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

## ----setup--------------------------------------------------------------------
library(bayesRecon)

## ----M5hier, fig.cap="**Figure 1**: graph of the M5 hierarchy.", out.width = '100%', echo = FALSE----
knitr::include_graphics("img/M5store_hier.png")

## ----InitializeHierarchy------------------------------------------------------
# Hierarchy composed by 3060 time series: 3049 bottom and 11 upper
n_b <- 3049
n_u <- 11
n <- n_b + n_u

# Load matrix A
A <- M5_CA1_basefc$A

# Load base forecasts:
base_fc_upper <- M5_CA1_basefc$upper
base_fc_bottom <- M5_CA1_basefc$bottom

# We will save all the results in the list rec_fc
rec_fc <- list(
  Gauss      = list(),
  Mixed_cond = list(),
  TD_cond    = list()
)

## ----readBaseForecasts--------------------------------------------------------
# Parameters of the upper base forecast distributions
mu_u <- unlist(lapply(base_fc_upper, "[[", "mu")) # upper means
# Compute the (shrinked) covariance matrix of the residuals
residuals.upper <- lapply(base_fc_upper, "[[", "residuals")
residuals.upper <- t(do.call("rbind", residuals.upper))
Sigma_u <- schaferStrimmer_cov(residuals.upper)$shrink_cov

# Parameters of the bottom base forecast distributions
mu_b <- c()
sd_b <- c()
for (fc_b in base_fc_bottom) {
  pmf <- fc_b$pmf
  mu_b <- c(mu_b, PMF_get_mean(pmf))
  sd_b <- c(sd_b, PMF_get_var(pmf)**0.5)
}
Sigma_b <- diag(sd_b**2)

# Mean and covariance matrix of the base forecasts
base_fc_mean <- c(mu_u, mu_b)
base_fc_cov <- matrix(0, nrow = n, ncol = n)
base_fc_cov[1:n_u, 1:n_u] <- Sigma_u
base_fc_cov[(n_u + 1):n, (n_u + 1):n] <- Sigma_b

## ----GaussianReconciliation---------------------------------------------------
# Gaussian reconciliation
start <- Sys.time()
gauss <- reconc_gaussian(A, base_fc_mean, base_fc_cov)
stop <- Sys.time()

rec_fc$Gauss <- list(
  mu_b = gauss$bottom_rec_mean,
  Sigma_b = gauss$bottom_rec_covariance,
  mu_u = A %*% gauss$bottom_rec_mean,
  Sigma_u = A %*% gauss$bottom_rec_covariance %*% t(A)
)

Gauss_time <- as.double(round(difftime(stop, start, units = "secs"), 2))
cat("Time taken by Gaussian reconciliation: ", Gauss_time, "s")

## ----MixedCondReconciliation--------------------------------------------------
seed <- 1
N_samples_IS <- 5e4

# Base forecasts
fc_upper_4rec <- list(mean = mu_u, cov = Sigma_u)
fc_bottom_4rec <- lapply(base_fc_bottom, "[[", "pmf") # list of PMFs

# MixCond reconciliation
start <- Sys.time()
mix_cond <- reconc_MixCond(A, fc_bottom_4rec, fc_upper_4rec,
  bottom_in_type = "pmf",
  num_samples = N_samples_IS, return_type = "pmf", seed = seed
)
stop <- Sys.time()

rec_fc$Mixed_cond <- list(
  bottom = mix_cond$bottom_rec_pmf,
  upper  = mix_cond$upper_rec_pmf,
  ESS    = mix_cond$ESS
)

MixCond_time <- as.double(round(difftime(stop, start, units = "secs"), 2))
cat("Computational time for Mix-cond reconciliation: ", MixCond_time, "s")

## ----TDcondReconciliation-----------------------------------------------------
N_samples_TD <- 1e4

# TDcond reconciliation
start <- Sys.time()
td <- reconc_TDcond(A, fc_bottom_4rec, fc_upper_4rec,
  bottom_in_type = "pmf", num_samples = N_samples_TD,
  return_type = "pmf", seed = seed
)
stop <- Sys.time()

## ----print computational time TD cond-----------------------------------------
rec_fc$TD_cond <- list(
  bottom = td$bottom_rec_pmf,
  upper  = td$upper_rec_pmf
)

TDCond_time <- as.double(round(difftime(stop, start, units = "secs"), 2))
cat("Computational time for TD-cond reconciliation: ", TDCond_time, "s")

