api options

api_options.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# current API updated to use parameters instead"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ema_workbench.em_framework import (ModelEnsemble, RealParameter,\n",
    "                                        TimeSeriesOutcome)\n",
    "from ema_workbench.util import ema_logging, save_results\n",
    "from ema_workbench.connectors.vensim import VensimModelStructureInterface \n",
    "\n",
    "class FluModel(VensimModelStructureInterface):\n",
    "    #base case model\n",
    "    model_file = r'\\FLUvensimV1basecase.vpm'\n",
    "        \n",
    "    #outcomes\n",
    "    outcomes = [TimeSeriesOutcome('deceased population region 1'),\n",
    "                TimeSeriesOutcome('infected fraction R1')]\n",
    " \n",
    "    #Plain Parametric Uncertainties \n",
    "    uncertainties = [\n",
    "        RealParameter(\"additional seasonal immune population fraction R1\", \n",
    "                        0, 0.5),\n",
    "        RealParameter(\"additional seasonal immune population fraction R2\",\n",
    "                        0, 0.5),\n",
    "        RealParameter(\"fatality ratio region 1\", 0.0001, 0.1),\n",
    "        RealParameter(\"fatality rate region 2\", 0.0001, 0.1),\n",
    "        RealParameter(\"initial immune fraction of the population of region 1\",\n",
    "                        0, 0.5),\n",
    "        RealParameter(\"initial immune fraction of the population of region 2\",\n",
    "                        0, 0.5),\n",
    "        RealParameter(\"normal interregional contact rate\", 0, 0.9),\n",
    "        RealParameter(\"permanent immune population fraction R1\", 0, 0.5),\n",
    "        RealParameter(\"permanent immune population fraction R2\", 0, 0.5),\n",
    "        RealParameter(\"recovery time region 1\", 0.1, 0.75),\n",
    "        RealParameter(\"recovery time region 2\", 0.1, 0.75),\n",
    "        RealParameter(\"susceptible to immune population delay time region 1\", \n",
    "                        0.5,2),\n",
    "        RealParameter(\"susceptible to immune population delay time region 2\",\n",
    "                        0.5,2),\n",
    "        RealParameter(\"root contact rate region 1\", 0.01, 5),\n",
    "        RealParameter(\"root contact ratio region 2\", 0.01, 5),\n",
    "        RealParameter(\"infection ratio region 1\", 0, 0.15),\n",
    "        RealParameter(\"infection rate region 2\", 0, 0.15),\n",
    "        RealParameter(\"normal contact rate region 1\", 10, 100),\n",
    "        RealParameter(\"normal contact rate region 2\", 10, 200)]\n",
    "\n",
    "if __name__ == \"__main__\":\n",
    "    ema_logging.log_to_stderr(ema_logging.INFO)\n",
    "        \n",
    "    model = FluModel(r'./models/flu', \"flucase\")\n",
    "    ensemble = ModelEnsemble()\n",
    "    ensemble.model_structure = model\n",
    "        \n",
    "    #turn on parallel processing\n",
    "    ensemble.parallel = True \n",
    "    \n",
    "    # run 1000 experiments\n",
    "    nr_runs = 1000\n",
    "    results = ensemble.perform_experiments(nr_runs)\n",
    "    \n",
    "    # save the results\n",
    "    save_results(results, r'./data/{} flu cases.tar.gz'.format(nr_runs))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# alternative API proposal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ema_workbench.em_framework import (ModelEnsemble, RealParameter,\n",
    "                                        TimeSeriesOutcome)\n",
    "from ema_workbench.util import ema_logging, save_results\n",
    "from ema_workbench.connectors.vensim import VensimModelStructureInterface \n",
    "\n",
    "if __name__ == \"__main__\":\n",
    "\n",
    "    ema_logging.log_to_stderr(ema_logging.INFO)\n",
    "    \n",
    "    # model specification\n",
    "    msi = VensimModelStructureInterface(\"flucase\", wd=r'./models/flu')\n",
    "    msi.model_file = r'\\FLUvensimV1basecase.vpm'\n",
    "    msi.outcomes = [TimeSeriesOutcome('deceased population region 1'),\n",
    "                    TimeSeriesOutcome('infected fraction R1')]\n",
    "    msi.uncertainties = [\n",
    "        RealParameter(\"additional seasonal immune population fraction R1\", \n",
    "                        0, 0.5),\n",
    "        RealParameter(\"additional seasonal immune population fraction R2\",\n",
    "                        0, 0.5),\n",
    "        RealParameter(\"fatality ratio region 1\", 0.0001, 0.1),\n",
    "        RealParameter(\"fatality rate region 2\", 0.0001, 0.1),\n",
    "        RealParameter(\"initial immune fraction of the population of region 1\",\n",
    "                        0, 0.5),\n",
    "        RealParameter(\"initial immune fraction of the population of region 2\",\n",
    "                        0, 0.5),\n",
    "        RealParameter(\"normal interregional contact rate\", 0, 0.9),\n",
    "        RealParameter(\"permanent immune population fraction R1\", 0, 0.5),\n",
    "        RealParameter(\"permanent immune population fraction R2\", 0, 0.5),\n",
    "        RealParameter(\"recovery time region 1\", 0.1, 0.75),\n",
    "        RealParameter(\"recovery time region 2\", 0.1, 0.75),\n",
    "        RealParameter(\"susceptible to immune population delay time region 1\", \n",
    "                        0.5,2),\n",
    "        RealParameter(\"susceptible to immune population delay time region 2\",\n",
    "                        0.5,2),\n",
    "        RealParameter(\"root contact rate region 1\", 0.01, 5),\n",
    "        RealParameter(\"root contact ratio region 2\", 0.01, 5),\n",
    "        RealParameter(\"infection ratio region 1\", 0, 0.15),\n",
    "        RealParameter(\"infection rate region 2\", 0, 0.15),\n",
    "        RealParameter(\"normal contact rate region 1\", 10, 100),\n",
    "        RealParameter(\"normal contact rate region 2\", 10, 200)]\n",
    "\n",
    "    # setup ensemble\n",
    "    ensemble = ModelEnsemble()\n",
    "    ensemble.model_structure = msi\n",
    "    \n",
    "    #turn on parallel processing\n",
    "    ensemble.parallel = True \n",
    "    \n",
    "    # run 1000 experiments\n",
    "    nr_runs = 1000\n",
    "    results = ensemble.perform_experiments(nr_runs)\n",
    "    \n",
    "    # save the results\n",
    "    save_results(results, r'./data/{} flu cases.tar.gz'.format(nr_runs))\n",
    "\n"
   ]
  }
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