1185 lines
42 KiB
R
1185 lines
42 KiB
R
# 80_UTILS_AGRONOMIC_SUPPORT.R
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# ============================================================================
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# AURA-SPECIFIC KPI UTILITIES (SCRIPT 80 - CLIENT TYPE: agronomic_support)
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#
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# Contains all 6 AURA KPI calculation functions and helpers:
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# - Field uniformity KPI (CV-based, spatial autocorrelation)
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# - Area change KPI (week-over-week CI changes)
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# - TCH forecasted KPI (tonnage projections from harvest data)
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# - Growth decline KPI (trend analysis)
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# - Weed presence KPI (field fragmentation detection)
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# - Gap filling KPI (interpolation quality)
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# - KPI reporting (summary tables, field details, text interpretation)
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# - KPI export (Excel, RDS, data export)
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#
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# Orchestrator: calculate_all_field_analysis_agronomic_support()
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# Dependencies: 00_common_utils.R (safe_log), sourced from common
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# Used by: 80_calculate_kpis.R (when client_type == "agronomic_support")
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# ============================================================================
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library(terra)
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library(sf)
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library(dplyr)
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library(tidyr)
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library(readxl)
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library(writexl)
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library(spdep)
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# ============================================================================
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# SHARED HELPER FUNCTIONS (NOW IN 80_UTILS_COMMON.R)
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# ============================================================================
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# The following helper functions have been moved to 80_utils_common.R:
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# - calculate_cv()
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# - calculate_change_percentages()
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# - calculate_spatial_autocorrelation()
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# - extract_ci_values()
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# - calculate_week_numbers()
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# - load_field_ci_raster()
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# - load_weekly_ci_mosaic()
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# - prepare_predictions()
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#
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# These are now sourced from common utils and shared by all client types.
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# ============================================================================
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# ============================================================================
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# AURA KPI CALCULATION FUNCTIONS (6 KPIS)
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# ============================================================================
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#' KPI 1: Calculate field uniformity based on CV and spatial autocorrelation
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#'
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#' Measures how uniform crop development is across the field.
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#' Low CV + high positive Moran's I = excellent uniformity
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#'
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#' @param ci_pixels_by_field List of CI pixel arrays for each field
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#' @param field_boundaries_sf SF object with field geometries
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#' @param ci_band Raster band with CI values
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#'
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#' @return Data frame with field_idx, cv_value, morans_i, uniformity_score, interpretation
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calculate_field_uniformity_kpi <- function(ci_pixels_by_field, field_boundaries_sf, ci_band = NULL,
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mosaic_dir = NULL, week_file = NULL) {
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result <- data.frame(
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field_idx = integer(),
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cv_value = numeric(),
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morans_i = numeric(),
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uniformity_score = numeric(),
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uniformity_category = character(),
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interpretation = character(),
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stringsAsFactors = FALSE
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)
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# Determine if we're using per-field structure
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is_per_field <- !is.null(mosaic_dir) && !is.null(week_file)
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for (field_idx in seq_len(nrow(field_boundaries_sf))) {
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ci_pixels <- ci_pixels_by_field[[field_idx]]
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if (is.null(ci_pixels) || length(ci_pixels) == 0) {
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result <- rbind(result, data.frame(
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field_idx = field_idx,
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cv_value = NA_real_,
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morans_i = NA_real_,
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uniformity_score = NA_real_,
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uniformity_category = "No data",
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interpretation = "No data",
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stringsAsFactors = FALSE
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))
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next
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}
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cv_val <- calculate_cv(ci_pixels)
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# Calculate Moran's I
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morans_i <- NA_real_
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if (is_per_field) {
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# Load individual field raster for per-field structure
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field_name <- field_boundaries_sf$field[field_idx]
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field_mosaic_path <- file.path(mosaic_dir, field_name, week_file)
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if (file.exists(field_mosaic_path)) {
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tryCatch({
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field_raster <- terra::rast(field_mosaic_path)[["CI"]]
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single_field <- field_boundaries_sf[field_idx, ]
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morans_result <- calculate_spatial_autocorrelation(field_raster, single_field)
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if (is.list(morans_result)) {
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morans_i <- morans_result$morans_i
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} else {
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morans_i <- morans_result
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}
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}, error = function(e) {
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message(paste(" Warning: Spatial autocorrelation failed for field", field_name, ":", e$message))
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})
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}
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} else if (!is.null(ci_band) && inherits(ci_band, "SpatRaster")) {
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# Use single raster for single-file structure
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tryCatch({
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single_field <- field_boundaries_sf[field_idx, ]
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morans_result <- calculate_spatial_autocorrelation(ci_band, single_field)
