## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
if (utils::packageVersion("scoringutils") < "2.0.0") {
    stop("The 'scoringutils' package version 2.0.0 or higher is required. Please update it.")
}
if (!requireNamespace("ggplot2", quietly = TRUE)) {
    stop("The vignette requires the 'ggplot2' package. Please install it to build the vignette.")
}

## ----warning=FALSE, message=FALSE---------------------------------------------
library(NobBS)
library(dplyr)
library(ggplot2)
library(scoringutils)

data(denguedat)

# Helper function to run nowcasting
run_nowcast <- function(data, now, win_size, specs) {
  NobBS(data, now, units = "1 week", onset_date = "onset_week",
        report_date = "report_week", moving_window = win_size, specs = specs)
}

quantiles <- c(0.025,seq(0.05,0.95,0.05),0.975)
q_len <- length(quantiles)
q_cols <- paste0('q_',quantiles)

# Poisson model specs
specs_poisson <- list(
  dist=c("Poisson"),
  quantiles=quantiles
)

#NB model specs
specs_nb = list(
  dist=c("NB"),
  quantiles=quantiles
)

# Initialize lists to store nowcasts
nowcasts_pois <- list()   # Nowcasts using poisson model
nowcasts_nb <- list()     # Nowcasts using negtive-binomial model

test_dates <- seq(as.Date("1994-08-29"),as.Date("1994-09-26"),by=7)

win_size <- 8

for (t in seq_along(test_dates)) {
  now <- test_dates[t]
  denguedat1 <- denguedat[denguedat$onset_week<=now,]
  nowcasts_pois[[t]] <- run_nowcast(denguedat1, now, win_size, specs_poisson)
  nowcasts_nb[[t]] <- run_nowcast(denguedat1, now, win_size, specs_nb)
}

## ----plot_estimates, fig.width=7, fig.height=4--------------------------------

plot_estimates <- function(nowcast1, nowcast2, cases_per_date, now) {
  # Ensure input data is valid
  if (is.null(nowcast1$estimates) || is.null(nowcast2$estimates)) {
    stop("Nowcast estimates are missing.")
  }
  
  # Extract estimates and credible intervals for nowcast without DoW effect
  onset_dates1 <- nowcast1$estimates$onset_date
  estimates1 <- nowcast1$estimates$estimate
  lower1 <- nowcast1$estimates$q_0.025  # 2.5% quantile (lower bound of 95% CI)
  upper1 <- nowcast1$estimates$q_0.975  # 97.5% quantile (upper bound of 95% CI)
  
  # Extract estimates and credible intervals for nowcast with DoW effect
  onset_dates2 <- nowcast2$estimates$onset_date
  estimates2 <- nowcast2$estimates$estimate
  lower2 <- nowcast2$estimates$q_0.025
  upper2 <- nowcast2$estimates$q_0.975
  
  # Extract eventual case counts
  case_dates <- cases_per_date$onset_week
  case_counts <- cases_per_date$count
  
  # Calculate plot range
  min_val <- min(c(lower1, lower2, case_counts), na.rm = TRUE)
  max_val <- max(c(upper1, upper2, case_counts), na.rm = TRUE) * 1.35
  
  # Create the plot
  plot(
    onset_dates1, estimates1, col = 'blue', type = 'l',
    xlab = 'Onset Date', ylab = 'Cases',
    ylim = c(min_val, max_val), lwd = 2,
    main = paste0('Incidence Estimates for ', now)
  )
  lines(onset_dates2, estimates2, col = 'red', lwd = 2)
  
  # Add 95% PI shaded regions for both nowcasts
  polygon(c(onset_dates1, rev(onset_dates1)), c(lower1, rev(upper1)), 
          col = rgb(0, 0, 1, 0.2), border = NA) 
  polygon(c(onset_dates2, rev(onset_dates2)), c(lower2, rev(upper2)), 
          col = rgb(1, 0, 0, 0.2), border = NA) 
  
  # Add true case counts as points
  points(case_dates, case_counts, col = 'black', pch = 20)
  
  # Add a legend
  legend(
    'topleft',
    legend = c('Estimates Poisson model', 
               'Estimates negative binomial model', 
               '95% PI (Poisson model)', 
               '95% PI (negative binomial model)',
               'Eventual cases'),
    col = c('blue', 'red', rgb(0, 0, 1, 0.2), rgb(1, 0, 0, 0.2), 'black'),
    lty = c(1, 1, NA, NA, NA), lwd = c(2, 2, NA, NA, NA), 
    pch = c(NA, NA, 15, 15, 20),
    pt.cex = c(NA, NA, 1.5, 1.5, 1), 
    cex = 0.9
  )
}

cases_per_week <- denguedat %>% group_by(onset_week) %>% summarize(count=n())

for (t in seq_along(test_dates)) {
  
  now <- test_dates[t]
  nowcast_pois <- nowcasts_pois[[t]]
  nowcast_nb <- nowcasts_nb[[t]]
  cases_per_week1 <- cases_per_week[cases_per_week$onset_week <= now, ]
  plot_estimates(nowcast_pois, nowcast_nb, cases_per_week1, now)
}

## ----quantile_estimates, warning=FALSE, message=FALSE-------------------------

data <- data.frame(onset_week=as.Date(character()),
                   now=as.Date(character()),
                   horizon=numeric(),
                   quantile_level=numeric(),
                   predicted=numeric(),
                   observed=numeric(),
                   model=character())

cases_per_week <- denguedat %>% group_by(onset_week) %>% summarize(count=n())

horizons <- c(-2,-1,0)

for (t in seq_along(test_dates)) {
  now <- test_dates[t]
  nowcast_pois <- nowcasts_pois[[t]]
  nowcast_nb <- nowcasts_nb[[t]]
  for(h in horizons) {
    date <- now + h*7
    true_value <- cases_per_week[cases_per_week$onset_week==date,]$count
    q_est_pois <- unname(unlist(nowcast_pois$estimates[nowcast_pois$estimates$onset_date==date,q_cols]))
    q_est_nb <- unname(unlist(nowcast_nb$estimates[nowcast_nb$estimates$onset_date==date,q_cols]))
    data_est <- data.frame(onset_week=rep(date,q_len*2),
                           now=rep(now,q_len*2),
                           horizon=rep(h,q_len*2),
                           quantile_level=rep(quantiles,2),
                           predicted=c(q_est_pois,q_est_nb),
                           observed=rep(true_value,q_len*2),
                           model=c(rep('Pois_model',q_len),rep('NB_model',q_len)))
    data <- rbind(data,data_est)
  }
}

print(head(data))
print(tail(data))

## ----warning=FALSE------------------------------------------------------------
nowcasts <- data %>%
          scoringutils::as_forecast_quantile()
scores <- scoringutils::score(nowcasts, 
             get_metrics(nowcasts,select=c("wis","overprediction","underprediction","dispersion")))

print(head(scores))

## ----fig.width=7, fig.height=4------------------------------------------------
scores_per_horizon <- scores %>%
          summarise_scores(by = c("horizon", "model"))

print(scores_per_horizon)
plot_wis(scores_per_horizon) + 
  facet_wrap(~ horizon, scales ='free') +
  ggtitle('WIS per Horizon')

## ----fig.width=7, fig.height=4------------------------------------------------
scores_per_now_date <- scores %>%
          summarise_scores(by = c("now", "model"))

print(scores_per_now_date)
plot_wis(scores_per_now_date) + 
  facet_wrap(~ now, scales ='free')  +
  ggtitle('WIS per Nowcasting Date')