Generate_Probability_Results.ipynb

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  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "dd419e6d",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import sys\n",
    "sys.path.insert(1, os.path.abspath(os.path.join(os.getcwd(), '../GillesPy2')))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "03f8aa88",
   "metadata": {},
   "outputs": [],
   "source": [
    "import json\n",
    "import pickle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "0c0a2ece",
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_parameters(job):\n",
    "    parameters = []\n",
    "    for param in job.params:\n",
    "        parameters.append({\n",
    "            'name': param['parameter'],\n",
    "            'range': param['range']\n",
    "        })\n",
    "    return parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "d9c77db4",
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_probs(job):\n",
    "    eliminations = {}\n",
    "    extinctions = {}\n",
    "    for key, sim in job.results.items():\n",
    "        eliminations[key] = sim.dftd_elimination\n",
    "        extinctions[key] = sim.devil_extinction\n",
    "    return eliminations, extinctions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "93619818",
   "metadata": {},
   "outputs": [],
   "source": [
    "def generate_prob_data_file(filename):\n",
    "    file_map = {\n",
    "        \"ParameterSweeps/DevilsDFTD2StageInfectionWithImmunityState.p\": \"Fig6A-B-data.json\",\n",
    "        \"ParameterSweeps/DevilsDFTD2StageInfectionWithVaccinationState.p\": \"Fig11A-C-data.json\",\n",
    "        \"ParameterSweeps/DevilsDFTD2StageInfectionWithCullingState.p\": \"Fig8-data.json\",\n",
    "        \"ParameterSweeps/DevilsDFTD2StageInfectionWithVaccinationAndCullingState.p\": \"Fig13A-F-data.json\"\n",
    "    }\n",
    "    try:\n",
    "        with open(filename, \"rb\") as state_file:\n",
    "            job = pickle.load(state_file)['job']\n",
    "        eliminations, extinctions = get_probs(job)\n",
    "        data = {\n",
    "            'parameters': get_parameters(job),\n",
    "            'elimination_probs': eliminations,\n",
    "            'extinction_probs': extinctions\n",
    "        }\n",
    "    except FileNotFoundError as err:\n",
    "        print(f\"{filename} is not currently available\")\n",
    "        return\n",
    "    \n",
    "    dst = os.path.join(\"figure_data\", file_map[filename])\n",
    "    with open(dst, \"w\") as data_file:\n",
    "        json.dump(data, data_file, sort_keys=True, indent=4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "a8b3ae94",
   "metadata": {},
   "outputs": [],
   "source": [
    "filenames = [\n",
    "    \"ParameterSweeps/DevilsDFTD2StageInfectionWithImmunityState.p\",\n",
    "    \"ParameterSweeps/DevilsDFTD2StageInfectionWithVaccinationState.p\",\n",
    "    \"ParameterSweeps/DevilsDFTD2StageInfectionWithCullingState.p\",\n",
    "    \"ParameterSweeps/DevilsDFTD2StageInfectionWithVaccinationAndCullingState.p\"\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "16d7bab1",
   "metadata": {},
   "outputs": [],
   "source": [
    "for filename in filenames:\n",
    "    generate_prob_data_file(filename)"
   ]
  }
 ],
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