Author: Ze Jiang, Md. Mamunur Rashid, Ashish Sharma, and Fiona Johnson

# WASP: An R package for Wavelet System Prediction

#### Ze Jiang, Md. Mamunur Rashid, Ashish Sharma, and Fiona Johnson

#### 14:05:38 22 January, 2026

# 1 Setup

# 2 Required packages

    library(WASP)
    library(ggplot2)

    #if(!require(SPEI)) devtools::install_github('sbegueria/SPEI@v1.7.1') # use 1.7.1
    #require(SPEI)
    library(readr)
    library(dplyr)
    #>
    #> Attaching package: 'dplyr'
    #> The following object is masked from 'package:kableExtra':
    #>
    #>     group_rows
    #> The following objects are masked from 'package:stats':
    #>
    #>     filter, lag
    #> The following objects are masked from 'package:base':
    #>
    #>     intersect, setdiff, setequal, union
    library(FNN)
    #>
    #> Attaching package: 'FNN'
    #> The following object is masked from 'package:WASP':
    #>
    #>     knn
    library(synthesis)
    #>
    #> Attaching package: 'synthesis'
    #> The following objects are masked from 'package:WASP':
    #>
    #>     data.gen.HL, data.gen.Rossler, data.gen.SW, data.gen.ar1,
    #>     data.gen.ar4, data.gen.ar9, data.gen.tar1, data.gen.tar2
    library(waveslim)
    #>
    #> waveslim: Wavelet Method for 1/2/3D Signals (version = 1.8.4)
    library(cowplot)
    library(gridGraphics)
    #> Loading required package: grid

# 3 DWT, MODWT and AT basic propertites

    # data generation
    x <- arima.sim(list(order = c(1, 0, 0), ar = 0.6), n = 512)
    # x <- as.numeric(scale(data.gen.Rossler(time = seq(0, 50, length.out = 512))$x, scale=F))

    # Daubechies wavelets
    for (wf in c("haar", "d4", "d8", "d16")) {
      print(paste0("Wavelet filter: ", wf))
      #----------------------------------------------------------------------------
      # wavelet family, extension mode and package
      # wf <- "haar" # wavelet family D8 or db4
      boundary <- "periodic"
      if (wf != "haar") v <- as.integer(parse_number(wf) / 2) else v <- 1

      # Maximum decomposition level J
      n <- length(x)
      J <- ceiling(log(n / (2 * v - 1)) / log(2)) - 1 # (Kaiser, 1994)

      cov <- rnorm(J + 1, sd = 2)
      Vr <- as.numeric(cov / norm(cov, type = "2") * sd(x))
      #----------------------------------------------------------------------------
      # DWT-MRA
      print("-----------DWT-MRA-----------")
      x.mra <- waveslim::mra(x, wf = wf, J = J, method = "dwt", boundary = boundary)
      x.mra.m <- matrix(unlist(x.mra), ncol = J + 1)

      x.n <- scale(x.mra.m) %*% Vr
      var(x.n) - var(x)

      message(paste0("Additive decompostion: ", isTRUE(all.equal(as.numeric(x), rowSums(x.mra.m)))))
      message(paste0("Variance decompostion: ", isTRUE(all.equal(var(x), sum(apply(x.mra.m, 2, var))))))

      #----------------------------------------------------------------------------
      # MODWT
      print("-----------MODWT-----------")
      x.modwt <- waveslim::modwt(x, wf = wf, n.levels = J, boundary = boundary)
      x.modwt.m <- matrix(unlist(x.modwt), ncol = J + 1)

      x.n <- scale(x.modwt.m) %*% Vr
      var(x.n) - var(x)

      message(paste0("Additive decompostion: ", isTRUE(all.equal(as.numeric(x), rowSums(x.modwt.m)))))
      message(paste0("Variance decompostion: ", isTRUE(all.equal(var(x), sum(apply(x.modwt.m, 2, var))))))

      #----------------------------------------------------------------------------
      # a trous
      print("-----------AT-----------")
      x.at <- at.wd(x, wf = wf, J = J, boundary = boundary)
      x.at.m <- matrix(unlist(x.at), ncol = J + 1)

