# Examine CI patterns for fields where detection failed
suppressPackageStartupMessages({
  library(readxl)
  library(dplyr)
  library(tidyr)
  library(lubridate)
  library(here)
  library(ggplot2)
})

project_dir <- "esa"
assign("project_dir", project_dir, envir = .GlobalEnv)
source(here("r_app", "parameters_project.R"))

# Load daily CI data
ci_data_raw <- readRDS(here("laravel_app/storage/app", project_dir, "Data/extracted_ci/cumulative_vals/All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>% ungroup()

time_series <- ci_data_raw %>%
  mutate(
    date = as.Date(Date),
    week = isoweek(date),
    year = isoyear(date)
  ) %>%
  select(field_id = field, date, week, year, mean_ci = FitData) %>%
  filter(!is.na(mean_ci), !is.na(date), !is.na(field_id)) %>%
  arrange(field_id, date)

# Load harvest data
harvest_actual <- read_excel('laravel_app/storage/app/esa/Data/harvest.xlsx') %>%
  mutate(
    season_start = as.Date(season_start),
    season_end = as.Date(season_end)
  ) %>%
  filter(field %in% unique(field_boundaries_sf$field)) %>%
  filter(!is.na(season_end))

cat("=== EXAMINING MISSED HARVESTS ===\n\n")

# Focus on specific fields mentioned: 00302, 00F28
test_fields <- c("00302", "00F28")

for (field_name in test_fields) {
  cat("\n\n===============================================\n")
  cat("FIELD:", field_name, "\n")
  cat("===============================================\n\n")
  
  # Get harvest dates for this field
  field_harvests <- harvest_actual %>% 
    filter(field == field_name) %>%
    arrange(season_end) %>%
    mutate(harvest_week = isoweek(season_end))
  
  cat("Harvest dates:\n")
  print(field_harvests %>% select(year, season_end, harvest_week))
  
  # Get time series for this field
  field_ts <- time_series %>% 
    filter(field_id == field_name) %>%
    arrange(date) %>%
    mutate(
      # Add rolling average
      ci_smooth = zoo::rollmean(mean_ci, k = 7, fill = NA, align = "center"),
      # Add week-over-week change
      ci_lag7 = lag(ci_smooth, 7),
      ci_drop = ci_lag7 - ci_smooth
    )
  
  # For each harvest, show ±30 days of data
  for (i in 1:nrow(field_harvests)) {
    h_date <- field_harvests$season_end[i]
    h_year <- field_harvests$year[i]
    
    cat("\n--- Harvest", i, ":", as.character(h_date), "(Year:", h_year, ") ---\n")
    
    window_data <- field_ts %>%
      filter(date >= (h_date - 30), date <= (h_date + 30)) %>%
      mutate(
        days_from_harvest = as.numeric(date - h_date),
        is_harvest_week = abs(days_from_harvest) <= 3
      )
    
    if (nrow(window_data) > 0) {
      cat("\nCI values around harvest (±30 days):\n")
      
      # Summary by week relative to harvest
      weekly_summary <- window_data %>%
        mutate(week_offset = floor(days_from_harvest / 7)) %>%
        group_by(week_offset) %>%
        summarise(
          n_days = n(),
          mean_ci = mean(mean_ci, na.rm = TRUE),
          min_ci = min(mean_ci, na.rm = TRUE),
          max_ci = max(mean_ci, na.rm = TRUE),
          mean_drop = mean(ci_drop, na.rm = TRUE),
          max_drop = max(ci_drop, na.rm = TRUE),
          .groups = "drop"
        ) %>%
        arrange(week_offset)
      
      print(weekly_summary)
      
      # Check detection conditions
      cat("\nDetection analysis:\n")
      
      # Count days meeting different thresholds
      low_ci_1.5 <- sum(window_data$mean_ci < 1.5, na.rm = TRUE)
      low_ci_2.0 <- sum(window_data$mean_ci < 2.0, na.rm = TRUE)
      low_ci_2.5 <- sum(window_data$mean_ci < 2.5, na.rm = TRUE)
      
      drop_0.3 <- sum(window_data$ci_drop > 0.3, na.rm = TRUE)
      drop_0.5 <- sum(window_data$ci_drop > 0.5, na.rm = TRUE)
      drop_0.8 <- sum(window_data$ci_drop > 0.8, na.rm = TRUE)
      
      cat("  Days with CI < 1.5:", low_ci_1.5, "\n")
      cat("  Days with CI < 2.0:", low_ci_2.0, "\n")
      cat("  Days with CI < 2.5:", low_ci_2.5, "\n")
      cat("  Days with drop > 0.3:", drop_0.3, "\n")
      cat("  Days with drop > 0.5:", drop_0.5, "\n")
      cat("  Days with drop > 0.8:", drop_0.8, "\n")
      
      # Check if there's a sustained low period
      consecutive_low <- window_data %>%
        mutate(is_low = mean_ci < 2.0) %>%
        filter(is_low) %>%
        mutate(
          date_diff = as.numeric(date - lag(date)),
          new_group = is.na(date_diff) | date_diff > 3
        ) %>%
        mutate(group_id = cumsum(new_group)) %>%
        group_by(group_id) %>%
        summarise(
          start = min(date),
          end = max(date),
          duration = n(),
          mean_ci = mean(mean_ci),
          .groups = "drop"
        ) %>%
        arrange(desc(duration))
      
      if (nrow(consecutive_low) > 0) {
        cat("\nLongest consecutive low CI periods (CI < 2.0):\n")
        print(head(consecutive_low, 3))
      } else {
        cat("\nNo sustained low CI periods found (CI < 2.0)\n")
      }
      
    } else {
      cat("No data available in this window\n")
    }
  }
}

cat("\n\n=== SUMMARY ===\n")
cat("This analysis shows why harvests were missed.\n")
cat("If CI doesn't drop low enough OR doesn't stay low for enough consecutive days,\n")
cat("the detection algorithm won't trigger.\n")