.cores <- length(core.vec[tree.vec == i])
    core.vec[tree.vec == i] <- seq(1, n.cores)
  }

  out <- data.frame(out, tree = tree.vec, core = core.vec)
  out <- out[order(out[, 4]), ] # sort by tree
  colnames(out) <- c("Site", "Tree", "Core", "tree", "core")
  return(out)
}