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if (is.list(morans_result)) {
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morans_i <- morans_result$morans_i
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} else {
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morans_i <- morans_result
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}
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}, error = function(e) {
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message(paste(" Warning: Spatial autocorrelation failed for field", field_idx, ":", e$message))
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})
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}
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# Normalize CV (0-1 scale, invert so lower CV = higher score)
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cv_normalized <- min(cv_val / 0.3, 1)
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cv_score <- 1 - cv_normalized
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# Normalize Moran's I (-1 to 1 scale, shift to 0-1)
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morans_normalized <- if (!is.na(morans_i)) {
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(morans_i + 1) / 2
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} else {
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0.5
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}
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uniformity_score <- 0.7 * cv_score + 0.3 * morans_normalized
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# Interpretation
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if (is.na(cv_val)) {
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interpretation <- "No data"
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uniformity_category <- "No data"
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} else if (cv_val < 0.08) {
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interpretation <- "Excellent uniformity"
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uniformity_category <- "Excellent"
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} else if (cv_val < 0.15) {
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interpretation <- "Good uniformity"
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uniformity_category <- "Good"
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} else if (cv_val < 0.25) {
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interpretation <- "Acceptable uniformity"
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uniformity_category <- "Acceptable"
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} else if (cv_val < 0.4) {
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interpretation <- "Poor uniformity"
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uniformity_category <- "Poor"
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} else {
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interpretation <- "Very poor uniformity"
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uniformity_category <- "Very poor"
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}
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result <- rbind(result, data.frame(
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field_idx = field_idx,
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cv_value = cv_val,
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morans_i = morans_i,
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uniformity_score = round(uniformity_score, 3),
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uniformity_category = uniformity_category,
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interpretation = interpretation,
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stringsAsFactors = FALSE
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))
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}
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return(result)
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}
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#' KPI 2: Calculate area change metric (week-over-week CI changes)
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#'
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#' Tracks the percentage change in CI between current and previous week
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#'
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#' @param current_stats Current week field statistics (from extract_field_statistics_from_ci)
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#' @param previous_stats Previous week field statistics
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#'
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#' @return Data frame with field-level CI changes
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calculate_area_change_kpi <- function(current_stats, previous_stats, field_boundaries_sf = NULL) {
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# Initialize field index vector
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field_idx_vec <- seq_len(nrow(current_stats))
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if (!is.null(field_boundaries_sf) && "Field_id" %in% names(current_stats)) {
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field_idx_vec <- match(current_stats$Field_id, field_boundaries_sf$field)
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}
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# Initialize result data frame
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result <- data.frame(
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field_idx = field_idx_vec,
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mean_ci_abs_change = NA_real_,
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interpretation = NA_character_,
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stringsAsFactors = FALSE
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)
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# Handle case where previous stats is NULL or empty
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if (is.null(previous_stats) || nrow(previous_stats) == 0) {
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result$interpretation <- "No previous data"
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return(result)
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}
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# Match fields between current and previous stats
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# Handle both naming conventions (Field_id vs field_idx)
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if ("Field_id" %in% names(current_stats)) {
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current_field_col <- "Field_id"
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prev_field_col <- "Field_id"
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ci_col <- "Mean_CI"
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} else {
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current_field_col <- "field_idx"
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prev_field_col <- "field_idx"
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ci_col <- "mean_ci"
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}
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# Create lookup for previous stats
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prev_lookup <- setNames(
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previous_stats[[ci_col]],
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previous_stats[[prev_field_col]]
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)
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# Calculate percentage change for each field
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for (i in seq_len(nrow(current_stats))) {
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current_field_id <- current_stats[[current_field_col]][i]
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current_ci <- current_stats[[ci_col]][i]
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# Find matching previous CI value
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prev_ci <- prev_lookup[[as.character(current_field_id)]]
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if (!is.null(prev_ci) && !is.na(prev_ci) && !is.na(current_ci)) {
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# Calculate absolute change (CI units)
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abs_change <- current_ci - prev_ci
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result$mean_ci_abs_change[i] <- round(abs_change, 2)
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# Add interpretation
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if (abs_change > 0.5) {
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result$interpretation[i] <- "Rapid growth"
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} else if (abs_change > 0.2) {
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result$interpretation[i] <- "Positive growth"
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} else if (abs_change >= -0.2) {
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result$interpretation[i] <- "Stable"
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} else if (abs_change >= -0.5) {
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result$interpretation[i] <- "Declining"
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} else {
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result$interpretation[i] <- "Rapid decline"
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}
