Line data    Source code

       1             : /* 
       2             : * Copyright (C) 2020-2024 MEmilio
       3             : *
       4             : * Authors: Daniel Abele, Jan Kleinert, Martin J. Kuehn
       5             : *
       6             : * Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
       7             : *
       8             : * Licensed under the Apache License, Version 2.0 (the "License");
       9             : * you may not use this file except in compliance with the License.
      10             : * You may obtain a copy of the License at
      11             : *
      12             : *     http://www.apache.org/licenses/LICENSE-2.0
      13             : *
      14             : * Unless required by applicable law or agreed to in writing, software
      15             : * distributed under the License is distributed on an "AS IS" BASIS,
      16             : * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
      17             : * See the License for the specific language governing permissions and
      18             : * limitations under the License.
      19             : */
      20             : 
      21             : #ifndef SIR_PARAMETERS_H
      22             : #define SIR_PARAMETERS_H
      23             : 
      24             : #include "memilio/epidemiology/age_group.h"
      25             : #include "memilio/epidemiology/uncertain_matrix.h"
      26             : #include "memilio/utils/custom_index_array.h"
      27             : #include "memilio/utils/parameter_set.h"
      28             : #include "memilio/utils/uncertain_value.h"
      29             : 
      30             : namespace mio
      31             : {
      32             : namespace osir
      33             : {
      34             : 
      35             : /**************************************
      36             :  * Define Parameters of the SIR model *
      37             :  **************************************/
      38             : 
      39             : /**
      40             :  * @brief probability of getting infected from a contact
      41             :  */
      42             : template <typename FP = ScalarType>
      43             : struct TransmissionProbabilityOnContact {
      44             :     using Type = CustomIndexArray<UncertainValue<FP>, AgeGroup>;
      45          72 :     static Type get_default(AgeGroup size)
      46             :     {
      47         144 :         return Type(size, 1.0);
      48             :     }
      49             :     static std::string name()
      50             :     {
      51             :         return "TransmissionProbabilityOnContact";
      52             :     }
      53             : };
      54             : 
      55             : /**
      56             :      * @brief the infectious time in day unit
      57             :      */
      58             : template <typename FP = ScalarType>
      59             : struct TimeInfected {
      60             :     using Type = CustomIndexArray<UncertainValue<FP>, AgeGroup>;
      61          72 :     static Type get_default(AgeGroup size)
      62             :     {
      63         144 :         return Type(size, 6.0);
      64             :     }
      65             :     static std::string name()
      66             :     {
      67             :         return "TimeInfected";
      68             :     }
      69             : };
      70             : 
      71             : /**
      72             :  * @brief the contact patterns within the society are modelled using a ContactMatrix
      73             :  */
      74             : template <typename FP = ScalarType>
      75             : struct ContactPatterns {
      76             :     using Type = UncertainContactMatrix<FP>;
      77          72 :     static Type get_default(AgeGroup size)
      78             :     {
      79          72 :         return Type(1, static_cast<Eigen::Index>((size_t)size));
      80             :     }
      81             :     static std::string name()
      82             :     {
      83             :         return "ContactPatterns";
      84             :     }
      85             : };
      86             : 
      87             : template <typename FP = ScalarType>
      88             : using ParametersBase = ParameterSet<TransmissionProbabilityOnContact<FP>, TimeInfected<FP>, ContactPatterns<FP>>;
      89             : 
      90             : /**
      91             :  * @brief Parameters of SIR model.
      92             :  */
      93             : template <typename FP = ScalarType>
      94             : class Parameters : public ParametersBase<FP>
      95             : {
      96             : public:
      97          72 :     Parameters(AgeGroup num_agegroups)
      98             :         : ParametersBase<FP>(num_agegroups)
      99          72 :         , m_num_groups{num_agegroups}
     100             :     {
     101          72 :     }
     102             : 
     103        4077 :     AgeGroup get_num_groups()
     104             :     {
     105        4077 :         return m_num_groups;
     106             :     }
     107             : 
     108             :     /**
     109             :      * @brief Checks whether all Parameters satisfy their corresponding constraints and applies them, if they do not.
     110             :      * Time spans cannot be negative and probabilities can only take values between [0,1]. 
     111             :      *
     112             :      * Attention: This function should be used with care. It is necessary for some test problems to run through quickly,
     113             :      *            but in a manual execution of an example, check_constraints() may be preferred. Note that the apply_constraints()
     114             :      *            function can and will not set Parameters to meaningful values in an epidemiological or virological context,
     115             :      *            as all models are designed to be transferable to multiple diseases. Consequently, only acceptable
     116             :      *            (like 0 or 1 for probabilities or small positive values for time spans) values are set here and a manual adaptation
     117             :      *            may often be necessary to have set meaningful values.