      # x.mra.modwt <- waveslim::mra(x,wf=wf, J=J, method="modwt", boundary=boundary)
      # x.mra.modwt <- matrix(unlist(x.mra.modwt), ncol=J+1)
      #
      # print(sum(abs(x.at.m-x.mra.modwt)))

      message(paste0("Additive decompostion: ", isTRUE(all.equal(as.numeric(x), rowSums(x.at.m)))))
      message(paste0("Variance decompostion: ", isTRUE(all.equal(var(x), sum(apply(x.at.m, 2, var))))))

      if (isTRUE(all.equal(x.at.m, x.modwt.m))) {
        message(paste0("AT and MODWT is equivalent using the", wf, "!"))
      }
    }
    #> [1] "Wavelet filter: haar"
    #> [1] "-----------DWT-MRA-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: TRUE
    #> [1] "-----------MODWT-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: TRUE
    #> [1] "-----------AT-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: TRUE
    #> AT and MODWT is equivalent using thehaar!
    #> [1] "Wavelet filter: d4"
    #> [1] "-----------DWT-MRA-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: TRUE
    #> [1] "-----------MODWT-----------"
    #> Additive decompostion: FALSE
    #> Variance decompostion: TRUE
    #> [1] "-----------AT-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: FALSE
    #> [1] "Wavelet filter: d8"
    #> [1] "-----------DWT-MRA-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: TRUE
    #> [1] "-----------MODWT-----------"
    #> Additive decompostion: FALSE
    #> Variance decompostion: TRUE
    #> [1] "-----------AT-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: FALSE
    #> [1] "Wavelet filter: d16"
    #> [1] "-----------DWT-MRA-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: TRUE
    #> [1] "-----------MODWT-----------"
    #> Additive decompostion: FALSE
    #> Variance decompostion: TRUE
    #> [1] "-----------AT-----------"
    #> Additive decompostion: TRUE
    #> Variance decompostion: FALSE

## 3.1 Summary of various properties for the three DWT methods

    tab1 <- data.frame(
      col1 = c("DWT-MRA", "MODWT", "AT"),
      col2 = c("$\\checkmark$", "", "$\\checkmark$"),
      col3 = c("$\\checkmark$", "$\\checkmark$", ""),
      col4 = c("", "$\\checkmark$", "$\\checkmark$"),
      col5 = c("$\\checkmark$", "", "")
    )

    colnames(tab1) <- c("Wavelet Method", "Additive decomposition", "Variance decomposition", "No dependence on future data", "Dyadic sample size")

    kable(tab1, caption = "Summary of various properties for the three DWT methods", booktabs = T, escape = F) %>%
      kable_styling(latex_options = c("HOLD_position"), position = "center") %>%
      column_spec(1, width = "6em") %>%
      column_spec(2:5, width = "7em") %>%
      footnote(general = "When Haar wavelet filter is used, MODWT and AT are equivalent and both of them preserves additive and variance decomposition.", footnote_as_chunk = T)

Table 3.1: Table 3.2: Summary of various properties for the three DWT methods
Wavelet Method | Additive decomposition | Variance decomposition | No dependence on future data | Dyadic sample size
--- | --- | --- | --- | ---
DWT-MRA | \(\checkmark\) | \(\checkmark\) |  | \(\checkmark\)
MODWT |  | \(\checkmark\) | \(\checkmark\) |
AT | \(\checkmark\) |  | \(\checkmark\) |
Note: When Haar wavelet filter is used, MODWT and AT are equivalent and both of them preserves additive and variance decomposition.

## 3.2 Illustration of three types of DWT methods

    p.list <- NULL
    wf.opts <- c("d16", "haar")
    for (k in seq_along(wf.opts)) {
      # data generation
      x <- arima.sim(list(order = c(1, 0, 0), ar = 0.6), n = 128)

      #----------------------------------------------------------------------------
      # wavelet family, extension mode and package
      wf <- wf.opts[k] # wavelet family D8 or db4
      boundary <- "periodic"
      if (wf != "haar") v <- as.integer(parse_number(wf) / 2) else v <- 1

      # Maximum decomposition level J
      n <- length(x)
      J <- ceiling(log(n / (2 * v - 1)) / log(2)) - 1 # (Kaiser, 1994)

      limits.x <- c(0, n)
      limits.y <- c(-3, 3)
      #----------------------------------------------------------------------------
      # DWT-MRA
      x.mra <- waveslim::mra(x, wf = wf, J = J, method = "dwt", boundary = boundary)
      x.mra.m <- matrix(unlist(x.mra), ncol = J + 1)

      p1 <- mra.plot(x, x.mra.m, limits.x, limits.y,
        ylab = "X", col = "red", type = "details",
        main = paste0("DWT-MRA", "(", wf, ")"), ps = 12
      )
      # p1 <- recordPlot()