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} else {
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result$interpretation[i] <- "No previous data"
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}
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}
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return(result)
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}
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#' KPI 3: Calculate TCH forecasted (tonnes of cane per hectare)
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#'
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#' Projects final harvest tonnage based on historical yield data and CI growth trajectory.
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#' Uses a Random Forest model trained on harvest data to predict yields for mature fields.
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#' Delegates to calculate_yield_prediction_kpi() in 80_utils_common.R.
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#'
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#' @param field_statistics Current field statistics (dataframe with Mean_CI or mean_ci column)
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#' @param harvesting_data Historical harvest data frame (with tonnage_ha column)
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#' @param field_boundaries_sf SF object with field geometries
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#' @param cumulative_CI_vals_dir Directory with combined CI RDS files (optional)
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#' @param data_dir Project data directory (from setup_project_directories or parameters_project.R)
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#' Used to build cumulative_CI_vals_dir path if not provided directly (optional)
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#' @param project_dir Deprecated: only used if data_dir not provided (optional)
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#'
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#' @return Data frame with field-level yield forecasts ready for orchestrator
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#' Columns: field_idx, tch_forecasted (yields in t/ha)
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calculate_tch_forecasted_kpi <- function(field_statistics, harvesting_data = NULL,
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field_boundaries_sf = NULL,
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cumulative_CI_vals_dir = NULL,
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data_dir = NULL,
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project_dir = NULL) {
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# Use common utils yield prediction function (handles all ML logic)
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# This replaces the previous linear model (TCH = 50 + CI*10) with proper ML prediction
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# Validate required parameters
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if (is.null(field_boundaries_sf)) {
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safe_log("field_boundaries_sf is NULL in calculate_tch_forecasted_kpi", "WARNING")
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return(data.frame(
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field_idx = integer(),
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tch_forecasted = numeric(),
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stringsAsFactors = FALSE
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))
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}
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# Determine cumulative CI directory
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if (is.null(cumulative_CI_vals_dir)) {
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# Priority 1: Use provided data_dir parameter
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if (!is.null(data_dir)) {
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cumulative_CI_vals_dir <- file.path(data_dir, "extracted_ci", "cumulative_vals")
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} else if (exists("data_dir", envir = .GlobalEnv)) {
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# Priority 2: Fallback to global data_dir from parameters_project.R
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cumulative_CI_vals_dir <- file.path(get("data_dir", envir = .GlobalEnv), "extracted_ci", "cumulative_vals")
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} else {
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# Priority 3: Last resort - log warning and fail gracefully
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safe_log("Missing project data directory configuration: provide data_dir parameter or ensure parameters_project.R has set data_dir globally", "WARNING")
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safe_log("No training data available for yield prediction", "WARNING")
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return(data.frame(
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field_idx = integer(),
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tch_forecasted = numeric(),
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stringsAsFactors = FALSE
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))
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}
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}
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# Call the shared yield prediction function from common utils
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yield_result <- calculate_yield_prediction_kpi(field_boundaries_sf, harvesting_data, cumulative_CI_vals_dir)
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# Extract field-level results from the list
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field_results <- yield_result$field_results
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# Convert to format expected by orchestrator
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# If no predictions, return empty data frame
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if (is.null(field_results) || nrow(field_results) == 0) {
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return(data.frame(
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field_idx = integer(),
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tch_forecasted = numeric(),
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stringsAsFactors = FALSE
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))
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}
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# Map field names to field_idx using field_boundaries_sf
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result <- field_results %>%
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mutate(
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field_idx = match(field, field_boundaries_sf$field),
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tch_forecasted = yield_forecast_t_ha
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) %>%
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filter(!is.na(field_idx)) %>%
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select(field_idx, tch_forecasted)
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# Ensure result has proper structure even if empty
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if (nrow(result) == 0) {
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return(data.frame(
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field_idx = integer(),
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tch_forecasted = numeric(),
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stringsAsFactors = FALSE
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))
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}
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return(result)
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}
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#' KPI 4: Calculate growth decline indicator
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#'
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#' Identifies fields with negative growth trajectory
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#'
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#' @param ci_values_list List of CI values for each field (multiple weeks)
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#'
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#' @return Data frame with field-level decline indicators
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calculate_growth_decline_kpi <- function(ci_values_list) {
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result <- data.frame(
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field_idx = seq_len(length(ci_values_list)),
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four_week_trend = NA_real_,
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trend_interpretation = NA_character_,
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decline_severity = NA_character_,
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stringsAsFactors = FALSE
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)
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for (field_idx in seq_len(length(ci_values_list))) {
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ci_vals <- ci_values_list[[field_idx]]
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if (is.null(ci_vals) || length(ci_vals) < 2) {
