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Enhance debugging output and improve date handling in TIFF removal script; update report utility functions for better map layout and historical data handling.

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This commit is contained in:
Timon 2026-02-11 09:48:07 +01:00
parent 2d6f062c27
commit b6fa1956c0
4 changed files with 353 additions and 210 deletions
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4
r_app/90_CI_report_with_kpis_agronomic_support.Rmd
View file

@ -664,7 +664,9 @@ tryCatch({
# Helper function to safely load per-field mosaic if it exists # Helper function to safely load per-field mosaic if it exists
load_per_field_mosaic <- function(base_dir, field_name, week, year) { load_per_field_mosaic <- function(base_dir, field_name, week, year) {
path <- file.path(base_dir, field_name, paste0("week_", sprintf("%02d", week), "_", year, ".tif")) path <- file.path(base_dir, field_name, paste0("week_", sprintf("%02d", week), "_", year, ".tif"))
cat(paste(" [DEBUG] Field:", field_name, "trying path:", path, "\n"))
if (file.exists(path)) { if (file.exists(path)) {
cat(paste(" ✓ File found\n"))
tryCatch({ tryCatch({
rast_obj <- terra::rast(path) rast_obj <- terra::rast(path)
# Extract CI band if present, otherwise first band # Extract CI band if present, otherwise first band
@ -677,6 +679,8 @@ tryCatch({
message(paste("Warning: Could not load", path, ":", e$message)) message(paste("Warning: Could not load", path, ":", e$message))
return(NULL) return(NULL)
}) })
} else {
cat(paste(" ✗ File NOT found\n"))
} }
return(NULL) return(NULL)
} }

295
r_app/DEBUG_remove_date_tiffs.R
View file

@ -1,30 +1,39 @@
# ============================================================================== #' DEBUG_REMOVE_DATE_TIFFS.R
# DEBUG_REMOVE_DATE_TIFFS.R #' ==============================================================================
# ============================================================================== #' PURPOSE:
# PURPOSE: #' Remove all TIFFs of a specific date OR date range from multiple storage folders.
# Remove all TIFFs of a specific date from multiple storage folders. #' Useful for debugging/re-running parts of the pipeline without full re-download.
# Useful for debugging/re-running parts of the pipeline without full re-download. #'
# #' USAGE:
# USAGE: #' Rscript DEBUG_remove_date_tiffs.R [project] [date] [options]
# Rscript DEBUG_remove_date_tiffs.R [project] [date] [--dry-run] [--skip-merged] [--skip-field-tiles] [--skip-field-tiles-ci] [--skip-daily-vals] #' Rscript DEBUG_remove_date_tiffs.R [project] --start-date [START] --end-date [END] [options]
# #'
# EXAMPLES: #' SINGLE DATE EXAMPLES:
# # Remove 2026-02-08 from all folders (WITH CONFIRMATION) #' # Remove 2026-02-08 from all folders (WITH CONFIRMATION)
# Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 #' Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08
# #'
# # Remove from all folders without confirmation #' # Remove from all folders without confirmation
# Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --no-confirm #' Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --no-confirm
# #'
# # Dry run - show what WOULD be deleted without deleting #' # Dry run - show what WOULD be deleted without deleting
# Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --dry-run #' Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --dry-run
# #'
# # Remove only from merged_tif and field_tiles, skip CI folders #' DATE RANGE EXAMPLES:
# Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --skip-field-tiles-ci --skip-daily-vals #' # Remove all dates from Nov 1, 2025 to Feb 11, 2026
# #' Rscript DEBUG_remove_date_tiffs.R aura --start-date 2025-11-01 --end-date 2026-02-11 --no-confirm
# # Remove from field_tiles_CI only #'
# Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --skip-merged --skip-field-tiles --skip-daily-vals #' # Dry run for date range
