Nothing
opar <- par(ask = interactive() &&
(.Device %in% c("X11", "GTK", "gnome", "windows","quartz")))
data(phyto)
# smooth the observed data
bobs <- dpill(obs$t, obs$y)
n <- tail(obs$t, n = 1) - obs$t[1] + 1
obss <- ksmooth(obs$t, obs$y, kernel = "normal", bandwidth = bobs,
n.points = n)
obss <- as.data.frame(obss)
names(obss) <- c("t", "y")
obss <- na.omit(obss[match(sim$t, obss$t),])
# plot data
basedate <- as.Date("1960/1/1")
plot(basedate + sim$t, sim$y, type="l", xaxt="n",
xlim=c(basedate + min(obs$t, sim$t), basedate + max(obs$t, sim$t)),
ylim=c(min(obs$y, sim$y), max(obs$y, sim$y)),
xlab="1994", ylab="Phytoplankton (mg/L)",
col="grey60", font=2, lwd=2, cex.lab=1.4, las=1)
lines(basedate + obss$t, obss$y, lwd=2)
points(basedate + obs$t, obs$y, lwd=2)
# positions and names to draw x-axes
lab.mon <- as.Date(c(paste("1994/", c(1,3,5,7,9,11), "/01", sep=""), "1995/1/1"))
lab.lab <- c("Jan","Mar","May","Jul","Sep","Nov","Jan")
axis(1, at=lab.mon, labels=lab.lab, font=2, cex.lab=1.4)
legend(as.Date("1994/09/01"), 50, c("measurement", "smoothed measurement", "simulation"),
lty=c(0,1,1), pch=c(1,NA,NA), lwd=2, col=c(1,1,"grey60"))
# semiquantitative comparison
sqc <- compareME(obs$y, sim$y, obs$t, sim$t, type = c("normalized"))
round(sqc$normalized, digits=3)
compareME(type="name")
# time transformation
tt <- timeTransME(obss$y, sim$y, obss$t, sim$t, ME = SMSE, time = "transform",
type = "normalized", trials = 5, timeME = MAE, timeMEtype = "dissimilarity")
cat("Error:", round(tt$totalME, digits = 3),"\n")
cat("Time stress:", round(tt$timeME, digits = 3),"\n")
# plot time transformation
basedate <- as.Date("1960/1/1")
plot(basedate + sim$t, sim$y, type="l", xaxt="n",
ylim=c(min(obs$y, sim$y), max(obs$y, sim$y)),
xlab="time", ylab="Phytoplankton (mg/L)",
col="grey60", font=2, lwd=2, cex.lab=1.2, las=1)
lines(basedate + obss$t, obss$y, lwd=2)
points(basedate + obs$t, obs$y, lwd=2)
lines(basedate + tt$x, tt$yp, lwd=2, col="grey60", lty=2)
# positions and names to draw x-axes
lab.mon <- as.Date(c(paste("1994/", c(1,3,5,7,9,11), "/01", sep=""), "1995/1/1"))
lab.lab <- c("Jan","Mar","May","Jul","Sep","Nov","Jan")
axis(1, at=lab.mon, labels=lab.lab, font=2, cex.lab=1.4)
legend(basedate + 12600, 50, c("measurement", "smoothed measurement", "simulation",
"transformed simulation"), lty=c(0,1,1,2), pch=c(1,NA,NA,NA), lwd=2, col=c(1,1,"grey60","grey60"))
# interval sequences
obs_f1 <- f.slope(obss$t, obss$y)
sim_f1 <- f.slope(sim$t, sim$y)
lcs <- LCS(obs_f1, sim_f1)
cat("QSI:",lcs$QSI,"\n")
qvlcs <- qvalLCS(obs$y, sim$y, obs$t, sim$t, smooth = "obs")
plot.qvalLCS(qvlcs)
par(opar)
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