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result$trend_interpretation[field_idx] <- "Insufficient data"
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next
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}
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ci_vals <- ci_vals[!is.na(ci_vals)]
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if (length(ci_vals) < 2) {
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result$trend_interpretation[field_idx] <- "Insufficient data"
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next
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}
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# Calculate linear trend
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weeks <- seq_along(ci_vals)
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lm_fit <- lm(ci_vals ~ weeks)
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slope <- coef(lm_fit)["weeks"]
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result$four_week_trend[field_idx] <- round(as.numeric(slope), 3)
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if (slope > 0.1) {
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result$trend_interpretation[field_idx] <- "Strong growth"
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result$decline_severity[field_idx] <- "None"
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} else if (slope > 0) {
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result$trend_interpretation[field_idx] <- "Weak growth"
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result$decline_severity[field_idx] <- "None"
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} else if (slope > -0.1) {
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result$trend_interpretation[field_idx] <- "Slight decline"
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result$decline_severity[field_idx] <- "Low"
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} else if (slope > -0.3) {
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result$trend_interpretation[field_idx] <- "Moderate decline"
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result$decline_severity[field_idx] <- "Medium"
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} else {
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result$trend_interpretation[field_idx] <- "Strong decline"
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result$decline_severity[field_idx] <- "High"
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}
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}
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return(result)
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}
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#'
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#' Combines two complementary metrics for comprehensive heterogeneity assessment:
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#' - Gini Coefficient: Distribution inequality of CI values (0=uniform, 1=unequal)
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#' - Moran's I: Spatial autocorrelation (-1 to +1, indicates clustering vs dispersal)
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#'
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#' @param ci_pixels_by_field List of CI pixel arrays for each field
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#' @param field_boundaries_sf SF object with field geometries
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#' @param mosaic_dir Directory path to per-field mosaic files (for Moran's I)
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#' @param week_file Week file pattern (for Moran's I calculation)
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#' @param mean_ci_values Optional vector of mean CI values per field
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#'
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#' @return Data frame with gini_coefficient, morans_i, patchiness_risk, patchiness_interpretation
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calculate_patchiness_kpi <- function(ci_pixels_by_field, field_boundaries_sf = NULL,
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mosaic_dir = NULL, week_file = NULL, mean_ci_values = NULL) {
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n_fields <- length(ci_pixels_by_field)
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result <- data.frame(
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field_idx = seq_len(n_fields),
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gini_coefficient = NA_real_,
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morans_i = NA_real_,
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patchiness_risk = NA_character_,
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patchiness_interpretation = NA_character_,
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stringsAsFactors = FALSE
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)
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# Determine if per-field structure available
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is_per_field <- !is.null(mosaic_dir) && !is.null(week_file) && !is.null(field_boundaries_sf)
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for (i in seq_len(n_fields)) {
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ci_pixels <- ci_pixels_by_field[[i]]
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if (is.null(ci_pixels) || length(ci_pixels) == 0) {
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result$patchiness_risk[i] <- "No data"
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result$patchiness_interpretation[i] <- "No data"
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next
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}
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ci_pixels <- ci_pixels[!is.na(ci_pixels)]
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if (length(ci_pixels) == 0) {
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result$patchiness_risk[i] <- "No data"
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result$patchiness_interpretation[i] <- "No data"
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next
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}
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# =========================================
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# METRIC 1: Calculate Gini Coefficient
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# =========================================
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gini <- NA_real_
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if (length(ci_pixels) > 1) {
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ci_sorted <- sort(ci_pixels)
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n <- length(ci_sorted)
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numerator <- 2 * sum(seq_len(n) * ci_sorted)
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denominator <- n * sum(ci_sorted)
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gini <- (numerator / denominator) - (n + 1) / n
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gini <- max(0, min(1, gini)) # Clamp to 0-1
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}
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result$gini_coefficient[i] <- gini
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# =========================================
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# METRIC 2: Calculate Moran's I (spatial clustering)
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# =========================================
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morans_i <- NA_real_
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if (is_per_field) {
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field_name <- field_boundaries_sf$field[i]
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field_mosaic_path <- file.path(mosaic_dir, field_name, week_file)
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|
|
if (file.exists(field_mosaic_path)) {
|
|
tryCatch({
|
|
field_raster <- terra::rast(field_mosaic_path)[["CI"]]
|
|
single_field <- field_boundaries_sf[i, ]
|
|
morans_result <- calculate_spatial_autocorrelation(field_raster, single_field)
|
|
|
|
if (is.list(morans_result)) {
|
|
morans_i <- morans_result$morans_i
|
|
} else {
|
|
morans_i <- morans_result
|
|
}
|
|
}, error = function(e) {
|
|
safe_log(paste("Warning: Moran's I failed for field", field_name, ":", e$message), "WARNING")
|
|
})
|
|
}
|
|
}
|
|
result$morans_i[i] <- morans_i
|
|
|
|
# =========================================
|
|
# RISK DETERMINATION: Gini + Moran's I combination
|
|
# =========================================
|
|
# Logic:
|
|
# - High Gini (>0.3) + High Moran's I (>0.85) = High patchiness (localized clusters)
|
|
# - High Gini + Low Moran's I = Medium patchiness (scattered heterogeneity)
|
|
# - Low Gini (<0.15) = Minimal patchiness (uniform)
|
|
# - Moderate Gini = Low to Medium patchiness
|
|
|
|
if (is.na(gini)) {
|
|
result$patchiness_risk[i] <- "No data"
|
|
} else if (gini < 0.15) {
|
|
result$patchiness_risk[i] <- "Minimal"
|
|
} else if (gini < 0.30) {
|
|
# Low-to-moderate Gini
|
|
if (!is.na(morans_i) && morans_i > 0.85) {
|
|
result$patchiness_risk[i] <- "Medium" # Some clustering
|
|
} else {
|
|
result$patchiness_risk[i] <- "Low"
|
|
}
|
|
} else if (gini < 0.50) {
|
|
# High Gini
|
|
if (!is.na(morans_i) && morans_i > 0.85) {
|
|
result$patchiness_risk[i] <- "High" # Localized problem clusters
|
|
} else {
|
|
result$patchiness_risk[i] <- "Medium" # Scattered issues
|
|
}
|
|
} else {
|
|
# Very high Gini (>0.5)
|
|
