1039 Add functions for the Person to choose whether to comply to mask,test and isolation

cpp/benchmarks/abm.cpp

@@ -61,9 +61,9 @@ mio::abm::Simulation make_simulation(size_t num_persons, std::initializer_list<u
         }
 
         //equal chance of (moderate) mask refusal and (moderate) mask eagerness
-        auto pct_mask_values = std::array{0.05 /*-1*/, 0.2 /*-0.5*/, 0.5 /*0*/, 0.2 /*0.5*/, 0.05 /*1*/};
-        auto mask_value      = -1 + 0.5 * mio::DiscreteDistribution<int>::get_instance()(prng, pct_mask_values);
-        person.set_mask_preferences({size_t(mio::abm::LocationType::Count), mask_value});
+        auto pct_compliance_values = std::array{0.05 /*-1*/, 0.2 /*-0.5*/, 0.5 /*0*/, 0.2 /*0.5*/, 0.05 /*1*/};
+        auto compliance_value      = -1 + 0.5 * mio::DiscreteDistribution<int>::get_instance()(prng, pct_compliance_values);
+        person.set_compliance(mio::abm::InterventionType::Mask, compliance_value);
     }
 
     //masks at locations
@@ -73,7 +73,7 @@ mio::abm::Simulation make_simulation(size_t num_persons, std::initializer_list<u
         auto pct_require_mask = 0.2;
         auto requires_mask    = loc.get_type() != mio::abm::LocationType::Home &&
                              mio::UniformDistribution<double>::get_instance()(world.get_rng()) < pct_require_mask;
-        loc.set_npi_active(requires_mask);
+        loc.set_mask_requirement(requires_mask);
     }
 
     //testing schemes

cpp/models/abm/intervention_type.h

@@ -0,0 +1,45 @@
+/* 
+* Copyright (C) 2020-2024 MEmilio
+*
+* Authors: Khoa Nguyen
+*
+* Contact: Martin J. Kuehn <[email protected]>
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+*     http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+*/
+
+#ifndef MIO_ABM_INTERVENTION_TYPE_H
+#define MIO_ABM_INTERVENTION_TYPE_H
+
+#include <cstdint>
+
+namespace mio
+{
+namespace abm
+{
+
+/**
+ * @brief Type of an Intervention.
+ */
+enum class InterventionType : std::uint32_t
+{
+    Mask = 0,
+    Testing,
+    Isolation,
+
+    Count
+};
+} // namespace abm
+} // namespace mio
+
+#endif

cpp/models/abm/location.cpp

@@ -17,7 +17,7 @@
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
-#include "abm/mask_type.h"
+#include "abm/intervention_type.h"
 #include "abm/mask.h"
 #include "abm/location.h"
 #include "abm/random_events.h"
@@ -37,7 +37,7 @@ Location::Location(LocationId loc_id, size_t num_agegroups, uint32_t num_cells)
     , m_parameters(num_agegroups)
     , m_cells(num_cells, num_agegroups)
     , m_required_mask(MaskType::Community)
-    , m_npi_active(false)
+    , m_is_mask_required(false)
 {
     assert(num_cells > 0 && "Number of cells has to be larger than 0.");
 }

cpp/models/abm/location.h

@@ -127,7 +127,7 @@ class Location
         , m_persons(other.m_persons)
         , m_cells(other.m_cells)
         , m_required_mask(other.m_required_mask)
-        , m_npi_active(other.m_npi_active)
+        , m_is_mask_required(other.m_is_mask_required)
         , m_geographical_location(other.m_geographical_location)
     {
     }
@@ -315,22 +315,21 @@ class Location
     }
 
     /**
-     * @brief Get the information whether NPIs are active at this Location.
-     * If true requires e.g. Mask%s when entering a Location.
-     * @return True if NPIs are active at this Location.
+     * @brief Get the information whether masks are required to enter this Location.
+     * @return True if masks are required to enter this Location.
      */
-    bool get_npi_active() const
+    bool is_mask_required() const
     {
-        return m_npi_active;
+        return m_is_mask_required;
     }
 
     /**
-     * @brief Activate or deactivate NPIs at this Location.
-     * @param[in] new_status Status of NPIs.
+     * @brief Activate or deactivate mask wearing requirement at this Location.
+     * @param[in] new_status Status of mask wearing requirement.
      */
-    void set_npi_active(bool new_status)
+    void set_mask_requirement(bool new_status)
     {
-        m_npi_active = new_status;
+        m_is_mask_required = new_status;
     }
 
     /**
@@ -404,7 +403,7 @@ class Location
     std::vector<observer_ptr<Person>> m_persons{}; ///< A vector of all Person%s at the Location.
     std::vector<Cell> m_cells{}; ///< A vector of all Cell%s that the Location is divided in.
     MaskType m_required_mask; ///< Least secure type of Mask that is needed to enter the Location.
-    bool m_npi_active; ///< If true requires e.g. Mask%s to enter the Location.
+    bool m_is_mask_required; ///< If true requires e.g. Mask%s to enter the Location.
     GeographicalLocation m_geographical_location; ///< Geographical location (longitude and latitude) of the Location.
 };
 

cpp/models/abm/mask.cpp

@@ -27,16 +27,21 @@ namespace mio
 {
 namespace abm
 {
-Mask::Mask(MaskType type)
+Mask::Mask(MaskType type, TimePoint t)
     : m_type(type)
-    , m_time_used(TimeSpan(0))
+    , m_time_first_usage(t)
 {
 }
 