# #' Rscript DEBUG_remove_date_tiffs.R aura --start-date 2025-11-01 --end-date 2026-02-11 --dry-run
# ============================================================================== #'
#' OPTIONS:
#' --dry-run Preview deletions without actually deleting
#' --no-confirm Delete without confirmation
#' --skip-merged Skip merged_tif folder
#' --skip-field-tiles Skip field_tiles folder
#' --skip-field-tiles-ci Skip field_tiles_CI folder
#' --skip-daily-vals Skip daily_vals folder
#'
#' ==============================================================================
# ============================================================================== # ==============================================================================
# CONFIGURATION - TOGGLE WHICH FOLDERS TO DELETE FROM (DEFAULT: ALL) # CONFIGURATION - TOGGLE WHICH FOLDERS TO DELETE FROM (DEFAULT: ALL)
@ -51,11 +60,12 @@ main <- function() {
# Validate minimum arguments # Validate minimum arguments
if (length(args) < 2) { if (length(args) < 2) {
cat("\n[ERROR] Missing arguments\n") cat("\n[ERROR] Missing arguments\n")
cat("Usage: Rscript DEBUG_remove_date_tiffs.R [project] [date] [options]\n\n") cat("Usage:\n")
cat(" Single date: Rscript DEBUG_remove_date_tiffs.R [project] [date] [options]\n")
cat(" Date range: Rscript DEBUG_remove_date_tiffs.R [project] --start-date [START] --end-date [END] [options]\n\n")
cat("Examples:\n") cat("Examples:\n")
cat(" Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08\n") cat(" Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08\n")
cat(" Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --dry-run\n") cat(" Rscript DEBUG_remove_date_tiffs.R aura --start-date 2025-11-01 --end-date 2026-02-11 --no-confirm\n\n")
cat(" Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --skip-field-tiles-ci\n\n")
cat("Options:\n") cat("Options:\n")
cat(" --dry-run Preview deletions without actually deleting\n") cat(" --dry-run Preview deletions without actually deleting\n")
cat(" --no-confirm Delete without confirmation\n") cat(" --no-confirm Delete without confirmation\n")
@ -68,15 +78,51 @@ main <- function() {
# Parse positional arguments # Parse positional arguments
project <- args[1] project <- args[1]
# Check if using date range or single date
date_str <- NULL
start_date_str <- NULL
end_date_str <- NULL
# Look for --start-date and --end-date flags
start_idx <- which(args == "--start-date")
end_idx <- which(args == "--end-date")
if (length(start_idx) > 0 && length(end_idx) > 0) {
# Date range mode
if (start_idx + 1 <= length(args)) {
start_date_str <- args[start_idx + 1]
}
if (end_idx + 1 <= length(args)) {
end_date_str <- args[end_idx + 1]
}
if (is.null(start_date_str) || is.null(end_date_str)) {
cat("\n[ERROR] --start-date and --end-date require date values\n")
quit(status = 1)
}
} else {
# Single date mode
if (length(args) < 2 || startsWith(args[2], "--")) {
cat("\n[ERROR] Missing date argument. Either provide:\n")
cat(" - A single date: Rscript ... [project] 2026-02-08\n")
cat(" - Or --start-date and --end-date flags\n\n")
quit(status = 1)
}
date_str <- args[2] date_str <- args[2]
}
# Parse optional flags # Parse optional flags
if (length(args) >= 3) { if (length(args) >= 3) {
for (i in 3:length(args)) { for (i in 3:length(args)) {
arg <- args[i] arg <- args[i]
# Skip NA or empty arguments # Skip NA, empty, or flag values (already processed)
if (is.na(arg) || nchar(arg) == 0) { if (is.na(arg) || nchar(arg) == 0 || arg %in% c("--start-date", "--end-date")) {
next
}
if (i > 1 && args[i-1] %in% c("--start-date", "--end-date")) {
# Skip date values (already processed)
next next
} }
@ -96,7 +142,11 @@ main <- function() {
} }
} }
# Validate date format # Validate and convert dates
dates_to_process <- c()
if (!is.null(date_str)) {
# Single date mode
date_obj <- tryCatch( date_obj <- tryCatch(
as.Date(date_str, format = "%Y-%m-%d"), as.Date(date_str, format = "%Y-%m-%d"),
error = function(e) NULL error = function(e) NULL
@ -106,12 +156,97 @@ main <- function() {
