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{
"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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"file_extension": ".py",
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"name": "python",
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