Merge pull request #432 from uncharted-aske/feature/add-computed-meas…

…ures-on-chime-models

Add computed measures on chime models and hard-code fitted params

client/src/services/DonuService.ts

@@ -201,6 +201,28 @@ export const getModelInterface = async (model: Model.Model, selectedModelGraphTy
 
  const response = await callDonuCache(request);
  if (response.status === Donu.ResponseStatus.success) {
+ if (selectedModelGraphType === Model.GraphTypes.PetriNetClassic) {
+ const result = response?.result as Donu.ModelDefinition;
+ if (modelGraph.model === 'SimpleSIR_metadata_gromet_PetriNetClassic.json') {
+ result.measures.push({
+ uid: 'beta*S*I',
+ value_type: 'float',
+ metadata: {
+ name: 'Daily New Infected',
+ type: 'float',
+ },
+ });
+ } else if (modelGraph.model === 'chime+.json') {
+ result.measures.push({
+ uid: 'computed',
+ value_type: 'float',
+ metadata: {
+ name: 'Daily New Infected',
+ type: 'float',
+ },
+ });
+ }
+ }
  /** TODO
  * This is a temporary mock up for Demonstration purposes.
  * The DONU API needs to be clearer on which outputs can be selected programatically.
@@ -276,6 +298,11 @@ export const getModelResult = async (
  step: config.step,
  };
 
+ if (selectedModelGraphType === Model.GraphTypes.PetriNetClassic) {
+ // HACK: Algebraic Julia doesn't work when value types are wrong
+ request['sim-type'] = Donu.SimulationType.GSL;
+ }
+
  /** TODO
  * This is a temporary mock up for Demonstration purposes.
  * The DONU API needs to be clearer on which outputs can be selected programatically.
@@ -303,7 +330,44 @@ export const getModelResult = async (
 
  const response = await callDonuCache(request);
  if (response.status === Donu.ResponseStatus.success) {
- return response?.result as Donu.SimulationResponse ?? null;
+ const result = response.result as Donu.SimulationResponse;
+ if (selectedModelGraphType === Model.GraphTypes.PetriNetClassic) {
+ if (modelGraph.model === 'SimpleSIR_metadata_gromet_PetriNetClassic.json') {
+ const beta = parameters['J:beta_rate'] as unknown as number;
+ const I = result[0].values['J:I'];
+ const S = result[0].values['J:S'];
+ const dailyNewInfectedValues = [];
+ for (let i = 0; i < result[0].times.length; i++) {
+ dailyNewInfectedValues.push(beta * S[i] * I[i]);
+ }
+ result[0].values['beta*S*I'] = dailyNewInfectedValues;
+ } else if (modelGraph.model === 'chime+.json') {
+ // const beta = parameters['J:beta_rate'] as unknown as number;
+ // const I = result[0].values['J:I'];
+ const S = result[0].values['J:S'];
+ const I_U = result[0].values['J:I_U'];
+ const I_V = result[0].values['J:I_V'];
+ const V = result[0].values['J:V'];
+
+ // eslint-disable-next-line camelcase
+ const inf_uu = parameters['J:inf_uu_rate'] as unknown as number;
+ // eslint-disable-next-line camelcase
+ const inf_vu = parameters['J:inf_vu_rate'] as unknown as number;
+ // eslint-disable-next-line camelcase
+ const inf_uv = parameters['J:inf_uv_rate'] as unknown as number;
+ // eslint-disable-next-line camelcase
+ const inf_vv = parameters['J:inf_vv_rate'] as unknown as number;
+
+ const dailyNewInfectedValues = [];
+ for (let i = 0; i < result[0].times.length; i++) {
+ // eslint-disable-next-line camelcase
+ dailyNewInfectedValues.push(S[i] * I_U[i] * inf_uu + S[i] * I_V[i] * inf_vu + V[i] * I_U[i] * inf_uv + V[i] * I_V[i] * inf_vv);
+ }
+ result[0].values.computed = dailyNewInfectedValues;
+ }
+ }
+
+ return result;
  } else {
  console.error('[DONU Service] — getModelResult', response.error); // eslint-disable-line no-console
  }
@@ -383,29 +447,19 @@ export const getDatasetResult = async (model: string): Promise<Donu.GetDatasetRe
 
  const response = await callDonuCache(request);
  if (response.status === Donu.ResponseStatus.success) {
- return response.result as Donu.GetDatasetResponse;
+ const result = _.cloneDeep(response.result) as Donu.GetDatasetResponse;
+ // HACK
+ if (model === 'GDA-Infections-FL.json') {
+ const dailyCases = result.columns.find(c => c.name === 'daily_cases');
+ dailyCases.values = dailyCases.values.slice(25);
+ }
+ return result;
  } else {
  console.error('[DONU Service] — getDatasetResult', response); // eslint-disable-line no-console
  }
 };
 
-// Get Dataset Response output
-// {
-// name: "GDA Infection Data",
-// description: "Infection data for FL",
-// columns: [
-// {
-// values: [0, 1, 2, 3, ...],
-// name: 'date',
-// description: 'date',
-// },
-// {
-// values: [129, 32, 0, 213, ...],
-// name: 'daily_cases',
-// description: 'daily_cases',
-// }
-// ]
-// }
+// Fit Model Measures' to Observational Data
 // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types
 export const fitMeasures = async (data: any, parameters: string[], source: string, type: Donu.Type): Promise<Donu.FitMeasuresResponse> => {
  const request: Donu.Request = {

client/src/views/Simulation/components/ParametersPanel.vue

@@ -253,10 +253,38 @@
  // this.model.modelGraph[0].model,
  // this.model.modelGraph[0].donuType,
  // );
- const fittedParameters = {
- 'J:rec_rate': 0.05,
- 'J:inf_rate': 0.4,
- };
+ let fittedParameters: {
+ [paramUid: string]: number;
+ } = {};
+ if (this.model.metadata?.name === 'CHIME_SIR_Base') {
+ fittedParameters = {
+ 'J:beta_rate': 1.7221469058282074e-7,
+ 'J:gamma_rate': 0.04954677073300576,
+ 'J:S_init': 720130.5394121626,
+ 'J:I_init': 6368.2763686775015,
+ 'J:R_init': 9.999999999999996e-11,
+ };
+ } else if (this.model.metadata?.name === 'CHIME_SVIIvR') {
+ fittedParameters = {
+ 'J:S_init': 874270.0703645574,
+ 'J:I_U_init': 2657.7553778002,
+ 'J:V_init': 45.90865845686915,
+ 'J:R_init': 0.10000000000000002,
+ 'J:I_V_init': 1.5201678216286594,
+ 'J:rec_v_rate': 2.3526228492762642e-5,
+ 'J:inf_vv_rate': 2.6041225138605557e-8,
+ 'J:inf_vu_rate': 2.8956286100930364e-9,
+ 'J:inf_uu_rate': 1.466296766065254e-7,
+ 'J:inf_uv_rate': 1.1577435141227581e-8,
+ 'J:vax_rate': 0.011287926731402404,
+ 'J:rec_u_rate': 1.7081993411296042e-5,
+ };
+ } else {
+ fittedParameters = {
+ 'J:rec_rate': 0.05,
+ 'J:inf_rate': 0.4,
+ };
+ }
 
  Object.entries(fittedParameters).forEach(([pid, value]) => {
  this.parameterValues[pid] = value;