Timon
d5fd4bb463
Major Changes: - NEW: Scripts 09 & 10 for KPI calculation and enhanced reporting - NEW: Shell script wrappers (01-10) for easier execution - NEW: R packages flextable and officer for enhanced Word reports - NEW: DEPLOYMENT_README.md with complete deployment guide - RENAMED: Numbered R scripts (02, 03, 04) for clarity - REMOVED: Old package management scripts (using renv only) - UPDATED: Workflow now uses scripts 09->10 instead of 05 Files Changed: 90+ files New Packages: flextable, officer New Scripts: 09_run_calculate_kpis.sh, 10_run_kpi_report.sh Documentation: DEPLOYMENT_README.md, EMAIL_TO_ADMIN.txt See DEPLOYMENT_README.md for full deployment instructions.
315 lines
9.4 KiB
Plaintext
315 lines
9.4 KiB
Plaintext
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R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
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Copyright (C) 2025 The R Foundation for Statistical Computing
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Platform: x86_64-w64-mingw32/x64
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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Natural language support but running in an English locale
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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- Project 'C:/Users/timon/Resilience BV/4020 SCane ESA DEMO - Documenten/General/4020 SCDEMO Team/4020 TechnicalData/WP3/smartcane_v2/smartcane' loaded. [renv 1.1.4]
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> # 09_CALCULATE_KPIS.R
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> # ===================
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> # This script calculates 6 Key Performance Indicators (KPIs) for sugarcane monitoring:
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> # 1. Field Uniformity Summary
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> # 2. Farm-wide Area Change Summary
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> # 3. TCH Forecasted
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> # 4. Growth Decline Index
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> # 5. Weed Presence Score
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> # 6. Gap Filling Score (placeholder)
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> #
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> # Usage: Rscript 09_calculate_kpis.R [end_date] [offset] [project_dir]
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> # - end_date: End date for KPI calculation (YYYY-MM-DD format), default: today
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> # - offset: Number of days to look back (not currently used for KPIs, but for consistency)
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> # - project_dir: Project directory name (e.g., "aura", "esa")
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>
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> # 1. Load required libraries
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> # -------------------------
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> suppressPackageStartupMessages({
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+ library(here)
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+ library(sf)
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+ library(terra)
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+ library(dplyr)
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+ library(tidyr)
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+ library(lubridate)
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+ library(readr)
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+ library(caret)
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+ library(CAST)
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+ library(randomForest)
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+ })
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>
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> # 2. Main function
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> # --------------
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> main <- function() {
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+ # Process command line arguments
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+ args <- commandArgs(trailingOnly = TRUE)
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+
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+ # Process end_date argument
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+ if (length(args) >= 1 && !is.na(args[1])) {
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+ end_date <- as.Date(args[1])
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+ if (is.na(end_date)) {
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+ warning("Invalid end_date provided. Using default (current date).")
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+ end_date <- Sys.Date()
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+ }
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+ } else {
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+ end_date <- Sys.Date()
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+ }
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+
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+ # Process offset argument (for consistency with other scripts, not currently used)
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+ if (length(args) >= 2 && !is.na(args[2])) {
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+ offset <- as.numeric(args[2])
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+ if (is.na(offset) || offset <= 0) {
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+ warning("Invalid offset provided. Using default (7 days).")
