library(lattice)
load("d.RData")

plot.trees <- function(v.id, layout = c(4, 3), stem = TRUE)
{
	df.b <- df.branch[df.branch$id %in% v.id,]
	df.t <- df.tree[df.tree$id %in% v.id,]
	df.b$id <- factor(df.b$id, levels = v.id)
	df.t$id <- factor(df.t$id, levels = v.id)
	min.x <- min(log(df.b$bdiameter08), na.rm = TRUE)
	max.x <- max(log(df.b$bdiameter08), na.rm = TRUE)
	max.y <- max(df.t$height08) + 10

	strip.tree <- function(which.panel, ...)
	{
		id <- v.id[which.panel]
		dt <- df.t[df.t$id == id,]
		panel.rect(
			0, 0, 1, 1,
			col = c("#ccffcc", "#ffcccc")[(dt["species"] == "mo") + 1]
		)
		panel.text(
			0.5, 0.5, 
			sprintf("%s (H = %.1f)", v.id[which.panel], dt["height08"])
		)
	}

	panel.tree <- function(x, y, subscripts, ...)
	{
		dfs <- df.b[subscripts,]
		id <- dfs[1, "id"]
		# lines (top at 2007, ground)
		panel.rect(
			min.x, -df.t[df.t$id == id, "dH"],
			max.x, 0,
			col = "#ddddff",
			border = NA
		)
		panel.rect(
			min.x, -df.t[df.t$id == id, "height08"],
			max.x, -max.y,
			col = "#eeeedd",
			border = NA
		)

		y <- dfs$bposition08
		# stem growth
		if (stem) {
			md <- 0.5
			panel.polygon(
				c(min.x, log(dfs$sdiameter08 * md), min.x),
				c(-min(y), -y, -max(y)),
				col = "#cccccc",
				border = NA
			)
			s07 <- !is.na(dfs$sdiameter07)
			panel.polygon(
				c(min.x, log(dfs$sdiameter07[s07] * md), min.x),
				c(-min(y[s07]), -y[s07], -max(y[s07])),
				col = "#eeeeee",
				border = NA
			)
		}

		# branch growth
		panel.segments(
			log(dfs$bdiameter08), -y,
			log(dfs$bdiameter07), -y,
			lwd = 2,
			col = "#00aa00"
		)
		# diamerter 08 and 07
		panel.points(
			log(dfs$bdiameter08), -y,
			pch = c(24,8, 23)[dfs$new08 + dfs$proleptic08 + 1],
			col = c("#000000", "#ff4000")[dfs$new08 + 1]
		)
		panel.points(
			log(dfs$bdiameter07), -y,
			pch = c(21, 4)[dfs$dead08 + 1],
			col = c("#000000", "#0000ff")[dfs$dead08 + 1]
		)
	}

	print(xyplot(
		-bposition08 ~ log(bdiameter08) | id,
		data = df.b,
		xlim = c(min.x, max.x),
		ylim = c(-max.y, 0),
		panel = panel.tree,
		strip = strip.tree,
		layout = layout,
		xlab = "log(D)",
		ylab = "Depth (cm)"
	))
}

plot.spc <- function(spc = "bp", ...)
{
	df.t <- df.tree[df.tree$species == spc,]
	v.id <- df.t[order(df.t$height08), "id"]
	plot.trees(v.id, ...)
}

plot.all <- function()
{
	for (spc in c("bp", "mo")) {
		file <- sprintf("trees%s.pdf", spc)
		cat("# output to", file, "...\n")
		pdf(
			file = file,
			paper = "A4",
			width = 8,
			height = 12
		)
		plot.spc(spc)
		dev.off()
	}
}