## ----InitializeMetrics--------------------------------------------------------
# Parameters for computing the scores
alpha <- 0.1 # MIS uses 90% coverage intervals
jitt <- 1e-9 # jitter for numerical stability

# Save actual values
actuals_u <- unlist(lapply(base_fc_upper, "[[", "actual"))
actuals_b <- unlist(lapply(base_fc_bottom, "[[", "actual"))
actuals <- c(actuals_u, actuals_b)

# Scaling factor for computing MASE
Q_u <- M5_CA1_basefc$Q_u
Q_b <- M5_CA1_basefc$Q_b
Q <- c(Q_u, Q_b)

# Initialize lists to save the results
mase <- list()
mis <- list()
rps <- list()

## ----metricFunctions,include=FALSE--------------------------------------------
# Functions for computing the scores of a PMF
AE_pmf <- function(pmf, actual) {
  return(abs(PMF_get_quantile(pmf, p = 0.5) - actual))
}
MIS_pmf <- function(pmf, actual, alpha) {
  u <- PMF_get_quantile(pmf, p = 1 - (alpha / 2))
  l <- PMF_get_quantile(pmf, p = alpha / 2)
  return(u - l + (2 / alpha) * (l - actual) * (actual < l) +
    (2 / alpha) * (actual - u) * (actual > u))
}
RPS_pmf <- function(pmf, actual) {
  cdf <- cumsum(pmf) / sum(pmf)
  M <- length(cdf)
  # if actual is outside the supp of pmf, add ones to the end of the cdf:
  if (actual >= M) {
    cdf <- c(cdf, rep(1, (actual - M + 1)))
    M <- length(cdf)
  }
  cdf_act <- (0:(M - 1)) >= actual # unit step function in actual
  crps_ <- sum((cdf - cdf_act)**2)
  return(crps_)
}

# Function for computing the MIS of (possibly truncated) Gaussian forecasts
MIS_gauss <- function(mus, sds, actuals, alpha, trunc = FALSE) {
  z <- qnorm(1 - (alpha / 2))
  u <- mus + z * sds
  l <- mus - z * sds
  # If it is truncated, set negative quantiles to zero
  if (trunc) {
    l[l < 0] <- 0
    u[u < 0] <- 0
  }
  return(u - l + (2 / alpha) * (l - actuals) * (actuals < l) +
    (2 / alpha) * (actuals - u) * (actuals > u))
}

## ----computeScores------------------------------------------------------------
# Compute scores for the base forecasts
# Upper
mu_u <- unlist(lapply(base_fc_upper, "[[", "mu"))
sd_u <- unlist(lapply(base_fc_upper, "[[", "sigma"))
mase$base[1:n_u] <- abs(mu_u - actuals_u) / Q_u
mis$base[1:n_u] <- MIS_gauss(mu_u, sd_u, actuals_u, alpha)
rps$base[1:n_u] <- scoringRules::crps(actuals_u, "norm", mean = mu_u, sd = sd_u)
# Bottom
pmfs <- lapply(base_fc_bottom, "[[", "pmf")
mase$base[(n_u + 1):n] <- mapply(AE_pmf, pmfs, actuals_b) / Q_b
mis$base[(n_u + 1):n] <- mapply(MIS_pmf, pmfs, actuals_b, MoreArgs = list(alpha = alpha))
rps$base[(n_u + 1):n] <- mapply(RPS_pmf, pmfs, actuals_b)

# Compute scores for Gauss reconciliation
mu <- c(rec_fc$Gauss$mu_u, rec_fc$Gauss$mu_b)
sd <- c(diag(rec_fc$Gauss$Sigma_u), diag(rec_fc$Gauss$Sigma_b))**0.5
sd <- sd + jitt
mase$Gauss <- abs(mu - actuals) / Q
mis$Gauss <- MIS_gauss(mu, sd, actuals, alpha)
rps$Gauss <- scoringRules::crps(actuals, "norm", mean = mu, sd = sd)

# Compute scores for Mix-cond reconciliation
pmfs <- c(rec_fc$Mixed_cond$upper, rec_fc$Mixed_cond$bottom)
mase$MixCond <- mapply(AE_pmf, pmfs, actuals) / Q
mis$MixCond <- mapply(MIS_pmf, pmfs, actuals, MoreArgs = list(alpha = alpha))
rps$MixCond <- mapply(RPS_pmf, pmfs, actuals)

