inst/doc/smoothing.R

In alkahest: Pre-Processing XY Data from Experimental Methods

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(alkahest)

## ----raw, fig.width=7, fig.height=5, fig.cap="Simulated data."----------------
## Simulate data
set.seed(12345)
x <- seq(-4, 4, length = 100)
y <- dnorm(x)
z <- y + rnorm(100, mean = 0, sd = 0.01) # Add some noise

## Plot raw data
plot(x, z, type = "l", xlab = "", ylab = "", las = 1)
lines(x, y, type = "l", lty = 2, col = "red")

## ----unweighted, fig.width=7, fig.height=6, fig.cap="Rectangular smoothing."----
unweighted <- smooth_rectangular(x, z, m = 3)

par(mar = c(3, 3, 1, 1) + 0.1, las = 1)
layout(matrix(c(1, 2), nrow = 2, ncol = 1), heights = c(2, 1))

plot(unweighted, type = "l", xlab = "", ylab = "") 
lines(x, y, type = "l", lty = 2, col = "red")

plot(x, y - unweighted$y, ylim = c(-0.03, 0.03), type = "l", xlab = "", ylab = "")
abline(h = 0, lty = 2)

## ----weighted, fig.width=7, fig.height=6, fig.cap="Triangular smoothing."-----
weighted <- smooth_triangular(x, z, m = 5)

par(mar = c(3, 3, 1, 1) + 0.1, las = 1)
layout(matrix(c(1, 2), nrow = 2, ncol = 1), heights = c(2, 1))

plot(weighted, type = "l", xlab = "", ylab = "")
lines(x, y, type = "l", lty = 2, col = "red")

plot(x, y - weighted$y, ylim = c(-0.03, 0.03), type = "l", xlab = "", ylab = "")
abline(h = 0, lty = 2)

## ----loess, fig.width=7, fig.height=6, fig.cap="Loess smoothing."-------------
loess <- smooth_loess(x, z, span = 0.2)

par(mar = c(3, 3, 1, 1) + 0.1, las = 1)
layout(matrix(c(1, 2), nrow = 2, ncol = 1), heights = c(2, 1))

plot(loess, type = "l", xlab = "", ylab = "")
lines(x, y, type = "l", lty = 2, col = "red")

plot(x, y - loess$y, ylim = c(-0.03, 0.03), type = "l", xlab = "", ylab = "")
abline(h = 0, lty = 2)

## ----savitzky, fig.width=7, fig.height=6, fig.cap="Savitzky–Golay filter."----
savitzky <- smooth_savitzky(x, z, m = 21, p = 2)

par(mar = c(3, 3, 1, 1) + 0.1, las = 1)
layout(matrix(c(1, 2), nrow = 2, ncol = 1), heights = c(2, 1))

plot(savitzky, type = "l", xlab = "", ylab = "")
lines(x, y, type = "l", lty = 2, col = "red")

plot(x, y - savitzky$y, ylim = c(-0.03, 0.03), type = "l", xlab = "", ylab = "")
abline(h = 0, lty = 2)

## ----whittaker, fig.width=7, fig.height=6, fig.cap="Whittaker smoothing."-----
whittaker <- smooth_whittaker(x, z, lambda = 1000, d = 3, sparse = TRUE)

par(mar = c(3, 3, 1, 1) + 0.1, las = 1)
layout(matrix(c(1, 2), nrow = 2, ncol = 1), heights = c(2, 1))

plot(whittaker, type = "l", xlab = "", ylab = "")
lines(x, y, type = "l", lty = 2, col = "red")

plot(x, y - whittaker$y, ylim = c(-0.03, 0.03), type = "l", xlab = "", ylab = "")
abline(h = 0, lty = 2)