result$patchiness_risk[i] <- "High"
|
|
}
|
|
|
|
# =========================================
|
|
# INTERPRETATION: Combined Gini + Moran's I narrative
|
|
# =========================================
|
|
result$patchiness_interpretation[i] <- dplyr::case_when(
|
|
is.na(gini) ~ "No data",
|
|
gini < 0.15 & (is.na(morans_i) | morans_i < 0.75) ~
|
|
"Excellent uniformity - minimal patchiness",
|
|
gini < 0.30 & (is.na(morans_i) | morans_i < 0.75) ~
|
|
"Good uniformity - low patchiness",
|
|
gini < 0.30 & !is.na(morans_i) & morans_i > 0.85 ~
|
|
"Moderate uniformity with localized clustering",
|
|
gini < 0.50 & (is.na(morans_i) | morans_i < 0.75) ~
|
|
"Poor uniformity - scattered heterogeneity",
|
|
gini < 0.50 & !is.na(morans_i) & morans_i > 0.85 ~
|
|
"Poor uniformity with clustered problem areas",
|
|
gini >= 0.50 ~
|
|
"Severe heterogeneity - requires field investigation",
|
|
TRUE ~ "Mixed heterogeneity"
|
|
)
|
|
}
|
|
|
|
return(result)
|
|
}
|
|
|
|
|
|
|
|
# ============================================================================
|
|
# KPI ORCHESTRATOR AND REPORTING
|
|
# ============================================================================
|
|
|
|
#' Create summary tables for all 6 KPIs
|
|
#'
|
|
#' @param all_kpis List containing results from all 6 KPI functions
|
|
#'
|
|
#' @return List of summary data frames ready for reporting
|
|
create_summary_tables <- function(all_kpis) {
|
|
kpi_summary <- list(
|
|
uniformity = all_kpis$uniformity %>%
|
|
select(field_idx, cv_value, uniformity_category, interpretation),
|
|
|
|
area_change = all_kpis$area_change %>%
|
|
select(field_idx, mean_ci_abs_change, interpretation),
|
|
|
|
tch_forecast = all_kpis$tch_forecasted %>%
|
|
select(field_idx, tch_forecasted),
|
|
|
|
growth_decline = all_kpis$growth_decline %>%
|
|
select(field_idx, four_week_trend, trend_interpretation, decline_severity),
|
|
|
|
patchiness = all_kpis$patchiness %>%
|
|
select(field_idx, gini_coefficient, morans_i, patchiness_interpretation, patchiness_risk),
|
|
|
|
gap_filling = if (!is.null(all_kpis$gap_filling) && nrow(all_kpis$gap_filling) > 0) {
|
|
all_kpis$gap_filling %>%
|
|
select(field_idx, gap_score, gap_level)
|
|
} else {
|
|
NULL
|
|
}
|
|
)
|
|
return(kpi_summary)
|
|
}
|
|
|
|
#' Create detailed field-by-field KPI report (ALL KPIs in one row)
|
|
#'
|
|
#' @param field_boundaries_sf SF object with field boundaries
|
|
#' @param all_kpis List with all KPI results
|
|
#' @param current_week Current week number
|
|
#' @param current_year Current year
|
|
#'
|
|
#' @return Data frame with one row per field, all KPI columns
|
|
create_field_detail_table <- function(field_boundaries_sf, all_kpis, current_week, current_year, current_stats = NULL) {
|
|
|
|
# Start with field identifiers AND field_idx for joining
|
|
result <- field_boundaries_sf %>%
|
|
sf::st_drop_geometry() %>%
|
|
mutate(
|
|
field_idx = row_number(),
|
|
Field_id = field,
|
|
Field_name = field,
|
|
Week = current_week,
|
|
Year = current_year
|
|
) %>%
|
|
select(field_idx, Field_id, Field_name, Week, Year)
|
|
|
|
# ============================================
|
|
# GROUP 0: MEAN CI (from field statistics)
|
|
# ============================================
|
|
if (!is.null(current_stats)) {
|
|
result <- result %>%
|
|
left_join(
|
|
current_stats %>%
|
|
select(Field_id, Mean_CI),
|
|
by = "Field_id"
|
|
)
|
|
} else {
|
|
result$Mean_CI <- NA_real_
|
|
}
|
|
|
|
# ============================================
|
|
# GROUP 1: FIELD UNIFORMITY (KPI 1)
|
|
# ============================================
|
|
result <- result %>%
|
|
left_join(
|
|
all_kpis$uniformity %>%
|
|
select(field_idx, CV = cv_value,
|
|
Uniformity_Category = uniformity_category,
|
|
Uniformity_Interpretation = interpretation),
|
|
by = "field_idx"
|
|
)
|
|
|
|
# ============================================
|
|
# GROUP 2: GROWTH & TREND ANALYSIS (KPI 2 + KPI 4)
|
|
# ============================================
|
|
# KPI 2: Area Change
|
|
result <- result %>%
|
|
left_join(
|
|
all_kpis$area_change %>%
|
|
select(field_idx, Weekly_CI_Change = mean_ci_abs_change,
|
|
Area_Change_Interpretation = interpretation),
|
|
by = "field_idx"
|
|
)
|
|
|
|
# KPI 4: Growth Decline
|
|
result <- result %>%
|
|
left_join(
|
|
all_kpis$growth_decline %>%
|
|
select(field_idx, Four_Week_Trend = four_week_trend,
|
|
Trend_Interpretation = trend_interpretation,
|
|
Decline_Severity = decline_severity),
|
|
by = "field_idx"
|
|
)
|
|
|
|
# ============================================
|
|
# GROUP 3: FIELD HETEROGENEITY/PATCHINESS (KPI 5)
|
|
# ============================================
|
|
# KPI 5: Field Patchiness (Gini + Moran's I combination)
|
|
result <- result %>%
|
|
left_join(
|
|
all_kpis$patchiness %>%
|
|
select(field_idx, Gini_Coefficient = gini_coefficient,
|
|
Morans_I = morans_i,
|
|
Patchiness_Interpretation = patchiness_interpretation,
|
|
Patchiness_Risk = patchiness_risk),
|
|
by = "field_idx"
|
|
)
|
|
|
|
# ============================================
|
|
# GROUP 4: YIELD FORECAST (KPI 3)
|
|
# ============================================
|
|
result <- result %>%
|
|
left_join(
|
|
all_kpis$tch_forecasted %>%
|
|
select(field_idx, TCH_Forecasted = tch_forecasted),
|
|
by = "field_idx"
|
|
)
|
|
|
|
# ============================================
|
|
# GROUP 5: DATA QUALITY / GAP FILLING (KPI 6)
|
|
# ============================================
|
|
# Add gap filling if available
|
|
if (!is.null(all_kpis$gap_filling) && nrow(all_kpis$gap_filling) > 0) {
|
|
result <- result %>%
|
|
left_join(
|
|
all_kpis$gap_filling %>%
|
|
select(field_idx, Gap_Score = gap_score, Gap_Level = gap_level),
|
|
by = "field_idx"
|
|
)
|
|
}
|
|
|
|
# Remove field_idx from final output
|
|
result <- result %>%
|
|
select(-field_idx)
|
|
|
|
# Round numeric columns
|
|
result <- result %>%
|
|
mutate(across(where(is.numeric), ~ round(., 2)))
|
|
|
|
return(result)
|
|
}
|
|
|
|
#' Generate KPI text interpretation for inclusion in Word report
|
|
#'
|
|
#' @param all_kpis List with all KPI results
|
|
#'
|
|
#' @return Character string with formatted KPI summary text
|
|
create_field_kpi_text <- function(all_kpis) {
|
|
text_parts <- c(
|
|
"## AURA KPI ANALYSIS SUMMARY\n",
|
|
"### Field Uniformity\n",
|
|
paste(all_kpis$uniformity$interpretation, collapse = "; "), "\n",
|
|
"### Growth Trends\n",
|
|
paste(all_kpis$growth_decline$trend_interpretation, collapse = "; "), "\n",
|
|
"### Weed/Pest Pressure\n",
|
|
paste(all_kpis$weed_presence$weed_pressure_risk, collapse = "; "), "\n"
|
|
)
|
|
|
|
return(paste(text_parts, collapse = ""))
|
|
}
|
|
|
|
#' Export detailed KPI data to Excel/RDS
|
|
#'
|
|
#' @param field_detail_df Data frame with all KPI columns (one row per field)
|
|
#' @param kpi_summary List with summary tables (optional, for metadata)
|
|
#' @param output_dir Directory for output files
|
|
#' @param week Week number
|
|
#' @param year Year
|
|
#' @param project_dir Project name
|
|
#' @return List of output file paths
|
|
export_kpi_data <- function(field_detail_df, kpi_summary, output_dir, week, year, project_dir) {
|
|
|
|
# Use the common export function from 80_utils_common.R
|
|
export_paths <- export_field_analysis_excel(
|
|
field_df = field_detail_df,
|
|
summary_df = NULL, # No separate summary sheet for agronomic support
|
|
project_dir = project_dir,
|
|
current_week = week,
|
|
year = year,
|
|
reports_dir = output_dir
|
|
)
|
|
|
|
return(export_paths)
|
|
}
|
|
|
|
# ============================================================================
|
|
# ORCHESTRATOR FUNCTION
|
|
# ============================================================================
|
|
|
|
#' Calculate all 6 AURA KPIs
|
|
#'
|
|
#' Main entry point for AURA KPI calculation.
|
|
#' This function orchestrates the 6 KPI calculations and returns all results.
|
|
#'
|
|
#' @param field_boundaries_sf SF object with field geometries
|
|
#' @param current_week ISO week number (1-53)
|
|
#' @param current_year ISO week year
|
|
#' @param current_mosaic_dir Directory containing current week's mosaic
|
|
#' @param previous_mosaic_dir Directory containing previous week's mosaic (optional)
|
|
#' @param ci_rds_path Path to combined CI RDS file
|
|
#' @param harvesting_data Data frame with harvest data (optional)
|
|
#' @param output_dir Directory for KPI exports
|
|
#'
|
|
#' @return List with results from all 6 KPI functions
|
|
#'
|
|
#' @details
|
|
#' This function:
|
|
#' 1. Loads current week mosaic and extracts field statistics
|
|
#' 2. (Optionally) loads previous week mosaic for comparison metrics
|
|
#' 3. Calculates all 6 AURA KPIs
|
|
#' 4. Creates summary tables
|
|
#' 5. Exports results to Excel/RDS
|
|
#'
|
|
calculate_all_field_analysis_agronomic_support <- function(
|
|
field_boundaries_sf,
|
|
current_week,
|
|
current_year,
|
|
current_mosaic_dir,
|
|
previous_mosaic_dir = NULL,
|
|
ci_rds_path = NULL,
|
|
harvesting_data = NULL,
|
|
output_dir = NULL,
|
|
data_dir = NULL,
|
|
project_dir = NULL
|
|
) {
|
|
|
|
message("\n============ AURA KPI CALCULATION (6 KPIs) ============")
|
|
|
|
# DETECT STRUCTURE FIRST - before any use of is_per_field
|
|
week_file <- sprintf("week_%02d_%d.tif", current_week, current_year)
|
|
|
|
# Safely identify immediate child directories (not including root)
|
|
# Use list.files + dir.exists filter instead of list.dirs for robustness
|
|
all_entries <- list.files(current_mosaic_dir, full.names = FALSE)
|
|
field_dirs <- all_entries[sapply(
|
|
file.path(current_mosaic_dir, all_entries),
|
|
dir.exists
|
|
)]
|
|
|
|
is_per_field <- length(field_dirs) > 0 &&
|
|
file.exists(file.path(current_mosaic_dir, field_dirs[1], week_file))
|
|
|
|
if (is_per_field) {
|
|
message("Detected per-field mosaic structure...")
