sc 114 library formatting and cleaning

r_app/10_create_per_field_tiffs.R

@@ -50,9 +50,9 @@
 #
 # ============================================================================
 
-
+# Spatial data handling
-library(terra)
+library(terra)  # For raster operations (reading/writing GeoTIFFs, cropping to field boundaries)
-library(sf)
+library(sf)     # For spatial operations (reading field boundaries GeoJSON, masking)
 
 # ==============================================================================
 # LOAD CENTRALIZED PARAMETERS & PATHS

r_app/20_ci_extraction.R

@@ -57,14 +57,17 @@
 # 1. Load required packages
 # -----------------------
 suppressPackageStartupMessages({
-  library(sf)
+  # Spatial data handling
-  library(terra)
+  library(sf)        # For reading/manipulating field boundaries (GeoJSON)
-  library(tidyverse)
+  library(terra)     # For raster operations (CI extraction from TIFFs)
-  library(lubridate)
+  
-  library(readxl)
+  # Data manipulation
-  library(here)
+  library(tidyverse) # For dplyr, ggplot2, readr (data wrangling and visualization)
-  library(furrr)
+  library(lubridate) # For date/time operations (parsing satellite dates)
-  library(future)
+  
+  # File I/O
+  library(readxl)    # For reading harvest.xlsx (harvest dates for field mapping)
+  library(here)      # For relative path resolution (platform-independent file paths)
 })
 
 # 2. Process command line arguments

r_app/21_convert_ci_rds_to_csv.R

@@ -50,10 +50,13 @@
 # ============================================================================
 
 suppressPackageStartupMessages({
-  library(tidyverse)
+  # File path handling
-  library(lubridate)
+  library(here)       # For relative path resolution (platform-independent file paths)
-  library(zoo)
+  
-  library(here)
+  # Data manipulation
+  library(tidyverse)  # For dplyr, readr (data wrangling and CSV I/O)
+  library(lubridate)  # For date/time operations (DOY calculation)
+  library(zoo)        # For zoo objects (gap filling, rolling operations)
 })
 
 # ============================================================================

r_app/30_interpolate_growth_model.R

@@ -53,9 +53,12 @@
 # 1. Load required packages
 # -----------------------
 suppressPackageStartupMessages({
-  library(tidyverse)
+  # File path handling
-  library(lubridate)
+  library(here)       # For relative path resolution (platform-independent file paths)
-  library(here)
+  
+  # Data manipulation
+  library(tidyverse)  # For dplyr (data wrangling, grouping, mutating)
+  library(lubridate)  # For date/time operations (date arithmetic, ISO week extraction)
 })
 
 # =============================================================================

r_app/40_mosaic_creation.R

@@ -60,11 +60,16 @@
 # 1. Load required packages
 # -----------------------
 suppressPackageStartupMessages({
-  library(sf)
+  # File path handling
-  library(terra)
+  library(here)       # For relative path resolution (platform-independent file paths)
-  library(tidyverse)
+  
-  library(lubridate)
+  # Spatial data handling
-  library(here)
+  library(sf)         # For spatial operations (field boundary masking)
+  library(terra)      # For raster operations (reading/writing/stacking GeoTIFFs)
+  
+  # Data manipulation
+  library(tidyverse)  # For dplyr, readr (data wrangling)
+  library(lubridate)  # For date/time operations (week extraction, date formatting)
 })
 
 # 2. Process command line arguments and run mosaic creation

r_app/80_calculate_kpis.R

@@ -127,23 +127,26 @@ WEEKS_FOR_CV_TREND_LONG <- 8
 # ============================================================================
 
