update abm vaccination tutorial

Author: charlie0614

cpp-tutorials/abm/parameter_setter.cpp

@@ -108,44 +108,10 @@ void set_local_parameters(mio::abm::Model& world)
         0.0087 0.0394 0.1417 0.3834 0.7064 0.0447
         0.0292 0.0648 0.1248 0.4179 0.3497 0.1544
     */
-    mio::CustomIndexArray<ScalarType, mio::AgeGroup, mio::AgeGroup> contacts_home(
-        {mio::AgeGroup(n_age_groups), mio::AgeGroup(n_age_groups)}, 0.);
-    contacts_home[{age_group_0_to_4, age_group_0_to_4}]     = 0.4413;
-    contacts_home[{age_group_0_to_4, age_group_5_to_14}]    = 0.0504;
-    contacts_home[{age_group_0_to_4, age_group_15_to_34}]   = 1.2383;
-    contacts_home[{age_group_0_to_4, age_group_35_to_59}]   = 0.8033;
-    contacts_home[{age_group_0_to_4, age_group_60_to_79}]   = 0.0494;
-    contacts_home[{age_group_0_to_4, age_group_80_plus}]    = 0.0017;
-    contacts_home[{age_group_5_to_14, age_group_0_to_4}]    = 0.0485;
-    contacts_home[{age_group_5_to_14, age_group_5_to_14}]   = 0.7616;
-    contacts_home[{age_group_5_to_14, age_group_15_to_34}]  = 0.6532;
-    contacts_home[{age_group_5_to_14, age_group_35_to_59}]  = 1.1614;
-    contacts_home[{age_group_5_to_14, age_group_60_to_79}]  = 0.0256;
-    contacts_home[{age_group_5_to_14, age_group_80_plus}]   = 0.0013;
-    contacts_home[{age_group_15_to_34, age_group_0_to_4}]   = 0.1800;
-    contacts_home[{age_group_15_to_34, age_group_5_to_14}]  = 0.1795;
-    contacts_home[{age_group_15_to_34, age_group_15_to_34}] = 0.8806;
-    contacts_home[{age_group_15_to_34, age_group_35_to_59}] = 0.6413;
-    contacts_home[{age_group_15_to_34, age_group_60_to_79}] = 0.0429;
-    contacts_home[{age_group_15_to_34, age_group_80_plus}]  = 0.0032;
-    contacts_home[{age_group_35_to_59, age_group_0_to_4}]   = 0.0495;
-    contacts_home[{age_group_35_to_59, age_group_5_to_14}]  = 0.2639;
-    contacts_home[{age_group_35_to_59, age_group_15_to_34}] = 0.5189;
-    contacts_home[{age_group_35_to_59, age_group_35_to_59}] = 0.8277;
-    contacts_home[{age_group_35_to_59, age_group_60_to_79}] = 0.0679;
-    contacts_home[{age_group_35_to_59, age_group_80_plus}]  = 0.0014;
-    contacts_home[{age_group_60_to_79, age_group_0_to_4}]   = 0.0087;
-    contacts_home[{age_group_60_to_79, age_group_5_to_14}]  = 0.0394;
-    contacts_home[{age_group_60_to_79, age_group_15_to_34}] = 0.1417;
-    contacts_home[{age_group_60_to_79, age_group_35_to_59}] = 0.3834;
-    contacts_home[{age_group_60_to_79, age_group_60_to_79}] = 0.7064;
-    contacts_home[{age_group_60_to_79, age_group_80_plus}]  = 0.0447;
-    contacts_home[{age_group_80_plus, age_group_0_to_4}]    = 0.0292;
-    contacts_home[{age_group_80_plus, age_group_5_to_14}]   = 0.0648;
-    contacts_home[{age_group_80_plus, age_group_15_to_34}]  = 0.1248;
-    contacts_home[{age_group_80_plus, age_group_35_to_59}]  = 0.4179;
-    contacts_home[{age_group_80_plus, age_group_60_to_79}]  = 0.3497;
-    contacts_home[{age_group_80_plus, age_group_80_plus}]   = 0.1544;
+    Eigen::MatrixXd contacts_home(n_age_groups, n_age_groups);
+    contacts_home << 0.4413, 0.0504, 1.2383, 0.8033, 0.0494, 0.0017, 0.0485, 0.7616, 0.6532, 1.1614, 0.0256, 0.0013,
+        0.1800, 0.1795, 0.8806, 0.6413, 0.0429, 0.0032, 0.0495, 0.2639, 0.5189, 0.8277, 0.0679, 0.0014, 0.0087, 0.0394,
+        0.1417, 0.3834, 0.7064, 0.0447, 0.0292, 0.0648, 0.1248, 0.4179, 0.3497, 0.1544;
 