      #----------------------------------------------------------------------------
      # MODWT
      x.modwt <- waveslim::modwt(x, wf = wf, n.levels = J, boundary = boundary)
      x.modwt.m <- matrix(unlist(x.modwt), ncol = J + 1)

      p2 <- mra.plot(x, x.modwt.m, limits.x, limits.y,
        ylab = "X", col = "red", type = "coefs",
        main = paste0("MODWT", "(", wf, ")"), ps = 12
      )

      #----------------------------------------------------------------------------
      # a trous
      x.at <- at.wd(x, wf = wf, J = J, boundary = boundary)
      x.at.m <- matrix(unlist(x.at), ncol = J + 1)

      p3 <- mra.plot(x, x.at.m, limits.x, limits.y,
        ylab = "X", col = "red", type = "coefs",
        main = paste0("AT", "(", wf, ")"), ps = 12
      )

      p.list[[k]] <- list(p1, p2, p3)
    }

### 3.2.1 Daubechies 16 wavelet

    #----------------------------------------------------------------------------
    # plot and save
    cowplot::plot_grid(
      plotlist = p.list[[1]], ncol = 3, labels = c("(a)", "(b)", "(c)"),
      label_size = 12
    )

Figure 3.1: Illustration of three types of DWT methods

### 3.2.2 Haar wavelet filter

    #----------------------------------------------------------------------------
    # plot and save
    cowplot::plot_grid(
      plotlist = p.list[[2]], ncol = 3, labels = c("(a)", "(b)", "(c)"),
      label_size = 12
    )

Figure 3.2: Illustration of three types of DWT methods

## 3.3 Wavelet transform: decompostion level

    sample <- seq(100, by = 200, length.out = 5)
    v <- 2 # vanishing moment
    tmp <- NULL
    for (n in sample) {
      J1 <- floor(log(n / (2 * v - 1)) / log(2))
      J # (Kaiser, 1994)
      J2 <- floor(log2(n / (2 * v - 1) - 1))
      J # Cornish, C. R., Bretherton, C. S., & Percival, D. B. (2006)
      J3 <- floor(log10(n))
      J # (Nourani et al., 2008)

      tmp <- cbind(tmp, c(J1, J2, J3))
    }

    tab <- tmp
    colnames(tab) <- sample
    rownames(tab) <- paste0("Method", 1:3)

    kable(tab,
      caption = "Decompostion level with varying sample size",
      booktabs = T, align = "c", digits = 3
    ) %>%
      kable_styling("striped", position = "center", full_width = FALSE) # %>%

Table 3.3: Table 3.4: Decompostion level with varying sample size
| 100 | 300 | 500 | 700 | 900
--- | --- | --- | --- | --- | ---
Method1 | 5 | 6 | 7 | 7 | 8
Method2 | 5 | 6 | 7 | 7 | 8
Method3 | 2 | 2 | 2 | 2 | 2

    # collapse_rows(columns = 1:2, valign = "middle")

# 4 Variance transformation

## 4.1 Optimal preditive accuracy (RMSE)

    if (TRUE) {
      ### Synthetic example
      # data generation
      set.seed(2020)
      sample <- 512
      # frequency, sampled from a given range
      fd <- c(3, 5, 10, 15, 25, 30, 55, 70, 95)
      # data <- WASP::data.gen.SW(nobs=sample,fp=25,fd=fd)
      data <- WASP::data.gen.SW(nobs = sample, fp = c(15, 25, 30), fd = fd)

      # ts = data.gen.Rossler(time = seq(0, 50, length.out = sample))
      # data <- list(x=ts$z, dp=cbind(ts$x, ts$y))
    } else {
      ### Real-world example
      data("obs.mon")
      data("rain.mon")

      if (TRUE) { # SPI12 as response
        #SPI.12 <- SPEI::spi(rain.mon[, 5], scale = 12)$fitted
        SPI.12 <- SPI.calc(window(rain.mon[, 5], start=c(1949,1), end=c(2009,12)),sc=12)
        x <- window(SPI.12, start = c(1950, 1), end = c(2009, 12))
        dp <- window(obs.mon, start = c(1950, 1), end = c(2009, 12))
      } else { # rainfall as response
        x <- window(rain.mon[, 5], start = c(1950, 1), end = c(2009, 12))
        dp <- window(obs.mon, start = c(1950, 1), end = c(2009, 12))
      }
      data <- list(x = x, dp = dp)
      sample <- length(x)
    }

