R/DeleteSeriesShorterThan.R

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

DeleteSeriesShorterThan <- function(rwl,
                                    filename,
                                    rwlStats = NULL,
                                    YEAR = 100,
                                    SaveShort = FALSE,
                                    Rwl = TRUE) {
  nSeries1 <- nSeries <- ncol(rwl)
  if (is.null(rwlStats)) {
    yr.range <- function(x) {
      yr.vec <- as.numeric(names(x))
      mask <- !is.na(x)
      range(yr.vec[mask])
    }
    series.stats <- data.frame(Series = colnames(rwl))
    series.stats$First <- apply(rwl, 2, yr.range)[1, ]
    series.stats$Last <- apply(rwl, 2, yr.range)[2, ]
    series.stats$Year <- series.stats$Last - series.stats$First + 1
    rwlStats <- series.stats
  }

  flag <- (rwlStats[, 4] >= YEAR)

  rwl1 <- subset(rwl, select = c(flag))
  if (ncol(rwl1) == 0) {
    cat("All series are shorter than ", YEAR, ".\n", sep = "")
    SaveShort <- FALSE
    Rwl <- FALSE
  }
  if (Rwl) {
    samp.depth <- apply(rwl1, 1, function(y) {
      sum(!is.na(y))
    })
    rwl1 <- subset(rwl1, samp.depth > 0)
    nSeries1 <- ncol(rwl1)
  }

  if (nSeries != nSeries1) {
    cat("The following series were shorter than ", YEAR, ":\n", sep = "")
    Flag <- rwlStats[, 4] < YEAR
    Flag <- colnames(rwl)[Flag]
    for (i in 1:length(Flag)) {
      cat(Flag[i], "\n")
    }

    b <- paste(filename, "+", YEAR, ".rwl", sep = "")
    write.rwl(rwl1, b)

    if (SaveShort) {
      rwl2 <- subset(rwl, select = c(!flag)) # To save series with less than YEAR
      samp.depth <- apply(rwl2, 1, function(y) {
        sum(!is.na(y))
      })
      rwl2 <- subset(rwl2, samp.depth > 0)

      b <- paste(filename, "-", YEAR, ".rwl", sep = "")
      write.rwl(rwl2, b)
    }
  } else {
    if (Rwl) {
      cat(paste("All series are longer than ", YEAR, ".\n", sep = ""))
    }
  }

  cat(rep("=", 98), "\n", sep = "")
  if (ncol(rwl1) >= 1) {
    return(rwl1)
  }
}