|
|
message("Using field-by-field extraction (similar to cane supply workflow)...")
|
|
|
|
# Use the same extraction method as cane supply
|
|
current_stats <- calculate_field_statistics(
|
|
field_boundaries_sf,
|
|
current_week,
|
|
current_year,
|
|
current_mosaic_dir,
|
|
report_date = Sys.Date()
|
|
)
|
|
|
|
# Extract CI pixels for each field from their individual mosaics
|
|
ci_pixels_by_field <- list()
|
|
for (i in seq_len(nrow(field_boundaries_sf))) {
|
|
field_name <- field_boundaries_sf$field[i]
|
|
field_mosaic_path <- file.path(current_mosaic_dir, field_name, week_file)
|
|
|
|
if (file.exists(field_mosaic_path)) {
|
|
tryCatch({
|
|
field_raster <- terra::rast(field_mosaic_path)
|
|
ci_band <- field_raster[["CI"]]
|
|
field_vect <- terra::vect(field_boundaries_sf[i, ])
|
|
ci_pixels_by_field[[i]] <- extract_ci_values(ci_band, field_vect)
|
|
}, error = function(e) {
|
|
message(paste(" Warning: Could not extract CI for field", field_name, ":", e$message))
|
|
ci_pixels_by_field[[i]] <- NULL
|
|
})
|
|
} else {
|
|
ci_pixels_by_field[[i]] <- NULL
|
|
}
|
|
}
|
|
|
|
# For uniformity calculations that need a reference raster, load first available
|
|
current_mosaic <- NULL
|
|
for (field_name in field_dirs) {
|
|
field_mosaic_path <- file.path(current_mosaic_dir, field_name, week_file)
|
|
if (file.exists(field_mosaic_path)) {
|
|
tryCatch({
|
|
current_mosaic <- terra::rast(field_mosaic_path)[["CI"]]
|
|
break
|
|
}, error = function(e) {
|
|
next
|
|
})
|
|
}
|
|
}
|
|
|
|
} else {
|
|
stop("ERROR: Per-field mosaic structure required (weekly_mosaic/{FIELD_NAME}/week_WW_YYYY.tif)")
|
|
}
|
|
|
|
# Load previous week mosaic (if available)
|
|
previous_stats <- NULL
|
|
target_prev <- calculate_target_week_and_year(current_week, current_year, offset_weeks = 1)
|
|
message(paste("Loading previous week mosaic (week", target_prev$week, target_prev$year, ")..."))
|
|
|
|
# Try loading previous week from the same per-field directory structure
|
|
prev_week_file <- sprintf("week_%02d_%d.tif", target_prev$week, target_prev$year)
|
|
prev_field_exists <- any(sapply(field_dirs, function(field) {
|
|
file.exists(file.path(current_mosaic_dir, field, prev_week_file))
|
|
}))
|
|
|
|
if (prev_field_exists) {
|
|
message(" Found previous week per-field mosaics, calculating statistics...")
|
|
previous_stats <- calculate_field_statistics(
|
|
field_boundaries_sf,
|
|
target_prev$week,
|
|
target_prev$year,
|
|
current_mosaic_dir,
|
|
report_date = Sys.Date() - 7
|
|
)
|
|
} else {
|
|
message(" Previous week mosaic not available - skipping area change KPI")
|
|
}
|
|
|
|
# Calculate 6 KPIs
|
|
message("\nCalculating KPI 1: Field Uniformity...")
|
|
uniformity_kpi <- calculate_field_uniformity_kpi(
|
|
ci_pixels_by_field,
|
|
field_boundaries_sf,
|
|
ci_band = NULL,
|
|
mosaic_dir = current_mosaic_dir,
|
|
week_file = week_file
|
|
)
|
|
|
|
message("Calculating KPI 2: Area Change...")
|
|
if (!is.null(previous_stats)) {
|
|
area_change_kpi <- calculate_area_change_kpi(current_stats, previous_stats, field_boundaries_sf)
|
|
} else {
|
|
area_change_kpi <- data.frame(
|
|
field_idx = seq_len(nrow(field_boundaries_sf)),
|
|
mean_ci_abs_change = NA_real_,
|
|
interpretation = rep("No previous data", nrow(field_boundaries_sf))
|
|
)
|
|
}
|
|
|
|
message("Calculating KPI 3: TCH Forecasted...")
|
|
tch_kpi <- calculate_tch_forecasted_kpi(current_stats, harvesting_data, field_boundaries_sf,
|
|
data_dir = data_dir, project_dir = project_dir)
|
|
|
|
message("Calculating KPI 4: Growth Decline...")
|
|
|
|
# Load historical field statistics to build weekly mean CI time series per field
|
|
# (growth_decline_kpi expects temporal series, not spatial pixel arrays)
|
|
weekly_mean_ci_by_field <- list()
|
|
|
|
# Build list of weekly mean CI values for each field (4-week lookback)
|
|
for (field_idx in seq_len(nrow(field_boundaries_sf))) {
|
|
weekly_ci_values <- c()
|
|
}
|
|
|
|
# Try to load historical data for trend calculation
|
|
if (!is.null(output_dir) && !is.null(project_dir)) {
|
|
tryCatch({
|
|
historical_data <- load_historical_field_data(
|
|
project_dir = project_dir,
|
|
current_week = current_week,
|
|
current_year = current_year,
|
|
reports_dir = output_dir,
|
|
num_weeks = 4,
|
|
auto_generate = FALSE,
|
|
field_boundaries_sf = field_boundaries_sf
|
|
)
|
|
|
|
if (!is.null(historical_data) && length(historical_data) > 0) {
|
|
message(" Building weekly mean CI time series from historical data...")