    # plot.ts(cbind(data$x,data$dp))

    tab.list <- list()
    mode.opts <- c("MRA", "MODWT", "AT")
    for (mode in mode.opts) {
      print(mode)

      # cov.opt <- switch(2,"auto","pos","neg")
      if (mode == "MRA") {
        method <- switch(1,
          "dwt",
          "modwt"
        )
      }

      # wavelet family, extension mode and package
      # wf <- switch(mode, "MRA"="haar", "MODWT"="haar", "AT"="haar")
      wf <- "haar"
      pad <- "zero"
      boundary <- "periodic"
      if (wf != "haar") v <- as.integer(parse_number(wf) / 2) else v <- 1

      # Maximum decomposition level J
      n <- sample
      J <- ceiling(log(n / (2 * v - 1)) / log(2)) - 1 # (Kaiser, 1994)

      tab <- NULL
      for (cov.opt in c("auto", "pos", "neg")) {
        # variance transform - calibration
        if (mode == "MRA") {
          dwt <- dwt.vt(data, wf, J, method, pad, boundary, cov.opt)
        } else if (mode == "MODWT") {
          dwt <- modwt.vt(data, wf, J, boundary, cov.opt)
        } else {
          dwt <- at.vt(data, wf, J, boundary, cov.opt)
        }

        # optimal prediction accuracy
        opti.rmse <- NULL
        dp.RMSE <- NULL
        dp.n.RMSE <- NULL
        S <- dwt$S
        ndim <- ncol(S)
        for (i in 1:ndim) {
          x <- dwt$x
          dp <- dwt$dp[, i]
          dp.n <- dwt$dp.n[, i]

          # ts.plot(cbind(dp,dp.n), col=1:2)

          dp.RMSE <- c(dp.RMSE, sqrt(mean(lm(x ~ dp)$residuals^2)))
          dp.n.RMSE <- c(dp.n.RMSE, sqrt(mean(lm(x ~ dp.n)$residuals^2)))

          # small difference due to the reconstruction
          opti.rmse <- c(opti.rmse, sqrt((n - 1) / n * (var(x) - sum(S[, i]^2) * var(dp) / var(dp.n))))
          # opti.rmse <- c(opti.rmse, sqrt((n-1)/n*(var(x)-sum(S[,i]^2))))
        }

        tab <- rbind(tab, data.frame(cov.opt, var=1:ndim, dp.RMSE, dp.n.RMSE, opti.rmse))
      }

      colnames(tab) <- c("Sign of covariance", "Variable", "Std", "VT", "Optimal")
      tab.list[[length(tab.list) + 1]] <- tab
    }
    #> [1] "MRA"
    #> [1] "MODWT"
    #> [1] "AT"

    # print(tab.list)

    kable(tab.list[[1]], caption = "Optimal RMSE using DWT-based VT",
          booktabs = T, align = "c", digits = 3) %>%
    kable_styling("striped", position = "center", full_width = FALSE)  %>%
    collapse_rows(columns = 1, valign = "middle")

Table 4.1: Table 4.2: Optimal RMSE using DWT-based VT
Sign of covariance | Variable | Std | VT | Optimal
--- | --- | --- | --- | ---
auto | 1 | 1.235 | 1.231 | 1.231
2 | 1.235 | 1.232 | 1.232
3 | 1.235 | 1.232 | 1.232
4 | 1.021 | 1.010 | 1.010
5 | 1.016 | 1.013 | 1.013
6 | 1.013 | 1.008 | 1.008
7 | 1.235 | 1.222 | 1.222
8 | 1.235 | 1.231 | 1.231
9 | 1.235 | 1.220 | 1.220
pos | 1 | 1.235 | 1.231 | 1.231
2 | 1.235 | 1.232 | 1.232
3 | 1.235 | 1.232 | 1.232
4 | 1.021 | 1.010 | 1.010
5 | 1.016 | 1.013 | 1.013
6 | 1.013 | 1.008 | 1.008
7 | 1.235 | 1.222 | 1.222
8 | 1.235 | 1.231 | 1.231
9 | 1.235 | 1.220 | 1.220
neg | 1 | 1.235 | 1.231 | 1.231
2 | 1.235 | 1.232 | 1.232
3 | 1.235 | 1.232 | 1.232
4 | 1.021 | 1.010 | 1.010
5 | 1.016 | 1.013 | 1.013
6 | 1.013 | 1.008 | 1.008
7 | 1.235 | 1.222 | 1.222
8 | 1.235 | 1.231 | 1.231
9 | 1.235 | 1.220 | 1.220