     /* baseline_school
         1.1165 0.2741 0.2235 0.1028 0.0007 0.0000
@@ -155,44 +121,10 @@ void set_local_parameters(mio::abm::Model& world)
         0.0004 0.0370 0.0115 0.0014 0.0039 0.0000
         0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
     */
-    mio::CustomIndexArray<ScalarType, mio::AgeGroup, mio::AgeGroup> contacts_school(
-        {mio::AgeGroup(n_age_groups), mio::AgeGroup(n_age_groups)}, 0.);
-    contacts_school[{age_group_0_to_4, age_group_0_to_4}]     = 1.1165;
-    contacts_school[{age_group_0_to_4, age_group_5_to_14}]    = 0.2741;
-    contacts_school[{age_group_0_to_4, age_group_15_to_34}]   = 0.2235;
-    contacts_school[{age_group_0_to_4, age_group_35_to_59}]   = 0.1028;
-    contacts_school[{age_group_0_to_4, age_group_60_to_79}]   = 0.0007;
-    contacts_school[{age_group_0_to_4, age_group_80_plus}]    = 0.0000;
-    contacts_school[{age_group_5_to_14, age_group_0_to_4}]    = 0.1627;
-    contacts_school[{age_group_5_to_14, age_group_5_to_14}]   = 1.9412;
-    contacts_school[{age_group_5_to_14, age_group_15_to_34}]  = 0.2431;
-    contacts_school[{age_group_5_to_14, age_group_35_to_59}]  = 0.1780;
-    contacts_school[{age_group_5_to_14, age_group_60_to_79}]  = 0.0130;
-    contacts_school[{age_group_5_to_14, age_group_80_plus}]   = 0.0000;
-    contacts_school[{age_group_15_to_34, age_group_0_to_4}]   = 0.0148;
-    contacts_school[{age_group_15_to_34, age_group_5_to_14}]  = 0.1646;
-    contacts_school[{age_group_15_to_34, age_group_15_to_34}] = 1.1266;
-    contacts_school[{age_group_15_to_34, age_group_35_to_59}] = 0.0923;
-    contacts_school[{age_group_15_to_34, age_group_60_to_79}] = 0.0074;
-    contacts_school[{age_group_15_to_34, age_group_80_plus}]  = 0.0000;
-    contacts_school[{age_group_35_to_59, age_group_0_to_4}]   = 0.0367;
-    contacts_school[{age_group_35_to_59, age_group_5_to_14}]  = 0.1843;
-    contacts_school[{age_group_35_to_59, age_group_15_to_34}] = 0.3265;
-    contacts_school[{age_group_35_to_59, age_group_35_to_59}] = 0.0502;
-    contacts_school[{age_group_35_to_59, age_group_60_to_79}] = 0.0021;
-    contacts_school[{age_group_35_to_59, age_group_80_plus}]  = 0.0005;
-    contacts_school[{age_group_60_to_79, age_group_0_to_4}]   = 0.0004;
-    contacts_school[{age_group_60_to_79, age_group_5_to_14}]  = 0.0370;
-    contacts_school[{age_group_60_to_79, age_group_15_to_34}] = 0.0115;
-    contacts_school[{age_group_60_to_79, age_group_35_to_59}] = 0.0014;
-    contacts_school[{age_group_60_to_79, age_group_60_to_79}] = 0.0039;
-    contacts_school[{age_group_60_to_79, age_group_80_plus}]  = 0.0000;
-    contacts_school[{age_group_80_plus, age_group_0_to_4}]    = 0.0000;
-    contacts_school[{age_group_80_plus, age_group_5_to_14}]   = 0.0000;
-    contacts_school[{age_group_80_plus, age_group_15_to_34}]  = 0.0000;
-    contacts_school[{age_group_80_plus, age_group_35_to_59}]  = 0.0000;
-    contacts_school[{age_group_80_plus, age_group_60_to_79}]  = 0.0000;
-    contacts_school[{age_group_80_plus, age_group_80_plus}]   = 0.0000;
+    Eigen::MatrixXd contacts_school(n_age_groups, n_age_groups);
+    contacts_school << 1.1165, 0.2741, 0.2235, 0.1028, 0.0007, 0.0000, 0.1627, 1.9412, 0.2431, 0.1780, 0.0130, 0.0000,
+        0.0148, 0.1646, 1.1266, 0.0923, 0.0074, 0.0000, 0.0367, 0.1843, 0.3265, 0.0502, 0.0021, 0.0005, 0.0004, 0.0370,
+        0.0115, 0.0014, 0.0039, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000;
 
