# R/selwold.R In mlesnoff/rnirs: Dimension reduction, Regression and Discrimination for Chemometrics

#### Documented in selwold

```selwold <- function(
r, start = 0,
type = c("raw", "smooth", "integral"),
alpha = .01, digits = 3,
plot = c("R", "diff", "none"),
xlab = "Index", ylab = "Value", main = "r",
...
) {

type <- match.arg(type)
plot <- match.arg(plot)

n <- length(r)

zindex <- seq(start, start + n - 1)

## val = Value on which are calculated diff and R
val <- switch(
type,
raw = r,
smooth = lowess(zindex, r, ...)\$y,
integral = cumsum(r + abs(min(r)))
)

zdiff <- -diff(val)
R <- zdiff / abs(val[-length(val)])
if(type == "integral")
R <- -R

zdiff <- c(zdiff, NA)
R <- c(R, NA)

opt <- zindex[r == min(r)][1]
sel <- zindex[R < alpha][1]
if(is.na(sel))
sel <- opt
sel <- min(opt, sel)

res <- data.frame(index = zindex, r = r)
res\$val <- val
res\$diff <- -zdiff
res\$R <- round(R, digits = digits)
row.names(res) <- seq_len(n)

if(plot %in% c("R", "diff")) {

fg <- "grey70"
col <- "#045a8d"
xmin <- min(zindex)
xmax <- max(zindex)
eps <- .8

if(n <= 55)
labs <- seq(xmin, xmax, by = 2)
else
labs <- seq(xmin, xmax, by = 10)

oldpar <- par(mfrow = c(1, 1))
par(mfrow = c(1, 2))

plot(
zindex, r,
type = "l", col = col, pch = 16,
xaxt = "n", las = 1, fg = fg, las = 1,
xlim = c(xmin - eps, xmax + eps), xaxs = "i",
xlab = xlab, ylab = ylab, main = main
)
points(zindex, r, pch = 16, col = col)
if(plot == "R")
if(sel < opt)
points(seq(sel + 1, opt), r[zindex %in% seq(sel + 1, opt)],
pch = 16, col = "grey", cex = 1.2)
points(opt, r[zindex == opt], pch = 16, col = "red", cex = 1.2)
axis(side = 1, at = labs, labels = labs, fg = fg)
abline(h = min(r), col = "grey")
on.exit(par(oldpar))

if(type == "smooth") {
lines(zindex, val, type = "l", col = "red")
legend("topright", legend = c("Raw", "Smoothed"),
box.col = "grey70", ncol = 1,
col = c("#045a8d", "red"), lty = 1, xjust = 1, yjust = 1)
}

if(plot == "R") {
plot(
zindex, R,
type = "l", pch = 16, col = col,
xaxt = "n", las = 1, fg = fg, las = 1,
xlim = c(xmin - eps, xmax - 1 + eps), xaxs = "i",
xlab = xlab, ylab = "R", main = "Relative gain"
)
points(zindex, R, pch = 16, col = col)
axis(side = 1, at = labs, labels = labs, fg = fg)
abline(h = c(0, alpha), col = c("grey", "blue"), lty = seq_len(2))
on.exit(par(oldpar))
}

if(plot == "diff") {
plot(
zindex, -zdiff,
type = "l", pch = 16, col = col,
xaxt = "n", las = 1, fg = fg, las = 1,
xlim = c(xmin - eps, xmax - 1 + eps), xaxs = "i",
xlab = xlab, ylab = "diff", main = "Difference"
)
points(zindex, -zdiff, pch = 16, col = col)
axis(side = 1, at = labs, labels = labs, fg = fg)
abline(h = median(-zdiff, na.rm = TRUE), col = "grey")
on.exit(par(oldpar))
}

par(oldpar)

}

list(res = res, opt = opt, sel = sel)

}
```
mlesnoff/rnirs documentation built on April 24, 2023, 4:17 a.m.