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+ offset <- 7
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+ }
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+ } else {
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+ offset <- 7
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+ }
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+
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+ # Process project_dir argument
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+ if (length(args) >= 3 && !is.na(args[3])) {
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+ project_dir <- as.character(args[3])
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+ } else {
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+ project_dir <- "esa" # Default project
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+ }
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+
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+ # Make project_dir available globally so parameters_project.R can use it
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+ assign("project_dir", project_dir, envir = .GlobalEnv)
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+
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+ # 3. Load utility functions and project configuration
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+ # --------------------------------------------------
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+
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+ tryCatch({
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+ source(here("r_app", "crop_messaging_utils.R"))
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+ }, error = function(e) {
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+ stop("Error loading crop_messaging_utils.R: ", e$message)
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+ })
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+
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+ tryCatch({
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+ source(here("r_app", "kpi_utils.R"))
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+ }, error = function(e) {
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+ stop("Error loading kpi_utils.R: ", e$message)
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+ })
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+
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+ # Load project parameters (this sets up all directory paths and field boundaries)
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+ tryCatch({
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+ source(here("r_app", "parameters_project.R"))
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+ }, error = function(e) {
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+ stop("Error loading parameters_project.R: ", e$message)
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+ })
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+
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+ # Load growth model utils if available (for yield prediction)
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+ tryCatch({
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+ source(here("r_app", "growth_model_utils.R"))
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+ }, error = function(e) {
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+ warning("growth_model_utils.R not found, yield prediction KPI will use placeholder data")
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+ })
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+
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+ # Check if required variables exist
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+ if (!exists("project_dir")) {
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+ stop("project_dir must be set before running this script")
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+ }
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+
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+ if (!exists("field_boundaries_sf") || is.null(field_boundaries_sf)) {
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+ stop("Field boundaries not loaded. Check parameters_project.R initialization.")
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+ }
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+
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+ # 4. Calculate all KPIs
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+ # -------------------
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+ output_dir <- file.path(reports_dir, "kpis")
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+
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+ kpi_results <- calculate_all_kpis(
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+ report_date = end_date,
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+ output_dir = output_dir,
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+ field_boundaries_sf = field_boundaries_sf,
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+ harvesting_data = harvesting_data,
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+ cumulative_CI_vals_dir = cumulative_CI_vals_dir,
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+ weekly_CI_mosaic = weekly_CI_mosaic,
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+ reports_dir = reports_dir,
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+ project_dir = project_dir
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+ )
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+
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+ # 5. Print summary
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+ # --------------
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+ cat("\n=== KPI CALCULATION SUMMARY ===\n")
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+ cat("Report Date:", as.character(kpi_results$metadata$report_date), "\n")
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+ cat("Current Week:", kpi_results$metadata$current_week, "\n")
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+ cat("Previous Week:", kpi_results$metadata$previous_week, "\n")
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+ cat("Total Fields Analyzed:", kpi_results$metadata$total_fields, "\n")
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+ cat("Calculation Time:", as.character(kpi_results$metadata$calculation_time), "\n")
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+
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+ cat("\nField Uniformity Summary:\n")
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+ print(kpi_results$field_uniformity_summary)
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+
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+ cat("\nArea Change Summary:\n")
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+ print(kpi_results$area_change)
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+
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+ cat("\nTCH Forecasted:\n")
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+ print(kpi_results$tch_forecasted)
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+
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+ cat("\nGrowth Decline Index:\n")
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+ print(kpi_results$growth_decline)
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+
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+ cat("\nWeed Presence Score:\n")
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+ print(kpi_results$weed_presence)
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+
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+ cat("\nGap Filling Score:\n")
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+ print(kpi_results$gap_filling)
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+
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+ cat("\n=== KPI CALCULATION COMPLETED ===\n")
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+ }
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>
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> # 6. Script execution
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> # -----------------
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> if (sys.nframe() == 0) {
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+ main()
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+ }
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[INFO] 2025-10-08 15:39:29 - Initializing project with directory: esa
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[1] "model using cumulative_CI,DOY will be trained now..."
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note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .
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+ Fold1: mtry=2
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- Fold1: mtry=2
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+ Fold2: mtry=2
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- Fold2: mtry=2
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+ Fold3: mtry=2
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- Fold3: mtry=2
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+ Fold4: mtry=2
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- Fold4: mtry=2
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+ Fold5: mtry=2
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- Fold5: mtry=2
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Aggregating results
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Fitting final model on full training set
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[1] "maximum number of models that still need to be trained: 3"
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[1] "model using cumulative_CI,CI_per_day will be trained now..."