     /* baseline_work
         0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
@@ -202,44 +134,10 @@ void set_local_parameters(mio::abm::Model& world)
         0.0000 0.0002 0.0194 0.0325 0.0003 0.0000
         0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
     */
-    mio::CustomIndexArray<ScalarType, mio::AgeGroup, mio::AgeGroup> contacts_work(
-        {mio::AgeGroup(n_age_groups), mio::AgeGroup(n_age_groups)}, 0.);
-    contacts_work[{age_group_0_to_4, age_group_0_to_4}]     = 0.0000;
-    contacts_work[{age_group_0_to_4, age_group_5_to_14}]    = 0.0000;
-    contacts_work[{age_group_0_to_4, age_group_15_to_34}]   = 0.0000;
-    contacts_work[{age_group_0_to_4, age_group_35_to_59}]   = 0.0000;
-    contacts_work[{age_group_0_to_4, age_group_60_to_79}]   = 0.0000;
-    contacts_work[{age_group_0_to_4, age_group_80_plus}]    = 0.0000;
-    contacts_work[{age_group_5_to_14, age_group_0_to_4}]    = 0.0000;
-    contacts_work[{age_group_5_to_14, age_group_5_to_14}]   = 0.0000;
-    contacts_work[{age_group_5_to_14, age_group_15_to_34}]  = 0.0000;
-    contacts_work[{age_group_5_to_14, age_group_35_to_59}]  = 0.0000;
-    contacts_work[{age_group_5_to_14, age_group_60_to_79}]  = 0.0000;
-    contacts_work[{age_group_5_to_14, age_group_80_plus}]   = 0.0000;
-    contacts_work[{age_group_15_to_34, age_group_0_to_4}]   = 0.0000;
-    contacts_work[{age_group_15_to_34, age_group_5_to_14}]  = 0.0127;
-    contacts_work[{age_group_15_to_34, age_group_15_to_34}] = 1.7570;
-    contacts_work[{age_group_15_to_34, age_group_35_to_59}] = 1.6050;
-    contacts_work[{age_group_15_to_34, age_group_60_to_79}] = 0.0133;
-    contacts_work[{age_group_15_to_34, age_group_80_plus}]  = 0.0000;
-    contacts_work[{age_group_35_to_59, age_group_0_to_4}]   = 0.0000;
-    contacts_work[{age_group_35_to_59, age_group_5_to_14}]  = 0.0020;
-    contacts_work[{age_group_35_to_59, age_group_15_to_34}] = 1.0311;
-    contacts_work[{age_group_35_to_59, age_group_35_to_59}] = 2.3166;
-    contacts_work[{age_group_35_to_59, age_group_60_to_79}] = 0.0098;
-    contacts_work[{age_group_35_to_59, age_group_80_plus}]  = 0.0000;
-    contacts_work[{age_group_60_to_79, age_group_0_to_4}]   = 0.0000;
-    contacts_work[{age_group_60_to_79, age_group_5_to_14}]  = 0.0002;
-    contacts_work[{age_group_60_to_79, age_group_15_to_34}] = 0.0194;
-    contacts_work[{age_group_60_to_79, age_group_35_to_59}] = 0.0325;
-    contacts_work[{age_group_60_to_79, age_group_60_to_79}] = 0.0003;
-    contacts_work[{age_group_60_to_79, age_group_80_plus}]  = 0.0000;
-    contacts_work[{age_group_80_plus, age_group_0_to_4}]    = 0.0000;
-    contacts_work[{age_group_80_plus, age_group_5_to_14}]   = 0.0000;
-    contacts_work[{age_group_80_plus, age_group_15_to_34}]  = 0.0000;
-    contacts_work[{age_group_80_plus, age_group_35_to_59}]  = 0.0000;
-    contacts_work[{age_group_80_plus, age_group_60_to_79}]  = 0.0000;
-    contacts_work[{age_group_80_plus, age_group_80_plus}]   = 0.0000;
+    Eigen::MatrixXd contacts_work(n_age_groups, n_age_groups);
+    contacts_work << 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000,
+        0.0000, 0.0127, 1.7570, 1.6050, 0.0133, 0.0000, 0.0000, 0.0020, 1.0311, 2.3166, 0.0098, 0.0000, 0.0000, 0.0002,
+        0.0194, 0.0325, 0.0003, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000;
 