cat(sprintf("[ERROR] Invalid date format: %s (expected YYYY-MM-DD)\n", date_str)) cat(sprintf("[ERROR] Invalid date format: %s (expected YYYY-MM-DD)\n", date_str))
quit(status = 1) quit(status = 1)
} }
dates_to_process <- date_obj
} else {
# Date range mode
start_date_obj <- tryCatch(
as.Date(start_date_str, format = "%Y-%m-%d"),
error = function(e) NULL
)
end_date_obj <- tryCatch(
as.Date(end_date_str, format = "%Y-%m-%d"),
error = function(e) NULL
)
if (is.null(start_date_obj) || is.na(start_date_obj)) {
cat(sprintf("[ERROR] Invalid start date format: %s (expected YYYY-MM-DD)\n", start_date_str))
quit(status = 1)
}
if (is.null(end_date_obj) || is.na(end_date_obj)) {
cat(sprintf("[ERROR] Invalid end date format: %s (expected YYYY-MM-DD)\n", end_date_str))
quit(status = 1)
}
if (start_date_obj > end_date_obj) {
cat(sprintf("[ERROR] Start date (%s) is after end date (%s)\n", start_date_str, end_date_str))
quit(status = 1)
}
# Generate sequence of dates
dates_to_process <- seq(start_date_obj, end_date_obj, by = "1 day")
}
# =========================================================================== # ===========================================================================
# BUILD LIST OF FOLDERS & FILES TO DELETE # PROCESS DATES
# =========================================================================== # ===========================================================================
total_dates <- length(dates_to_process)
total_files_deleted <- 0
total_errors <- 0
cat("\n")
cat(strrep("=", 70), "\n")
cat("DELETE TIFFS - SUMMARY\n")
cat(strrep("=", 70), "\n")
cat(sprintf("Project: %s\n", project))
if (total_dates == 1) {
cat(sprintf("Date: %s\n", format(dates_to_process[1], "%Y-%m-%d")))
} else {
cat(sprintf("Date range: %s to %s (%d dates)\n",
format(dates_to_process[1], "%Y-%m-%d"),
format(dates_to_process[total_dates], "%Y-%m-%d"),
total_dates))
}
cat(sprintf("Dry run: %s\n", if (DRY_RUN) "YES" else "NO"))
cat("\n")
# Confirm before proceeding
if (REQUIRE_CONFIRMATION && !DRY_RUN) {
cat("⚠️ This will PERMANENTLY DELETE files from the above date(s)!\n")
cat("Use --no-confirm flag to skip this prompt\n")
# Check if running in interactive mode
if (interactive()) {
response <- readline(prompt = "Type 'yes' to confirm, or anything else to cancel: ")
if (tolower(response) != "yes") {
cat("[CANCELLED] No files deleted\n")
cat(strrep("=", 70), "\n\n")
quit(status = 0)
}
} else {
cat("\n[ERROR] Non-interactive mode detected (running via Rscript)\n")
cat("Cannot prompt for confirmation. Use --no-confirm flag to proceed\n\n")
cat(strrep("=", 70), "\n\n")
quit(status = 1)
}
}
# ===========================================================================
# LOOP THROUGH DATES AND DELETE
# ===========================================================================
cat("Processing...\n\n")
for (date_idx in seq_along(dates_to_process)) {
current_date <- dates_to_process[date_idx]
date_str <- format(current_date, "%Y-%m-%d")
base_path <- file.path("laravel_app", "storage", "app", project) base_path <- file.path("laravel_app", "storage", "app", project)
files_to_delete <- list() files_to_delete <- list()
# FOLDER 1: merged_tif/{DATE}.tif # FOLDER 1: merged_tif/{DATE}.tif
@ -170,76 +305,17 @@ main <- function() {
} }
} }
# =========================================================================== # Delete files for this date
# SUMMARY & CONFIRMATION
# ===========================================================================
cat("\n")
cat(strrep("=", 70), "\n")
cat("DELETE DATE TIFFS - SUMMARY\n")
cat(strrep("=", 70), "\n")
cat(sprintf("Project: %s\n", project))
cat(sprintf("Date: %s\n", date_str))
cat(sprintf("Dry run: %s\n", if (DRY_RUN) "YES" else "NO"))
cat(sprintf("Files to delete: %d\n", length(files_to_delete)))
cat("\n")
if (length(files_to_delete) == 0) {
cat("[INFO] No files found to delete\n")
cat(strrep("=", 70), "\n\n")
quit(status = 0)
}
# Count files by folder type for compact summary
folder_counts <- table(sapply(names(files_to_delete), function(key) strsplit(key, "/")[[1]][1]))