    kable(tab.list[[2]], caption = "Optimal RMSE using MODWT/AT-based VT",
          booktabs = T, align = "c", digits = 3) %>%
    kable_styling("striped", position = "center", full_width = FALSE)  %>%
    collapse_rows(columns = 1, valign = "middle")

Table 4.3: Table 4.4: Optimal RMSE using MODWT/AT-based VT
Sign of covariance | Variable | Std | VT | Optimal
--- | --- | --- | --- | ---
auto | 1 | 1.235 | 1.235 | 1.235
2 | 1.235 | 1.234 | 1.234
3 | 1.235 | 1.235 | 1.235
4 | 1.021 | 1.021 | 1.021
5 | 1.016 | 1.022 | 1.022
6 | 1.013 | 1.016 | 1.016
7 | 1.235 | 1.221 | 1.221
8 | 1.235 | 1.228 | 1.228
9 | 1.235 | 1.234 | 1.234
pos | 1 | 1.235 | 1.235 | 1.235
2 | 1.235 | 1.234 | 1.234
3 | 1.235 | 1.235 | 1.235
4 | 1.021 | 1.021 | 1.021
5 | 1.016 | 1.022 | 1.022
6 | 1.013 | 1.016 | 1.016
7 | 1.235 | 1.221 | 1.221
8 | 1.235 | 1.228 | 1.228
9 | 1.235 | 1.234 | 1.234
neg | 1 | 1.235 | 1.235 | 1.235
2 | 1.235 | 1.234 | 1.234
3 | 1.235 | 1.235 | 1.235
4 | 1.021 | 1.021 | 1.021
5 | 1.016 | 1.022 | 1.022
6 | 1.013 | 1.016 | 1.016
7 | 1.235 | 1.221 | 1.221
8 | 1.235 | 1.228 | 1.228
9 | 1.235 | 1.234 | 1.234

## 4.2 Transformed predictor variables

    #-------------------------------------------------------------------
    if (TRUE) {
      set.seed(2020)
      ### synthetic example - Rossler
      sample <- 10000
      s <- 0.1
      ts.list <- list()
      for (i in seq_along(s)) {
        ts.r <- data.gen.Rossler(a = 0.2, b = 0.2, w = 5.7, start = c(-2, -10, 0.2), time = seq(0, 50, length.out = sample))

        # add noise
        ts.r$x <- ts(ts.r$x + rnorm(n = sample, mean = 0, sd = s[i]))
        ts.r$y <- ts(ts.r$y + rnorm(n = sample, mean = 0, sd = s[i]))
        ts.r$z <- ts(ts.r$z + rnorm(n = sample, mean = 0, sd = s[i]))

        ts.list[[i]] <- ts.r
      }

      data.list <- lapply(ts.list, function(ts) list(x = ts$z, dp = cbind(ts$x, ts$y)))

      lab.names <- c("x", "y")
      xlim<- c(0,n);ylim <- c(-55, 55)
    } else {

      ### Real-world example
      data("obs.mon")
      data("rain.mon")

      #SPI.12 <- SPEI::spi(rain.mon[, 5], scale = 12)$fitted
      SPI.12 <- SPI.calc(window(rain.mon[, 5], start=c(1949,1), end=c(2009,12)),sc=12)
      x <- window(SPI.12, start = c(1950, 1), end = c(2009, 12))
      dp <- window(obs.mon, start = c(1950, 1), end = c(2009, 12))

      data.list <- list(list(x = x, dp = dp))
      sample <- length(x)

      lab.names <- colnames(obs.mon)
      xlim<- NULL;ylim <- NULL
    }

    #-------------------------------------------------------------------
    p.list <- list()
    dp.list <- list()
    if (wf != "haar") mode.opts <- c("MRA", "MODWT", "AT")[1:3] else mode.opts <- c("MRA", "MODWT","AT")[1:2]
    for (mode in mode.opts) {
      cov.opt <- switch(1,
        "auto",
        "pos",
        "neg"
      )
      flag <- switch(1,
        "biased",
        "unbiased"
      )
      if (mode == "MRA") {
        method <- switch(1,
          "dwt",
          "modwt"
        )
      }