     /* baseline_other
         0.5170 0.3997 0.7957 0.9958 0.3239 0.0428
@@ -249,78 +147,46 @@ void set_local_parameters(mio::abm::Model& world)
         0.0371 0.0393 0.4171 0.9666 0.7495 0.0257
         0.0791 0.0800 0.3480 0.5588 0.2769 0.0180
     */
-    mio::CustomIndexArray<ScalarType, mio::AgeGroup, mio::AgeGroup> contacts_other(
-        {mio::AgeGroup(n_age_groups), mio::AgeGroup(n_age_groups)}, 0.);
-    contacts_other[{age_group_0_to_4, age_group_0_to_4}]     = 0.5170;
-    contacts_other[{age_group_0_to_4, age_group_5_to_14}]    = 0.3997;
-    contacts_other[{age_group_0_to_4, age_group_15_to_34}]   = 0.7957;
-    contacts_other[{age_group_0_to_4, age_group_35_to_59}]   = 0.9958;
-    contacts_other[{age_group_0_to_4, age_group_60_to_79}]   = 0.3239;
-    contacts_other[{age_group_0_to_4, age_group_80_plus}]    = 0.0428;
-    contacts_other[{age_group_5_to_14, age_group_0_to_4}]    = 0.0632;
-    contacts_other[{age_group_5_to_14, age_group_5_to_14}]   = 0.9121;
-    contacts_other[{age_group_5_to_14, age_group_15_to_34}]  = 0.3254;
-    contacts_other[{age_group_5_to_14, age_group_35_to_59}]  = 0.4731;
-    contacts_other[{age_group_5_to_14, age_group_60_to_79}]  = 0.2355;
-    contacts_other[{age_group_5_to_14, age_group_80_plus}]   = 0.0148;
-    contacts_other[{age_group_15_to_34, age_group_0_to_4}]   = 0.0336;
-    contacts_other[{age_group_15_to_34, age_group_5_to_14}]  = 0.1604;
-    contacts_other[{age_group_15_to_34, age_group_15_to_34}] = 1.7529;
-    contacts_other[{age_group_15_to_34, age_group_35_to_59}] = 0.8622;
-    contacts_other[{age_group_15_to_34, age_group_60_to_79}] = 0.1440;
-    contacts_other[{age_group_15_to_34, age_group_80_plus}]  = 0.0077;
-    contacts_other[{age_group_35_to_59, age_group_0_to_4}]   = 0.0204;
-    contacts_other[{age_group_35_to_59, age_group_5_to_14}]  = 0.1444;
-    contacts_other[{age_group_35_to_59, age_group_15_to_34}] = 0.5738;
-    contacts_other[{age_group_35_to_59, age_group_35_to_59}] = 1.2127;
-    contacts_other[{age_group_35_to_59, age_group_60_to_79}] = 0.3433;
-    contacts_other[{age_group_35_to_59, age_group_80_plus}]  = 0.0178;
-    contacts_other[{age_group_60_to_79, age_group_0_to_4}]   = 0.0371;
-    contacts_other[{age_group_60_to_79, age_group_5_to_14}]  = 0.0393;
-    contacts_other[{age_group_60_to_79, age_group_15_to_34}] = 0.4171;
-    contacts_other[{age_group_60_to_79, age_group_35_to_59}] = 0.9666;
-    contacts_other[{age_group_60_to_79, age_group_60_to_79}] = 0.7495;
-    contacts_other[{age_group_60_to_79, age_group_80_plus}]  = 0.0257;
-    contacts_other[{age_group_80_plus, age_group_0_to_4}]    = 0.0791;
-    contacts_other[{age_group_80_plus, age_group_5_to_14}]   = 0.0800;
-    contacts_other[{age_group_80_plus, age_group_15_to_34}]  = 0.3480;
-    contacts_other[{age_group_80_plus, age_group_35_to_59}]  = 0.5588;
-    contacts_other[{age_group_80_plus, age_group_60_to_79}]  = 0.2769;
-    contacts_other[{age_group_80_plus, age_group_80_plus}]   = 0.0180;
+    Eigen::MatrixXd contacts_other(n_age_groups, n_age_groups);
+    contacts_other << 0.5170, 0.3997, 0.7957, 0.9958, 0.3239, 0.0428, 0.0632, 0.9121, 0.3254, 0.4731, 0.2355, 0.0148,
+        0.0336, 0.1604, 1.7529, 0.8622, 0.1440, 0.0077, 0.0204, 0.1444, 0.5738, 1.2127, 0.3433, 0.0178, 0.0371, 0.0393,
+        0.4171, 0.9666, 0.7495, 0.0257, 0.0791, 0.0800, 0.3480, 0.5588, 0.2769, 0.0180;
 
