#!/bin/bash

weeks_ago="0"
data_dir="chemba"

# Parse command line arguments
for arg in "$@"; do
    case $arg in
        --weeks_ago=*)
            weeks_ago="${arg#*=}"
            ;;
        --data_dir=*)
            data_dir="${arg#*=}"
            ;;
        *)
            echo "Unknown option: $arg"
            exit 1
            ;;
    esac
    shift
done

echo "Weeks ago: $weeks_ago"

# Check if required arguments are set
if [ -z "$weeks_ago" ] || [ -z "$data_dir" ]; then
    echo "Missing arguments. Use: build_mosiac.sh --weeks_ago=3 --data_dir=chemba"
    exit 1
fi

echo 2_CI_data_prep.R $weeks_ago $data_dir

cd ../r_app
Rscript 2_CI_data_prep.R $weeks_ago $data_dir