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note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .
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+ Fold1: mtry=2
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- Fold1: mtry=2
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+ Fold2: mtry=2
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- Fold2: mtry=2
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+ Fold3: mtry=2
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- Fold3: mtry=2
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+ Fold4: mtry=2
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- Fold4: mtry=2
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+ Fold5: mtry=2
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- Fold5: mtry=2
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Aggregating results
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Fitting final model on full training set
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[1] "maximum number of models that still need to be trained: 2"
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[1] "model using DOY,CI_per_day will be trained now..."
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note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .
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+ Fold1: mtry=2
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- Fold1: mtry=2
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+ Fold2: mtry=2
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- Fold2: mtry=2
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+ Fold3: mtry=2
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- Fold3: mtry=2
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+ Fold4: mtry=2
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- Fold4: mtry=2
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+ Fold5: mtry=2
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- Fold5: mtry=2
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Aggregating results
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Fitting final model on full training set
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[1] "maximum number of models that still need to be trained: 1"
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[1] "vars selected: cumulative_CI,DOY with RMSE 24.808"
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[1] "model using additional variable CI_per_day will be trained now..."
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note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 .
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+ Fold1: mtry=2
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- Fold1: mtry=2
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+ Fold1: mtry=3
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- Fold1: mtry=3
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+ Fold2: mtry=2
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- Fold2: mtry=2
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+ Fold2: mtry=3
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- Fold2: mtry=3
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+ Fold3: mtry=2
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- Fold3: mtry=2
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+ Fold3: mtry=3
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- Fold3: mtry=3
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+ Fold4: mtry=2
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- Fold4: mtry=2
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+ Fold4: mtry=3
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- Fold4: mtry=3
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+ Fold5: mtry=2
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- Fold5: mtry=2
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+ Fold5: mtry=3
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- Fold5: mtry=3
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Aggregating results
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Selecting tuning parameters
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Fitting mtry = 3 on full training set
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[1] "maximum number of models that still need to be trained: 0"
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[1] "vars selected: cumulative_CI,DOY with RMSE 24.808"
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field_groups count value
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75% Top 25% 3 96.2
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50% Average 7 93.0
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25% Lowest 25% 2 84.0
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Total area forecasted 12 219.0
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=== KPI CALCULATION SUMMARY ===
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Report Date: 2025-10-08
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Current Week: 40
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Previous Week: 39
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Total Fields Analyzed: 12
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Calculation Time: 2025-10-08 15:39:34.583434
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Field Uniformity Summary:
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uniformity_level count percent
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1 Excellent 0 0
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2 Good 0 0
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3 Moderate 0 0
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4 Poor 0 0
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Area Change Summary:
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change_type hectares percent
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1 Improving areas 0 0
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2 Stable areas 0 0
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3 Declining areas 0 0
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4 Total area 0 100
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TCH Forecasted:
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field_groups count value
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75% Top 25% 3 96.2
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50% Average 7 93.0
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25% Lowest 25% 2 84.0
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Total area forecasted 12 219.0
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Growth Decline Index:
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risk_level count percent
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1 High 0 0
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2 Low 0 0
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3 Moderate 0 0
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4 Very-high 0 0
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Weed Presence Score:
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weed_risk_level field_count percent
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1 Canopy closed - Low weed risk 4 33.3
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2 High 0 0.0
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3 Low 0 0.0
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4 Moderate 0 0.0
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Gap Filling Score:
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# A tibble: 1 × 3
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gap_level field_count percent
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<chr> <int> <dbl>
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1 <NA> 12 100
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=== KPI CALCULATION COMPLETED ===
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There were 50 or more warnings (use warnings() to see the first 50)
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>
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> proc.time()
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user system elapsed
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11.93 0.93 13.45
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