     118             :      *
     119             :      * @return Returns true if one ore more constraint were corrected, false otherwise.  
     120             :      */
     121          27 :     bool apply_constraints()
     122             :     {
     123          27 :         double tol_times = 1e-1;
     124             : 
     125          27 :         int corrected = false;
     126             : 
     127          54 :         for (auto i = AgeGroup(0); i < AgeGroup(m_num_groups); i++) {
     128          27 :             if (this->template get<TimeInfected<FP>>()[i] < tol_times) {
     129          18 :                 log_warning(
     130             :                     "Constraint check: Parameter TimeInfected changed from {:.4f} to {:.4f}. Please note that "
     131             :                     "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
     132             :                     "and reset parameters.",
     133           9 :                     this->template get<TimeInfected<FP>>()[i], tol_times);
     134           9 :                 this->template get<TimeInfected<FP>>()[i] = tol_times;
     135           9 :                 corrected                                 = true;
     136             :             }
     137          54 :             if (this->template get<TransmissionProbabilityOnContact<FP>>()[i] < 0.0 ||
     138          27 :                 this->template get<TransmissionProbabilityOnContact<FP>>()[i] > 1.0) {
     139          18 :                 log_warning(
     140             :                     "Constraint check: Parameter TransmissionProbabilityOnContact changed from {:0.4f} to {:d} ",
     141          18 :                     this->template get<TransmissionProbabilityOnContact<FP>>()[i], 0.0);
     142           9 :                 this->template get<TransmissionProbabilityOnContact<FP>>() = 0.0;
     143           9 :                 corrected                                                  = true;
     144             :             }
     145             :         }
     146          27 :         return corrected;
     147             :     }
     148             : 
     149             :     /**
     150             :      * @brief Checks whether all Parameters satisfy their corresponding constraints and logs an error 
     151             :      * if constraints are not satisfied.
     152             :      * @return Returns true if one constraint is not satisfied, otherwise false.   
     153             :      */
     154          81 :     bool check_constraints() const
     155             :     {
     156          81 :         double tol_times = 1e-1;
     157             : 
     158         144 :         for (auto i = AgeGroup(0); i < AgeGroup(m_num_groups); i++) {
     159             : 
     160          81 :             if (this->template get<TimeInfected<FP>>()[i] < tol_times) {
     161          18 :                 log_error(
     162             :                     "Constraint check: Parameter TimeInfected {:.4f} smaller or equal {:.4f}. Please note that "
     163             :                     "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
     164             :                     "and reset parameters.",
     165          18 :                     this->template get<TimeInfected<FP>>()[i], 0.0);
     166           9 :                 return true;
     167             :             }
     168         144 :             if (this->template get<TransmissionProbabilityOnContact<FP>>()[i] < 0.0 ||
     169          72 :                 this->template get<TransmissionProbabilityOnContact<FP>>()[i] > 1.0) {
     170          18 :                 log_error("Constraint check: Parameter TransmissionProbabilityOnContact {:.4f} smaller {:.4f} or "
     171             :                           "greater {:.4f}",
     172          18 :                           this->template get<TransmissionProbabilityOnContact<FP>>()[i], 0.0, 1.0);
     173           9 :                 return true;
     174             :             }
     175             :         }
     176          63 :         return false;
     177             :     }
     178             : 
     179             : private:
     180             :     Parameters(ParametersBase<FP>&& base)
     181             :         : ParametersBase<FP>(std::move(base))
     182             :         , m_num_groups(this->template get<ContactPatterns<FP>>().get_cont_freq_mat().get_num_groups())
     183             :     {
     184             :     }
     185             : 
     186             : public:
     187             :     /**
     188             :      * deserialize an object of this class.
     189             :      * @see mio::deserialize
     190             :      */
     191             :     template <class IOContext>
     192             :     static IOResult<Parameters> deserialize(IOContext& io)
     193             :     {
     194             :         BOOST_OUTCOME_TRY(auto&& base, ParametersBase<FP>::deserialize(io));
     195             :         return success(Parameters(std::move(base)));
     196             :     }
     197             : 
     198             : private:
     199             :     AgeGroup m_num_groups;
     200             : };
     201             : 
     202             : } // namespace osir
     203             : } // namespace mio
     204             : 
     205             : #endif // SIR_PARAMETERS_H