      # wavelet family, extension mode and package
      # wf <- switch(mode, "MRA"="haar", "MODWT"="haar", "AT"="haar")
      wf <- "d16"
      pad <- "zero"
      boundary <- "periodic"
      if (wf != "haar") v <- as.integer(parse_number(wf) / 2) else v <- 1

      # Maximum decomposition level J
      n <- sample
      J <- ceiling(log(n / (2 * v - 1)) / log(2)) - 1 # (Kaiser, 1994)
      # J <- floor(log(n/(2*v-1))/log(2))

      # variance transform - calibration
      if (mode == "MRA") {
        dwt.list <- lapply(data.list, function(x) dwt.vt(x, wf, J, method, pad, boundary, cov.opt, flag))
      } else if (mode == "MODWT") {
        dwt.list <- lapply(data.list, function(x) modwt.vt(x, wf, J, boundary, cov.opt, flag))
      } else {
        dwt.list <- lapply(data.list, function(x) at.vt(x, wf, J, boundary, cov.opt, flag))
      }

      for (j in 1:length(dwt.list)) {
        dwt <- dwt.list[[j]]

        par(
          mfrow = c(ncol(dwt$dp), 1), mar = c(0, 2.5, 2, 1),
          oma = c(2, 1, 0, 0), # move plot to the right and up
          mgp = c(1.5, 0.5, 0), # move axis labels closer to axis
          pty = "m", bg = "transparent",
          ps = 12
        )

        # plot(dwt$x, type="l", xlab=NA, ylab="SPI12", col="red")
        # plot(dwt$x, type="l", xlab=NA, ylab="Rain", col="red")
        for (i in 1:ncol(dwt$dp)) {
          ts.plot(cbind(dwt$dp[, i], dwt$dp.n[, i]),
            xlab = NA, ylab = paste0(lab.names[i]),
            xlim = xlim, ylim = ylim,
            col = c("black", "blue"), lwd = c(1, 2)
          )
        }

        p.list[[length(p.list) + 1]] <- recordPlot()

        dp.list[[length(dp.list) + 1]] <- dwt$dp.n
      }
    }
    #> [1] "Difference between reconstructed and original series: 2.28840755511772e-08"
    #> [1] "Difference between reconstructed and original series: 2.18861104239743e-08"
    #> [1] "Difference between reconstructed and original series: 45963.8818333333"
    #> [1] "Difference between reconstructed and original series: 46239.1064980564"

    #----------------------------------------------------------------------------
    # plot and save
    fig <- cowplot::plot_grid(plotlist = p.list, nrow = 1, labels = c("(a)", "(b)", "(c)"))
    fig

Figure 4.1: Orignal and VT predictors. (a): DWT-MRA (b): MODWT/AT

# 5 Stepwise variance transformation

    #-------------------------------------------------------------------
    ### Real-world example
    data("obs.mon")
    data("rain.mon")
    op <- par()
    station.id <- 5
    lab.names <- colnames(obs.mon)[c(1, 3, 4, 5, 7)]

    if (TRUE) { # SPI12 as response
      #SPI.12 <- SPEI::spi(rain.mon, scale = 12)$fitted
      SPI.12 <- SPI.calc(window(rain.mon, start=c(1949,1), end=c(2009,12)),sc=12)
      x <- window(SPI.12, start = c(1950, 1), end = c(2009, 12))
      dp <- window(obs.mon[, lab.names], start = c(1950, 1), end = c(2009, 12))
    } else { # rainfall as response
      x <- window(rain.mon, start = c(1950, 1), end = c(2009, 12))
      dp <- window(obs.mon[, lab.names], start = c(1950, 1), end = c(2009, 12))
    }

    data.list <- lapply(station.id, function(id) list(x = x[, id], dp = dp))

    ylim <- data.frame(
      GPH = c(700, 900), TDP700 = c(5, 25), TDP500 = c(5, 25), EPT = c(300, 330),
      UWND = c(-5, 25), VWND = c(-5, 10), MSLP = c(-1, 1)
    )[c(1, 3, 4, 5, 7)]

    #-------------------------------------------------------------------
    p.list <- list()
    RMSE <- NULL
    mode.opts <- c("MRA", "MODWT", "AT")[1:2]
    for (mode in mode.opts) {
      cov.opt <- switch(1,
        "auto",
        "pos",
        "neg"
      )
      if (mode == "MRA") {
        method <- switch(1,
          "dwt",
          "modwt"
        )
      }