 suppressPackageStartupMessages({
-  library(here)
+  # File path handling
-  library(sf)
+  library(here)      # For relative path resolution (platform-independent file paths)
-  library(terra)
+  
-  library(dplyr)
+  # Spatial data handling
-  library(tidyr)
+  library(sf)        # For reading/manipulating field boundaries (GeoJSON)
-  library(lubridate)
+  library(terra)     # For raster operations (reading mosaic TIFFs)
-  library(readr)
+  
-  library(readxl)
+  # Data manipulation
-  library(writexl)
+  library(dplyr)     # For data wrangling (filter, mutate, group_by, summarize)
-  library(purrr)
+  library(tidyr)     # For data reshaping (pivot_longer, pivot_wider, gather)
-  library(furrr)
+  library(lubridate) # For date/time operations (week extraction, date arithmetic)
-  library(future)
+  
-  library(caret)
+  # File I/O
-  library(CAST)
+  library(readr)     # For reading CSV files (harvest predictions from Python)
-  library(randomForest)
+  library(readxl)    # For reading harvest.xlsx (harvest dates for field mapping)
+  library(writexl)   # For writing Excel outputs (KPI summary tables)
+  
+  # ML/Analysis (optional - only for harvest model inference)
   tryCatch({
-    library(torch)
+    library(torch)   # For PyTorch model inference (harvest readiness prediction)
   }, error = function(e) {
     message("Note: torch package not available - harvest model inference will be skipped")
   })

r_app/90_CI_report_with_kpis_simple.Rmd

@@ -38,21 +38,26 @@ reporting_script <- TRUE
 
 # Load all packages at once with suppressPackageStartupMessages
 suppressPackageStartupMessages({
-  library(here)
+  # File path handling
-  library(sf)
+  library(here)       # For relative path resolution (platform-independent file paths)
-  library(terra)
+  
-  library(tidyverse)
+  # Spatial data handling
-  library(tmap)
+  library(sf)         # For reading/manipulating field boundaries (GeoJSON)
-  library(lubridate)
+  library(terra)      # For raster operations (reading mosaic TIFFs for visualization)
-  library(zoo)
+  
-  library(rsample)
+  # Data manipulation
-  library(caret)
+  library(tidyverse)  # For dplyr, ggplot2, tidyr (data wrangling and visualization)
-  library(randomForest)
+  library(tidyr)      # For data reshaping (pivot_longer, pivot_wider for wide-to-long conversion)
-  library(CAST)
+  library(lubridate)  # For date/time operations (week extraction, date formatting)
-  library(knitr)
+  library(zoo)        # For zoo objects (time series manipulation, na.locf for gap filling)
-  library(tidyr)
+  
-  library(flextable)
+  # Visualization
-  library(officer)
+  library(tmap)       # For interactive maps (field boundary visualization)
+  
+  # Reporting
+  library(knitr)      # For R Markdown document generation (code execution and output)
+  library(flextable)  # For formatted tables in Word output (professional table styling)
+  library(officer)    # For Word document manipulation (custom formatting, headers, footers)
 })
 
 # Load custom utility functions

r_app/91_CI_report_with_kpis_Angata.Rmd

@@ -38,20 +38,25 @@ reporting_script <- TRUE
 
 # Load all packages at once with suppressPackageStartupMessages
 suppressPackageStartupMessages({
-  library(here)
+  # File path handling
-  library(sf)
+  library(here)       # For relative path resolution (platform-independent file paths)
-  library(terra)
+  
-  library(tidyverse)
+  # Spatial data handling
-  library(tmap)
+  library(sf)         # For reading/manipulating field boundaries (GeoJSON)
-  library(lubridate)
+  library(terra)      # For raster operations (reading mosaic TIFFs for visualization)
-  library(zoo)
+  
-  library(rsample)
+  # Data manipulation
-  library(caret)
+  library(tidyverse)  # For dplyr, ggplot2, tidyr (data wrangling and visualization)
-  library(randomForest)
+  library(tidyr)      # For data reshaping (pivot_longer, pivot_wider for wide-to-long conversion)
-  library(CAST)
+  library(lubridate)  # For date/time operations (week extraction, date formatting)
-  library(knitr)
+  library(zoo)        # For zoo objects (time series manipulation, na.locf for gap filling)
-  library(tidyr)
+  
-  library(flextable)
+  # Visualization
+  library(tmap)       # For interactive maps (field boundary visualization)
+  
+  # Reporting
+  library(knitr)      # For R Markdown document generation (code execution and output)
+  library(flextable)  # For formatted tables in Word output (professional table styling)
 })
 
 # Load custom utility functions