-void Mask::change_mask(MaskType new_mask_type)
+void Mask::change_mask(MaskType new_mask_type, TimePoint t)
 {
-    m_type      = new_mask_type;
-    m_time_used = TimeSpan(0);
+    m_type             = new_mask_type;
+    m_time_first_usage = t;
+}
+
+const TimeSpan Mask::get_time_used(TimePoint curr_time) const
+{
+    return curr_time - m_time_first_usage;
 }
 
 } // namespace abm

cpp/models/abm/mask.h

@@ -38,8 +38,9 @@ class Mask
     /**
      * @brief Construct a new Mask of a certain type.
      * @param[in] type The type of the Mask.
+     * @param[in] t The TimePoint of the Mask's initial usage.
      */
-    Mask(MaskType type);
+    Mask(MaskType type, TimePoint t);
 
     /**
      * @brief Get the MaskType of this Mask.
@@ -51,30 +52,20 @@ class Mask
 
     /**
      * @brief Get the length of time this Mask has been used.
+     * @param[in] curr_time The current TimePoint.
      */
-    const TimeSpan& get_time_used() const
-    {
-        return m_time_used;
-    }
-
-    /**
-     * @brief Increase the time this Mask was used by a timestep.
-     * @param[in] dt The length of the timestep.
-     */
-    void increase_time_used(TimeSpan dt)
-    {
-        m_time_used += dt;
-    }
+    const TimeSpan get_time_used(TimePoint curr_time) const;
 
     /**
      * @brief Change the type of the Mask and reset the time it was used.
      * @param[in] new_mask_type The type of the new Mask.
+     * @param[in] t The TimePoint of mask change.
      */
-    void change_mask(MaskType new_mask_type);
+    void change_mask(MaskType new_mask_type, TimePoint t);
 
 private:
     MaskType m_type; ///< Type of the Mask.
-    TimeSpan m_time_used; ///< Length of time the Mask has been used.
+    TimePoint m_time_first_usage; ///< TimePoint of the Mask's initial usage.
 };
 } // namespace abm
 } // namespace mio

cpp/models/abm/mask_type.h

@@ -33,7 +33,8 @@ namespace abm
  */
 enum class MaskType : std::uint32_t
 {
-    Community = 0,
+    None = 0,
+    Community,
     Surgical,
     FFP2,
 

cpp/models/abm/parameters.h

@@ -43,7 +43,7 @@ namespace abm
  * @brief Time that a Person is infected but not yet infectious.
  */
 struct IncubationPeriod {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -55,7 +55,7 @@ struct IncubationPeriod {
 };
 
 struct InfectedNoSymptomsToSymptoms {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -67,7 +67,7 @@ struct InfectedNoSymptomsToSymptoms {
 };
 
 struct InfectedNoSymptomsToRecovered {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -79,7 +79,7 @@ struct InfectedNoSymptomsToRecovered {
 };
 
 struct InfectedSymptomsToRecovered {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -91,7 +91,7 @@ struct InfectedSymptomsToRecovered {
 };
 
 struct InfectedSymptomsToSevere {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -103,7 +103,7 @@ struct InfectedSymptomsToSevere {
 };
 
 struct SevereToCritical {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -115,7 +115,7 @@ struct SevereToCritical {
 };
 
 struct SevereToRecovered {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -127,7 +127,7 @@ struct SevereToRecovered {
 };
 
 struct CriticalToRecovered {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -139,7 +139,7 @@ struct CriticalToRecovered {
 };
 
 struct CriticalToDead {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -151,7 +151,7 @@ struct CriticalToDead {
 };
 
 struct RecoveredToSusceptible {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -212,7 +212,7 @@ struct InfectivityDistributions {
  * @brief Probability that an Infection is detected.
  */
 struct DetectInfection {
-    using Type = CustomIndexArray< UncertainValue<>, VirusVariant, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, VirusVariant, AgeGroup>;
     static Type get_default(AgeGroup size)
     {
         return Type({VirusVariant::Count, size}, 1.);
@@ -227,10 +227,15 @@ struct DetectInfection {
  * @brief Effectiveness of a Mask of a certain MaskType% against an Infection%.
  */
 struct MaskProtection {
-    using Type = CustomIndexArray< UncertainValue<>, MaskType>;
+    using Type = CustomIndexArray<UncertainValue<>, MaskType>;
     static Type get_default(AgeGroup /*size*/)
     {
-        return Type({MaskType::Count}, 1.);
+        Type defaut_value                 = Type(MaskType::Count, 0.0);
+        // Initial values according to http://dx.doi.org/10.15585/mmwr.mm7106e1
+        defaut_value[MaskType::FFP2]      = 0.83;
+        defaut_value[MaskType::Surgical]  = 0.66;
+        defaut_value[MaskType::Community] = 0.56;
+        return defaut_value;
     }
     static std::string name()
     {
@@ -312,8 +317,8 @@ struct HighViralLoadProtectionFactor {
  * @brief Parameters that describe the reliability of a test.
  */
 struct TestParameters {
-     UncertainValue<> sensitivity;
-     UncertainValue<> specificity;
+    UncertainValue<> sensitivity;
+    UncertainValue<> specificity;
 };
 
 struct GenericTest {
@@ -392,7 +397,7 @@ struct QuarantineDuration {
  * @brief Parameter for the exponential distribution to decide if a Person goes shopping.
  */
 struct BasicShoppingRate {
-    using Type = CustomIndexArray< UncertainValue<>, AgeGroup>;
+    using Type = CustomIndexArray<UncertainValue<>, AgeGroup>;
     static auto get_default(AgeGroup size)
     {
         return Type({size}, 1.0);