cat("Files to delete by folder:\n")
for (folder in names(folder_counts)) {
cat(sprintf(" %s: %d file%s\n", folder, folder_counts[folder], if (folder_counts[folder] != 1) "s" else ""))
}
cat(sprintf(" Total: %d file%s\n", length(files_to_delete), if (length(files_to_delete) != 1) "s" else ""))
cat("\n")
# Ask for confirmation (unless --no-confirm flag was used)
if (REQUIRE_CONFIRMATION && !DRY_RUN) {
# Check if running in interactive mode
if (!interactive()) {
cat("\n[ERROR] Non-interactive mode detected (running via Rscript)\n")
cat("Cannot prompt for confirmation. Use --no-confirm flag to proceed:\n")
cat(" Rscript DEBUG_remove_date_tiffs.R angata 2026-02-08 --no-confirm\n\n")
cat(strrep("=", 70), "\n\n")
quit(status = 1)
}
cat("⚠️ This will PERMANENTLY DELETE the above files!\n")
cat("Use --no-confirm flag to skip this prompt\n")
# Use readline() for interactive input (only works in interactive R/RStudio)
response <- readline(prompt = "Type 'yes' to confirm, or anything else to cancel: ")
if (tolower(response) != "yes") {
cat("[CANCELLED] No files deleted\n")
cat(strrep("=", 70), "\n\n")
quit(status = 0)
}
}
# ===========================================================================
# DELETE OR DRY-RUN
# ===========================================================================
deleted_count <- 0 deleted_count <- 0
error_count <- 0 error_count <- 0
for (i in seq_along(files_to_delete)) { for (i in seq_along(files_to_delete)) {
folder_key <- names(files_to_delete)[i]
file_path <- files_to_delete[[i]] file_path <- files_to_delete[[i]]
if (!DRY_RUN) { if (!DRY_RUN) {
# file.remove() returns logical; check the return value
success <- tryCatch({ success <- tryCatch({
file.remove(file_path) file.remove(file_path)
}, error = function(e) { }, error = function(e) {
# If unexpected exception, treat as failure
FALSE FALSE
}) })
@ -248,6 +324,21 @@ main <- function() {
} else { } else {
error_count <- error_count + 1 error_count <- error_count + 1
} }
} else {
deleted_count <- length(files_to_delete)
}
}
total_files_deleted <- total_files_deleted + deleted_count
total_errors <- total_errors + error_count
# Progress indicator (every 5 dates or on last date)
if (total_dates == 1 || date_idx %% 5 == 0 || date_idx == total_dates) {
if (DRY_RUN) {
cat(sprintf("[%d/%d] %s: Would delete %d files\n", date_idx, total_dates, date_str, deleted_count))
} else {
cat(sprintf("[%d/%d] %s: Deleted %d files\n", date_idx, total_dates, date_str, deleted_count))
}
} }
} }
@ -256,14 +347,20 @@ main <- function() {
# =========================================================================== # ===========================================================================
cat("\n") cat("\n")
cat(strrep("=", 70), "\n")
cat("SUMMARY\n")
cat(strrep("=", 70), "\n")
cat(sprintf("Dates processed: %d\n", total_dates))
if (DRY_RUN) { if (DRY_RUN) {
cat(sprintf("[DRY RUN] Would have deleted %d files\n", length(files_to_delete))) cat(sprintf("Files that would be deleted: %d\n", total_files_deleted))
} else { } else {
cat(sprintf("Deleted: %d files\n", deleted_count)) cat(sprintf("Total files deleted: %d\n", total_files_deleted))
if (error_count > 0) { if (total_errors > 0) {
cat(sprintf("Errors: %d files\n", error_count)) cat(sprintf("Errors: %d\n", total_errors))
} }
} }
cat(strrep("=", 70), "\n\n") cat(strrep("=", 70), "\n\n")
quit(status = 0) quit(status = 0)

6
r_app/MANUAL_PIPELINE_RUNNER.R
View file

@ -438,9 +438,9 @@
# rmarkdown::render( # rmarkdown::render(
rmarkdown::render( rmarkdown::render(
"r_app/90_CI_report_with_kpis_agronomic_support.Rmd", "r_app/90_CI_report_with_kpis_agronomic_support.Rmd",
params = list(data_dir = "john", report_date = as.Date("2026-02-04")), params = list(data_dir = "aura", report_date = as.Date("2026-01-01")),
output_file = "SmartCane_Report_agronomic_support_john_2026-02-04.docx", output_file = "SmartCane_Report_agronomic_support_aura_2026-01-01.docx",