|
|
|
|
# Initialize list with empty vectors for each field
|
|
for (field_idx in seq_len(nrow(field_boundaries_sf))) {
|
|
weekly_mean_ci_by_field[[field_idx]] <- c()
|
|
}
|
|
|
|
# Extract Mean_CI from each historical week (reverse order to go chronologically)
|
|
for (hist_idx in rev(seq_along(historical_data))) {
|
|
hist_week <- historical_data[[hist_idx]]
|
|
hist_data <- hist_week$data
|
|
|
|
# Extract Mean_CI column if available
|
|
if ("Mean_CI" %in% names(hist_data)) {
|
|
# Match fields between historical data and field_boundaries
|
|
for (field_idx in seq_len(nrow(field_boundaries_sf))) {
|
|
field_name <- field_boundaries_sf$field[field_idx]
|
|
|
|
# Find matching row in historical data by field name/ID
|
|
field_row <- which(
|
|
(hist_data$Field_id == field_name | hist_data$Field_name == field_name) &
|
|
!is.na(hist_data$Mean_CI)
|
|
)
|
|
|
|
if (length(field_row) > 0) {
|
|
mean_ci_val <- as.numeric(hist_data$Mean_CI[field_row[1]])
|
|
if (!is.na(mean_ci_val)) {
|
|
weekly_mean_ci_by_field[[field_idx]] <- c(weekly_mean_ci_by_field[[field_idx]], mean_ci_val)
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
message(paste(" ✓ Loaded weekly Mean_CI for", sum(sapply(weekly_mean_ci_by_field, length) > 0), "fields"))
|
|
}
|
|
}, error = function(e) {
|
|
message(paste(" Note: Could not load historical field data for trend analysis:", e$message))
|
|
})
|
|
}
|
|
|
|
# If no historical data available, create empty vectors (will result in "Insufficient data")
|
|
if (length(weekly_mean_ci_by_field) == 0 || all(sapply(weekly_mean_ci_by_field, length) == 0)) {
|
|
message(" Warning: No historical weekly CI data available - attempting to load from RDS cache...")
|
|
# LOAD HISTORICAL WEEKS FOR TREND CALCULATION (4-week and 8-week analysis)
|
|
# Try to load previous weeks from cache (same as cane_supply workflow)
|
|
ci_values_4week_per_field <- list()
|
|
for (field_idx in seq_len(nrow(field_boundaries_sf))) {
|
|
ci_values_4week <- numeric()
|
|
field_name <- field_boundaries_sf$field[field_idx]
|
|
|
|
# Load up to 4 previous weeks
|
|
for (lookback in 3:0) {
|
|
target_week <- current_week - lookback
|
|
target_year <- current_year
|
|
if (target_week < 1) {
|
|
target_week <- target_week + 52
|
|
target_year <- target_year - 1
|
|
}
|
|
|
|
# Try to load from cached RDS files
|
|
if (!is.null(output_dir)) {
|
|
rds_filename <- sprintf("%s_field_analysis_week%02d_%d.rds", project_dir, target_week, target_year)
|
|
rds_path <- file.path(output_dir, rds_filename)
|
|
# Normalize path safely (for cases where file may not exist yet)
|
|
rds_path_normalized <- tryCatch(
|
|
normalizePath(rds_path, winslash = "/"),
|
|
error = function(e) rds_path # Fall back to original path if normalizePath fails
|
|
)
|
|
|
|
message(paste(" Trying to load:", rds_path_normalized))
|
|
|
|
if (file.exists(rds_path_normalized)) {
|
|
tryCatch({
|
|
rds_content <- readRDS(rds_path_normalized)
|
|
# RDS files are saved as lists with 'field_analysis' key (not 'field_data')
|
|
if (is.list(rds_content) && "field_analysis" %in% names(rds_content)) {
|
|
cached_data <- rds_content$field_analysis
|
|
} else if (is.list(rds_content) && "field_data" %in% names(rds_content)) {
|
|
# Fallback for older RDS format
|
|
cached_data <- rds_content$field_data
|
|
} else if (is.data.frame(rds_content)) {
|
|
cached_data <- rds_content
|
|
} else {
|
|
cached_data <- NULL
|
|
}
|
|
|
|
if (!is.null(cached_data) && is.data.frame(cached_data) && "Mean_CI" %in% names(cached_data)) {
|
|
matching_row <- which(cached_data$Field_id == field_name | cached_data$Field_name == field_name)
|
|
if (length(matching_row) > 0 && !is.na(cached_data$Mean_CI[matching_row[1]])) {
|
|
ci_val <- as.numeric(cached_data$Mean_CI[matching_row[1]])
|
|
message(paste(" ✓ Loaded week", target_week, "CI =", ci_val))
|
|
ci_values_4week <- c(ci_values_4week, ci_val)
|
|
}
|
|
}
|
|
}, error = function(e) {
|
|
message(paste(" Error loading:", e$message))
|
|
})
|
|
}
|
|
}
|
|
}
|
|
|
|
# Add current week CI
|
|
if (!is.null(current_stats) && nrow(current_stats) > 0) {
|
|
matching_row <- which(
|
|
(current_stats$Field_id == field_name | current_stats$Field_name == field_name) &
|
|
!is.na(current_stats$Mean_CI)
|
|
)
|
|
if (length(matching_row) > 0) {
|
|
ci_val <- as.numeric(current_stats$Mean_CI[matching_row[1]])
|
|
message(paste(" ✓ Loaded current week CI =", ci_val))
|
|
ci_values_4week <- c(ci_values_4week, ci_val)
|
|
}
|
|
}
|
|
|
|
ci_values_4week_per_field[[field_idx]] <- ci_values_4week
|
|
}
|
|
|
|
# Use 4-week CI series for trend calculation (or current week if unavailable)
|
|
for (field_idx in seq_len(nrow(field_boundaries_sf))) {
|
|
weekly_mean_ci_by_field[[field_idx]] <- ci_values_4week_per_field[[field_idx]]
|
|
if (length(weekly_mean_ci_by_field[[field_idx]]) == 0) {
|
|
weekly_mean_ci_by_field[[field_idx]] <- NA_real_
|
|
}
|
|
}
|
|
|
|
message(paste(" ✓ Loaded trend data for", sum(sapply(weekly_mean_ci_by_field, length) > 0), "fields"))
|
|
}
|
|
|
|
# Calculate growth decline using weekly time series (not spatial pixel arrays)
|
|
growth_decline_kpi <- calculate_growth_decline_kpi(weekly_mean_ci_by_field)
|
|
|
|
message("Calculating KPI 5: Field Patchiness...")