# Compute scores for TD-cond reconciliation
pmfs <- c(rec_fc$TD_cond$upper, rec_fc$TD_cond$bottom)
mase$TDcond <- mapply(AE_pmf, pmfs, actuals) / Q
mis$TDcond <- mapply(MIS_pmf, pmfs, actuals, MoreArgs = list(alpha = alpha))
rps$TDcond <- mapply(RPS_pmf, pmfs, actuals)

## ----skillScoreFunction,include=FALSE-----------------------------------------
# Function for computing the skill score
skill.score <- function(ref, met) {
  s <- (2 * (ref - met) / (ref + met)) * 100
  s[is.na(s)] <- 0 # if both numerator and denominator are 0, set skill score to 0
  return(s)
}

## ----ComputeScores------------------------------------------------------------
scores <- list(
  mase = mase,
  mis = mis,
  rps = rps
)
scores_ <- names(scores)

ref_met <- "base"
methods_ <- c("Gauss", "MixCond", "TDcond")

# For each score and method we compute the skill score with respect to the base forecasts
skill_scores <- list()
for (s in scores_) {
  skill_scores[[s]] <- list()
  for (met in methods_) {
    skill_scores[[s]][["upper"]][[met]] <- skill.score(
      scores[[s]][[ref_met]][1:n_u],
      scores[[s]][[met]][1:n_u]
    )
    skill_scores[[s]][["bottom"]][[met]] <- skill.score(
      scores[[s]][[ref_met]][(n_u + 1):n],
      scores[[s]][[met]][(n_u + 1):n]
    )
  }
}

## ----AverageScores------------------------------------------------------------
mean_skill_scores <- list()

for (s in scores_) {
  mean_skill_scores[[s]] <- rbind(
    data.frame(lapply(skill_scores[[s]][["upper"]], mean)),
    data.frame(lapply(skill_scores[[s]][["bottom"]], mean))
  )
  rownames(mean_skill_scores[[s]]) <- c("upper", "bottom")
}

## ----printMASETable-----------------------------------------------------------
knitr::kable(mean_skill_scores$mase, digits = 2, caption = "Mean skill score on MASE.", align = "lccc")

## ----PrintMIStable------------------------------------------------------------
knitr::kable(mean_skill_scores$mis, digits = 2, caption = "Mean skill score on MIS.")

## ----printRPStable------------------------------------------------------------
knitr::kable(mean_skill_scores$rps, digits = 2, caption = "Mean skill score on RPS.")

## ----MASEboxplots, fig.cap="**Figure 2**: boxplot of MASE skill scores for upper and bottom time series.", fig.width=7,fig.height=8----
custom_colors <- c(
  "#a8a8e4",
  "#a9c7e4",
  "#aae4df"
)

# Boxplots of MASE skill scores
par(mfrow = c(2, 1))
boxplot(skill_scores$mase$upper,
  main = "MASE upper time series",
  col = custom_colors, ylim = c(-80, 80)
)
abline(h = 0, lty = 3)
boxplot(skill_scores$mase$bottom,
  main = "MASE bottom time series",
  col = custom_colors, ylim = c(-200, 200)
)
abline(h = 0, lty = 3)

## ----setupParams,eval=TRUE,include=FALSE--------------------------------------
par(mfrow = c(1, 1))

## ----MISboxplots, fig.cap="**Figure 3**: boxplot of MIS skill scores for upper and bottom time series.", fig.width=7,fig.height=8----
# Boxplots of MIS skill scores
par(mfrow = c(2, 1))
boxplot(skill_scores$mis$upper,
  main = "MIS upper time series",
  col = custom_colors, ylim = c(-150, 150)
)
abline(h = 0, lty = 3)
boxplot(skill_scores$mis$bottom,
  main = "MIS bottom time series",
  col = custom_colors, ylim = c(-200, 200)
)
abline(h = 0, lty = 3)

## ----eval=TRUE,include=FALSE--------------------------------------------------
par(mfrow = c(1, 1))

## ----RPSboxplots,fig.cap="**Figure 4**: boxplot of RPS skill scores for upper and bottom time series.", fig.width=7,fig.height=8----
# Boxplots of RPS skill scores
par(mfrow = c(2, 1))
boxplot(skill_scores$rps$upper,
  main = "RPS upper time series",
  col = custom_colors, ylim = c(-80, 80)
)
abline(h = 0, lty = 3)
boxplot(skill_scores$rps$bottom,
  main = "RPS bottom time series",
  col = custom_colors, ylim = c(-200, 200)
)
abline(h = 0, lty = 3)

## ----eval=TRUE,include=FALSE--------------------------------------------------
par(mfrow = c(1, 1))