-    mio::CustomIndexArray<ScalarType, mio::AgeGroup, mio::AgeGroup> contacts_random(
-        {mio::AgeGroup(n_age_groups), mio::AgeGroup(n_age_groups)}, 1.0);
+    Eigen::MatrixXd contacts_random = Eigen::MatrixXd::Ones(n_age_groups, n_age_groups);
 
     for (auto& loc : world.get_locations()) {
         switch (loc.get_type()) {
-        case mio::abm::LocationType::Home:
-            loc.get_infection_parameters().get<mio::abm::ContactRates>() = contacts_home;
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 1.4; //17 hours //intensity
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 15.0; // Intensity
-            break;
-        case mio::abm::LocationType::School:
-            loc.get_infection_parameters().get<mio::abm::ContactRates>() = contacts_school;
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 4.8; //5h
-            break;
-        case mio::abm::LocationType::Work:
-            loc.get_infection_parameters().get<mio::abm::ContactRates>() = contacts_work;
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 3.0 * 0.5; // 7h
-            break;
-        case mio::abm::LocationType::SocialEvent:
-            loc.get_infection_parameters().get<mio::abm::ContactRates>() = contacts_other;
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 1.2; //aufteilung
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 2.0; // intensity
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 6.0; // 4 hours
-            break;
-        case mio::abm::LocationType::BasicsShop:
-            loc.get_infection_parameters().get<mio::abm::ContactRates>() = contacts_other;
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 0.8; //aufteilung
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 0.33; // intensity
-            loc.get_infection_parameters().get<mio::abm::ContactRates>().array() *= 12.0; // 2 hours
-            break;
-        default:
-            loc.get_infection_parameters().get<mio::abm::ContactRates>() = contacts_random;
-            break;
+            {
+            case mio::abm::LocationType::Home:
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() = contacts_home;
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *=
+                    1.4; //17 hours //intensity
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 15.0; // Intensity
+                break;
+            case mio::abm::LocationType::School:
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() = contacts_school;
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 4.8; //5h
+                break;
+            case mio::abm::LocationType::Work:
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() = contacts_work;
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 3.0 * 0.5; // 7h
+                break;
+            case mio::abm::LocationType::SocialEvent:
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() = contacts_other;
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 1.2; //aufteilung
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 2.0; // intensity
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 6.0; // 4 hours
+                break;
+            case mio::abm::LocationType::BasicsShop:
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() = contacts_other;
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 0.8; //aufteilung
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 0.33; // intensity
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() *= 12.0; // 2 hours
+                break;
+            default:
+                loc.get_infection_parameters().get<mio::abm::ContactRates>().get_baseline() = contacts_random;
+                break;
+            }
         }
     }
 }

cpp-tutorials/abm/tutorial_abm_vaccination.cpp

@@ -202,10 +202,8 @@ int main(int argc, char* argv[])
     const auto age_group_60_to_79 = mio::AgeGroup(4); // seniors
     const auto age_group_80_plus  = mio::AgeGroup(5); // elderly
 
-    // *** Create the model and set infection parameters (same as Tutorial 1). ***
+    // *** Create the model (same as Tutorial 1). ***
     auto model = mio::abm::Model(num_age_groups);
-    set_local_parameters(model);
-    set_world_parameters(model.parameters);
 
     // Define which age groups are eligible to go to school and to work.
     // The AgeGroupGotoSchool / AgeGroupGotoWork arrays default to false for
@@ -321,6 +319,10 @@ int main(int argc, char* argv[])
     // One workplace for all working adults.
     auto work = model.add_location(mio::abm::LocationType::Work);
 
+    // *** Set paramters for all locations (same as Tutorial 1). ***
+    set_local_parameters(model);
+    set_world_parameters(model.parameters);
+
     // *** Assign initial infection states. ***
     //
     //  Index | InfectionState          | Probability
@@ -420,8 +422,8 @@ int main(int argc, char* argv[])
         // Read real-world vaccination counts from a JSON file and apply
         // them day-by-day to the model's persons.
         const std::string vacc_json_path = "./vacc_county_ageinf_ma7.json";
-        const int county_id       = 1002;
-        const mio::Date sim_start = mio::Date(2020, 10, 1);
+        const int county_id              = 1002;
+        const mio::Date sim_start        = mio::Date(2020, 10, 1);
 
         auto vacc_map = prepare_vaccination_data(vacc_json_path, num_age_groups, county_id);
 

cpp-tutorials/git_tag.cmake

@@ -1 +1 @@
-set(GIT_TAG_MEMILIO "cd1068790c12e99a84584585bb9874673a06ab9f")
+set(GIT_TAG_MEMILIO "20cee90e7ce55b0107f0607df36e50b9e4a49889")