|
|
# Calculate patchiness using both Gini coefficient and Moran's I spatial clustering
|
|
patchiness_kpi <- calculate_patchiness_kpi(
|
|
ci_pixels_by_field,
|
|
field_boundaries_sf = field_boundaries_sf,
|
|
mosaic_dir = current_mosaic_dir,
|
|
week_file = week_file,
|
|
mean_ci_values = current_stats$Mean_CI
|
|
)
|
|
|
|
message("Calculating KPI 6: Gap Filling...")
|
|
# Build list of per-field files for this week
|
|
per_field_files <- c()
|
|
for (field_name in field_dirs) {
|
|
field_mosaic_path <- file.path(current_mosaic_dir, field_name, week_file)
|
|
if (file.exists(field_mosaic_path)) {
|
|
per_field_files <- c(per_field_files, field_mosaic_path)
|
|
}
|
|
}
|
|
|
|
if (length(per_field_files) > 0) {
|
|
# Use the common wrapper function (same as cane supply)
|
|
gap_scores_result <- calculate_gap_scores(per_field_files, field_boundaries_sf)
|
|
|
|
# Guard against NULL or empty result from calculate_gap_scores
|
|
if (is.null(gap_scores_result) || nrow(gap_scores_result) == 0) {
|
|
message(" Warning: calculate_gap_scores returned NULL/empty - creating fallback")
|
|
gap_scores_result <- data.frame(
|
|
Field_id = field_boundaries_sf$field,
|
|
gap_score = NA_real_,
|
|
stringsAsFactors = FALSE
|
|
)
|
|
}
|
|
|
|
# Convert to the format expected by orchestrator
|
|
gap_filling_kpi <- gap_scores_result %>%
|
|
mutate(field_idx = match(Field_id, field_boundaries_sf$field)) %>%
|
|
select(field_idx, gap_score) %>%
|
|
mutate(
|
|
gap_level = dplyr::case_when(
|
|
gap_score < 10 ~ "Minimal",
|
|
gap_score < 25 ~ "Moderate",
|
|
TRUE ~ "Significant"
|
|
),
|
|
mean_ci = NA_real_,
|
|
outlier_threshold = NA_real_
|
|
)
|
|
} else {
|
|
# Fallback: no per-field files
|
|
gap_filling_kpi <- data.frame(
|
|
field_idx = seq_len(nrow(field_boundaries_sf)),
|
|
gap_score = NA_real_,
|
|
gap_level = NA_character_,
|
|
mean_ci = NA_real_,
|
|
outlier_threshold = NA_real_
|
|
)
|
|
}
|
|
|
|
# Compile results
|
|
all_kpis <- list(
|
|
uniformity = uniformity_kpi,
|
|
area_change = area_change_kpi,
|
|
tch_forecasted = tch_kpi,
|
|
growth_decline = growth_decline_kpi,
|
|
patchiness = patchiness_kpi,
|
|
gap_filling = gap_filling_kpi
|
|
)
|
|
|
|
# Deduplicate KPI dataframes to ensure one row per field_idx
|
|
# (sometimes joins or calculations can create duplicate rows)
|
|
message("Deduplicating KPI results (keeping first occurrence per field)...")
|
|
all_kpis$uniformity <- all_kpis$uniformity %>%
|
|
distinct(field_idx, .keep_all = TRUE)
|
|
all_kpis$area_change <- all_kpis$area_change %>%
|
|
distinct(field_idx, .keep_all = TRUE)
|
|
all_kpis$tch_forecasted <- all_kpis$tch_forecasted %>%
|
|
distinct(field_idx, .keep_all = TRUE)
|
|
all_kpis$growth_decline <- all_kpis$growth_decline %>%
|
|
distinct(field_idx, .keep_all = TRUE)
|
|
all_kpis$patchiness <- all_kpis$patchiness %>%
|
|
distinct(field_idx, .keep_all = TRUE)
|
|
all_kpis$gap_filling <- all_kpis$gap_filling %>%
|
|
distinct(field_idx, .keep_all = TRUE)
|
|
|
|
# Built single-sheet field detail table with all KPIs
|
|
message("\nBuilding comprehensive field detail table...")
|
|
field_detail_df <- create_field_detail_table(
|
|
field_boundaries_sf = field_boundaries_sf,
|
|
all_kpis = all_kpis,
|
|
current_week = current_week,
|
|
current_year = current_year,
|
|
current_stats = current_stats
|
|
)
|
|
|
|
# Create summary tables
|
|
message("\nCreating summary tables...")
|
|
kpi_summary <- create_summary_tables(all_kpis)
|
|
|
|
# Export
|
|
message("\nExporting KPI data (single-sheet format)...")
|
|
export_paths <- export_kpi_data(
|
|
field_detail_df = field_detail_df,
|
|
kpi_summary = kpi_summary,
|
|
output_dir = output_dir,
|
|
week = current_week,
|
|
year = current_year,
|
|
project_dir = project_dir
|
|
)
|
|
|
|
message(paste("\n✓ AURA KPI calculation complete. Week", current_week, current_year))
|
|
|
|
return(list(
|
|
field_analysis_df = field_detail_df,
|
|
kpis = all_kpis,
|
|
summary_tables = kpi_summary,
|
|
export_paths = export_paths,
|
|
metadata = list(
|
|
week = current_week,
|
|
year = current_year,
|
|
project = project_dir
|
|
)
|
|
))
|
|
}
|