output_dir = "laravel_app/storage/app/john/reports" output_dir = "laravel_app/storage/app/aura/reports"
) )
# #
# COMMAND #2 - CANE SUPPLY REPORT (ANGATA, CHEMBA, XINAVANE, ESA): # COMMAND #2 - CANE SUPPLY REPORT (ANGATA, CHEMBA, XINAVANE, ESA):

104
r_app/report_utils.R
View file

@ -73,8 +73,12 @@ create_CI_map <- function(pivot_raster, pivot_shape, pivot_spans, show_legend =
reverse = TRUE reverse = TRUE
)) ))
# Add layout elements # Add layout elements
map <- map + tm_layout(main.title = paste0("Max CI week ", week,"\n", age, " weeks (", age * 7, " days) old"), map <- map + tm_title(text = paste0("Max CI week ", week,"\n", age, " weeks (", age * 7, " days) old"),
main.title.size = 0.7) size = 0.7)
# Add layout configuration to prevent legend rescaling
map <- map + tm_layout(legend.position = c("left", "bottom"),
legend.outside = FALSE,
inner.margins = 0.05)
# Add borders if requested # Add borders if requested
if (borders) { if (borders) {
@ -137,8 +141,12 @@ create_CI_diff_map <- function(pivot_raster, pivot_shape, pivot_spans, show_lege
reverse = TRUE reverse = TRUE
)) ))
# Add layout elements # Add layout elements
map <- map + tm_layout(main.title = paste0("CI change week ", week_1, " - week ", week_2, "\n", age, " weeks (", age * 7, " days) old"), map <- map + tm_title(text = paste0("CI change week ", week_1, " - week ", week_2, "\n", age, " weeks (", age * 7, " days) old"),
main.title.size = 0.7) size = 0.7)
# Add layout configuration to prevent legend rescaling
map <- map + tm_layout(legend.position = c("right", "bottom"),
legend.outside = FALSE,
inner.margins = 0.05)
# Add borders if requested # Add borders if requested
if (borders) { if (borders) {
@ -195,25 +203,23 @@ ci_plot <- function(pivotName,
if (missing(current_ci) || is.null(current_ci)) { if (missing(current_ci) || is.null(current_ci)) {
stop("current_ci is required") stop("current_ci is required")
} }
if (missing(ci_minus_1) || is.null(ci_minus_1)) { # Note: ci_minus_1, ci_minus_2, last_week_diff, three_week_diff are now optional
stop("ci_minus_1 is required") # (may be NULL if historical data is not available for early seasons)
}
if (missing(ci_minus_2) || is.null(ci_minus_2)) {
stop("ci_minus_2 is required")
}
if (missing(last_week_diff) || is.null(last_week_diff)) {
stop("last_week_diff is required")
}
if (missing(three_week_diff) || is.null(three_week_diff)) {
stop("three_week_diff is required")
}
if (missing(harvesting_data) || is.null(harvesting_data)) { if (missing(harvesting_data) || is.null(harvesting_data)) {
stop("harvesting_data is required") stop("harvesting_data is required")
} }
# Warn if critical rasters are missing
if (is.null(ci_minus_1) || is.null(ci_minus_2)) {
safe_log(paste("Warning: Historical CI data missing for field", pivotName, "- will show current week only"), "WARNING")
}
if (is.null(last_week_diff) || is.null(three_week_diff)) {
safe_log(paste("Warning: Difference rasters missing for field", pivotName, "- difference maps skipped"), "WARNING")
}
# Extract pivot shape and age data # Extract pivot shape and age data
tryCatch({ tryCatch({
pivotShape <- field_boundaries %>% terra::subset(field %in% pivotName) %>% sf::st_transform(terra::crs(current_ci)) pivotShape <- field_boundaries %>% dplyr::filter(field %in% pivotName) %>% sf::st_transform(terra::crs(current_ci))
age <- harvesting_data %>% age <- harvesting_data %>%
dplyr::filter(field %in% pivotName) %>% dplyr::filter(field %in% pivotName) %>%
sort("year") %>% sort("year") %>%
@ -247,33 +253,69 @@ ci_plot <- function(pivotName,
sf::st_transform(sf::st_crs(pivotShape)) %>% sf::st_transform(sf::st_crs(pivotShape)) %>%
dplyr::filter(field %in% pivotName) dplyr::filter(field %in% pivotName)
# Create the maps for different timepoints # Create maps conditionally based on data availability
CImap_m2 <- create_CI_map(singlePivot_m2, AllPivots2, joined_spans2, # Always create current week map (required)
show_legend = TRUE, legend_is_portrait = TRUE,
