Set up Dockerfile for running the R script

.gitignore

@@ -143,3 +143,5 @@ version.py
 # pixi environments
 .pixi
 *.egg-info
+
+outputs/

DESCRIPTION

@@ -20,7 +20,8 @@ Imports:
     pbapply,
     furrr,
     parallel,
-    logger
+    logger,
+    tidyverse
 Suggests:
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

Dockerfile

@@ -0,0 +1,39 @@
+FROM rocker/r-ver:4.2.0
+
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    libgit2-dev \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libfontconfig1-dev \
+    zlib1g-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libfreetype6-dev \
+    libpng-dev \
+    libtiff5-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libproj-dev \
+    libudunits2-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN Rscript -e "install.packages('terra', repos='https://cloud.r-project.org')"
+RUN Rscript -e "install.packages('remotes', repos='https://cloud.r-project.org')"
+RUN Rscript -e "install.packages('devtools', repos='https://cloud.r-project.org', dependencies=TRUE)"
+
+WORKDIR /home/biodiversity-horizons
+
+COPY DESCRIPTION .
+COPY NAMESPACE .
+
+COPY R ./R
+
+RUN Rscript -e "remotes::install_local('.', dependencies=TRUE)"
+
+COPY scripts ./scripts
+
+# By default, run the script with "data-raw/" as path, "multisession", and (availableCores()-1) workers.
+# The user can override by passing in arguments at runtime, e.g.:
+CMD ["Rscript", "scripts/VISS_Sample_Data.R", "data-raw/", "multisession"]

scripts/VISS_Sample_Data.R

@@ -7,21 +7,49 @@ library(pbapply)
 library(sf)
 library(parallel)
 library(logger)
+library(future)
 
 # 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/"
+# Parse command-line arguments
+args <- commandArgs(trailingOnly = TRUE)
+
+# Set Data path
+if (length(args) >= 1) {
+  path <- args[1]
+} else {
+  # Default to data-raw/ if not provided
+  if (interactive()) {
+    path <- "data-raw/"
+    message("No data path argument provided. Using default: ", path)
+  } else {
+    stop("No data folder argument provided.\nUsage: Rscript VISS_Sample_Data.R /path/to/data [plan_type] [workers]")
+  }
+}
 log_info("Data path set to: {path}")
 
+# Plan type
+if (length(args) >= 2) {
+  plan_type <- args[2]
+} else {
+  plan_type <- "multisession"
+}
+
+# Number of workers
+if (length(args) >= 3) {
+  workers <- as.numeric(args[3])
+} else {
+  workers <- availableCores() - 1
+}
+
 # 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"))
+historical_climate <- readRDS(file.path(path, "historical_climaate_data.rds"))
+future_climate     <- readRDS(file.path(path, "future_climaate_data.rds"))
+grid               <- readRDS(file.path(path, "grid.rds"))
+primates_shp       <- readRDS(file.path(path, "primates_shapefiles.rds"))
 log_info("Data loaded successfully.")
 
 # Log data details
@@ -58,8 +86,8 @@ 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)
+log_info("Computing thermal limits for each species using {workers} workers and a '{plan_type}' parallelization plan.")
+plan(plan_type, workers = workers)
 
 niche_limits <- future_map_dfr(
   primates_range_data,
@@ -72,7 +100,7 @@ log_info("Thermal limit computation complete.")
 # 4. Calculate exposure
 log_info("Calculating exposure for each species.")
 exposure_list <- future_map(
-  1:length(primates_range_data),
+  seq_along(primates_range_data),
   ~ exposure(.x, primates_range_data, future_climate_df, niche_limits),
   .progress = TRUE
 )
@@ -84,11 +112,10 @@ 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 < 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.")
+cl <- future::makeClusterPSOCK(workers, port = 12000, outfile = NULL, verbose = TRUE)
 clusterEvalQ(cl, library(dplyr))
 clusterExport(cl, "exposure_times")
 
@@ -110,14 +137,25 @@ res_final <- res_final %>%
   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)
 
+# 6. Save the output to "outputs/" directory
+output_dir <- "outputs"
+if (!dir.exists(output_dir)) {
+  dir.create(output_dir, recursive = TRUE)
+}
+
+saveRDS(
+  res_final,
+  file.path(output_dir, "res_final.rds")
+)
+log_info("Saved results to {file.path(output_dir, 'res_final.rds')}")
+
 # Reset parallel processing plan
 future::plan("sequential")
 log_info("VISS Sample Data script completed successfully.")