      # wavelet family, extension mode and package
      wf <- switch(mode,
        "MRA" = "d4",
        "MODWT" = "haar",
        "AT" = "haar"
      )
      pad <- "zero"
      boundary <- "periodic"
      if (wf != "haar") v <- as.integer(parse_number(wf) / 2) else v <- 1

      # Maximum decomposition level J
      n <- nrow(x)
      J <- ceiling(log(n / (2 * v - 1)) / log(2)) - 1 # (Kaiser, 1994)

      # high order variance transformation
      dwt.list <- lapply(data.list, function(data) stepwise.VT(data, mode = mode, wf = wf, J=J))

      for (j in seq_len(length(dwt.list))) {
        dwt <- dwt.list[[j]]
        cpy <- dwt$cpy

        MSE <- NULL
        for (i in seq_len(length(cpy))) {
          m1 <- sqrt(FNN::knn.reg(train = dwt$dp[, 1:i], y = dwt$x)$PRESS / n)
          m2 <- sqrt(FNN::knn.reg(train = dwt$dp.n[, 1:i], y = dwt$x)$PRESS / n)

          MSE <- rbind(MSE, c(m1, m2))
        }

        RMSE <- rbind(RMSE, data.frame(mode, MSE))

        par(
          mfrow = c(length(cpy), 1), mar = c(0, 4, 2, 1),
          oma = c(2, 1, 0, 0), # move plot to the right and up
          mgp = c(1.5, 0.5, 0), # move axis labels closer to axis
          pty = "m", bg = "transparent",
          ps = 8
        )

        # plot(dwt$x, type="l", xlab=NA, ylab="SPI12", ylim=c(-3,3),col="red")
        # plot(dwt$x, type="l", xlab=NA, ylab="Rain", col="red")
        for (i in seq_len(length(cpy))) {
          ts.plot(dwt$dp[, i], dwt$dp.n[, i],
            xlab = NA, ylab = paste0(lab.names[cpy[i]]), # ylim=ylim[,i],
            col = c("black", "blue"), lwd = c(1, 2)
          )
        }

        p.list[[length(p.list) + 1]] <- recordPlot()
      }
    }
    #> [1] "Variance difference between transformed and original series by percentage: 17.2789507251337"
    par(op)
    #-------------------------------------------------------------------
    # plot and save
    cowplot::plot_grid(plotlist = p.list, nrow = 1, labels = c("(a)", "(b)", "(c)"))

Figure 5.1: Orignal and SVT predictors. (a): DWT-MRA (b): MODWT/AT

    #-------------------------------------------------------------------
    # RMSE when more predictors are included
    #tab1 <- round(RMSE, 3)
    #tab1 <- cbind(1:nrow(tab1), tab1)
    #colnames(tab1) <- c("No. of Predictors", rep(c("Original", "Transformed"), length(mode.opts)))
    # kable(tab1, caption = "Comparison of prediction accuracy using Std and SVT", booktabs = T) %>%
    #   kable_styling(latex_options = c("HOLD_position"), position = "center", full_width = FALSE)  %>%
    #   #  add_header_above(c(" " = 1, "DWT-MRA" = 2, "MODWT" = 2, "AT" = 2))
    #   add_header_above(c(" " = 1, "DWT-MRA" = 2, "MODWT/AT" = 2))
    tab <- RMSE %>% group_by(mode) %>% mutate(id = row_number())
    tab1 <- tab[,c(1,4,2,3)]
    colnames(tab1) <- c("Method","No. of Predictors","Original","Transformed")
    kable(tab1, caption = "Comparison of prediction accuracy using Std and SVT", booktabs = T,
          digits = 3) %>%
      kable_styling(latex_options = c("HOLD_position"), position = "center", full_width = FALSE)  %>%
      collapse_rows(columns = 1)

Table 5.1: Table 5.2: Comparison of prediction accuracy using Std and SVT
Method | No. of Predictors | Original | Transformed
--- | --- | --- | ---
MRA | 1 | 1.132 | 0.995
2 | 1.101 | 0.849
3 | 1.101 | 0.835
4 | 1.108 | 0.747
MODWT | 1 | 1.121 | 0.999
2 | 1.121 | 0.903
3 | 1.067 | 0.825