week = week_minus_2, age = age - 2, borders = borders, colorblind = colorblind_friendly)
CImap_m1 <- create_CI_map(singlePivot_m1, AllPivots2, joined_spans2,
show_legend = FALSE, legend_is_portrait = FALSE,
week = week_minus_1, age = age - 1, borders = borders, colorblind = colorblind_friendly)
CImap <- create_CI_map(singlePivot, AllPivots2, joined_spans2, CImap <- create_CI_map(singlePivot, AllPivots2, joined_spans2,
show_legend = FALSE, legend_is_portrait = FALSE, show_legend = FALSE, legend_is_portrait = FALSE,
week = week, age = age, borders = borders, colorblind = colorblind_friendly) week = week, age = age, borders = borders, colorblind = colorblind_friendly)
# Create difference maps - only show legend on the second one to avoid redundancy
# Create historical maps only if data is available
maps_to_arrange <- list(CImap)
widths_to_use <- c(1)
field_heading_note <- ""
# Try to create 2-week ago map
if (!is.null(singlePivot_m2)) {
CImap_m2 <- create_CI_map(singlePivot_m2, AllPivots2, joined_spans2,
show_legend = TRUE, legend_is_portrait = TRUE,
week = week_minus_2, age = age - 2, borders = borders, colorblind = colorblind_friendly)
maps_to_arrange <- c(list(CImap_m2), maps_to_arrange)
widths_to_use <- c(0.4, widths_to_use)
}
# Try to create 1-week ago map
if (!is.null(singlePivot_m1)) {
CImap_m1 <- create_CI_map(singlePivot_m1, AllPivots2, joined_spans2,
show_legend = FALSE, legend_is_portrait = FALSE,
week = week_minus_1, age = age - 1, borders = borders, colorblind = colorblind_friendly)
maps_to_arrange <- c(maps_to_arrange, list(CImap_m1))
widths_to_use <- c(widths_to_use, 0.3)
}
# Try to create 1-week difference map
if (!is.null(abs_CI_last_week)) {
CI_max_abs_last_week <- create_CI_diff_map(abs_CI_last_week, AllPivots2, joined_spans2, CI_max_abs_last_week <- create_CI_diff_map(abs_CI_last_week, AllPivots2, joined_spans2,
show_legend = FALSE, legend_is_portrait = FALSE, show_legend = FALSE, legend_is_portrait = FALSE,
week_1 = week, week_2 = week_minus_1, age = age, borders = borders, colorblind = colorblind_friendly) week_1 = week, week_2 = week_minus_1, age = age, borders = borders, colorblind = colorblind_friendly)
maps_to_arrange <- c(maps_to_arrange, list(CI_max_abs_last_week))
widths_to_use <- c(widths_to_use, 0.3)
}
# Try to create 3-week difference map
if (!is.null(abs_CI_three_week)) {
CI_max_abs_three_week <- create_CI_diff_map(abs_CI_three_week, AllPivots2, joined_spans2, CI_max_abs_three_week <- create_CI_diff_map(abs_CI_three_week, AllPivots2, joined_spans2,
show_legend = TRUE, legend_is_portrait = TRUE, show_legend = TRUE, legend_is_portrait = TRUE,
week_1 = week, week_2 = week_minus_3, age = age, borders = borders, colorblind = colorblind_friendly) week_1 = week, week_2 = week_minus_3, age = age, borders = borders, colorblind = colorblind_friendly)
# Arrange the maps with equal widths maps_to_arrange <- c(maps_to_arrange, list(CI_max_abs_three_week))
tst <- tmap_arrange(CImap_m2, CImap_m1, CImap, CI_max_abs_last_week, CI_max_abs_three_week, widths_to_use <- c(widths_to_use, 0.4)
nrow = 1, widths = c(0.23, 0.18, 0.18, 0.18, 0.23)) }
# Normalize widths to sum to 1
widths_to_use <- widths_to_use / sum(widths_to_use)
# Add note if historical data is limited
if (length(maps_to_arrange) == 1) {
field_heading_note <- " (Current week only - historical data not yet available)"
} else if (length(maps_to_arrange) < 5) {
field_heading_note <- " (Limited historical data)"
}
# Arrange the maps with normalized widths
tst <- do.call(tmap_arrange, c(maps_to_arrange, list(nrow = 1, widths = widths_to_use)))
# Output heading and map to R Markdown # Output heading and map to R Markdown
age_months <- round(age / 4.348, 1) age_months <- round(age / 4.348, 1)
cat(paste("## Field", pivotName, "-", age, "weeks/", age_months, "months after planting/harvest", "\n\n")) cat(paste("## Field", pivotName, "-", age, "weeks/", age_months, "months after planting/harvest", field_heading_note, "\n\n"))
print(tst) print(tst)
}, error = function(e) { }, error = function(e) {