Add logging to scripts/VISS_Sample_Data

scripts/VISS_Sample_Data.R

@@ -6,30 +6,59 @@ library(exactextractr)
 library(pbapply)
 library(sf)
 library(parallel)
+library(logger)
+
+# Initialize logger
+log_threshold(INFO)
+log_info("Starting VISS Sample Data script.")
 
 # Set the folder containing the files as the working directory
 path <- "data-raw/"
+log_info("Data path set to: {path}")
 
 # Load data
+log_info("Loading data...")
 historical_climate <- readRDS(paste0(path, "historical_climaate_data.rds"))
 future_climate <- readRDS(paste0(path, "future_climaate_data.rds"))
 grid <- readRDS(paste0(path, "grid.rds"))
 primates_shp <- readRDS(paste0(path, "primates_shapefiles.rds"))
+log_info("Data loaded successfully.")
+
+# Log data details
+log_info("Historical climate data has {nrow(historical_climate)} rows.")
+log_info("Future climate data has {nrow(future_climate)} rows.")
+log_info("Grid data contains {nrow(grid)} rows.")
+log_info("Primates shapefile contains {nrow(primates_shp)} rows.")
 
+# Load all functions from the package
+log_info("Loading package functions...")
 devtools::load_all()
+log_info("Package functions loaded successfully.")
 
 # 1. Transform the distribution polygons to match the grid
+log_info("Transforming distribution polygons to match the grid.")
 primates_range_data <- prepare_range(primates_shp, grid)
+log_info("Processed {length(primates_range_data)} species.")
 
 # 2. Extract climate data using the grid
+log_info("Extracting historical climate data...")
 historical_climate_df <- extract_climate_data(historical_climate, grid)
+log_info(
+  "Historical climate extraction done: {nrow(historical_climate_df)} rows."
+)
+
+log_info("Extracting future climate data...")
 future_climate_df <- extract_climate_data(future_climate, grid)
+log_info("Future climate extraction done: {nrow(future_climate_df)} rows.")
 
 # Rename columns
+log_info("Renaming columns for climate data.")
 colnames(historical_climate_df) <- c("world_id", 1850:2014)
 colnames(future_climate_df) <- c("world_id", 2015:2100)
+log_info("Column renaming complete.")
 
 # 3. Compute the thermal limits for each species
+log_info("Computing thermal limits for each species.")
 plan("multisession", workers = availableCores() - 1)
 
 niche_limits <- future_map_dfr(
@@ -38,20 +67,28 @@ niche_limits <- future_map_dfr(
   .id = "species",
   .progress = TRUE
 )
+log_info("Thermal limit computation complete.")
 
 # 4. Calculate exposure
-plan("multisession", workers = availableCores() - 1)
-exposure_list <- future_map(1:length(primates_range_data), ~ exposure(.x, primates_range_data, future_climate_df, niche_limits), .progress = TRUE) #nolint
+log_info("Calculating exposure for each species.")
+exposure_list <- future_map(
+  1:length(primates_range_data),
+  ~ exposure(.x, primates_range_data, future_climate_df, niche_limits),
+  .progress = TRUE
+)
 names(exposure_list) <- names(primates_range_data)
+log_info("Exposure calculation complete.")
 
 # 5. Calculate exposure times
+log_info("Calculating exposure times.")
 exposure_df <- exposure_list %>%
   bind_rows() %>%
   mutate(sum = rowSums(select(., starts_with("2")))) %>%
-  filter(sum < 82) %>%  # Select only cells with less than 82 suitable years
+  filter(sum < 82) %>%  # Select only cells with < 82 suitable years
   select(-sum)
 
 cl <- makeCluster(availableCores() - 1)
+log_info("Parallel cluster created with {availableCores() - 1} workers.")
 clusterEvalQ(cl, library(dplyr))
 clusterExport(cl, "exposure_times")
 
@@ -64,16 +101,23 @@ res_final <- pbapply(
       original_state = 1,
       consecutive_elements = 5
     )
-  }
+  },
+  cl = cl
 )
 
 res_final <- res_final %>%
   bind_rows() %>%
   na.omit()
 
+log_info("Exposure time calculation complete.")
+
 stopCluster(cl)
+log_info("Cluster stopped.")
 
 # Final data frame with exposure times for each species at each grid cell
+log_info("Final data frame contains {nrow(res_final)} rows.")
 print(res_final)
 
+# Reset parallel processing plan
 future::plan("sequential")
+log_info("VISS Sample Data script completed successfully.")