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             : #ifndef SEIR_PARAMETERS_H
      21             : #define SEIR_PARAMETERS_H
      22             : 
      23             : #include "memilio/config.h"
      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/uncertain_value.h"
      28             : #include "memilio/utils/parameter_set.h"
      29             : 
      30             : namespace mio
      31             : {
      32             : namespace oseir
      33             : {
      34             : 
      35             : /***************************************
      36             :  * Define Parameters of the SEIR model *
      37             :  ***************************************/
      38             : 
      39             : /**
      40             :  * @brief probability of getting infected from a contact
      41             :  */
      42             : template <typename FP = double>
      43             : struct TransmissionProbabilityOnContact {
      44             :     using Type = CustomIndexArray<UncertainValue<FP>, AgeGroup>;
      45         154 :     static Type get_default(AgeGroup size)
      46             :     {
      47         308 :         return Type(size, 1.);
      48             :     }
      49             :     static std::string name()
      50             :     {
      51             :         return "TransmissionProbabilityOnContact";
      52             :     }
      53             : };
      54             : 
      55             : /**
      56             :  * @brief the latent time in day unit
      57             :  */
      58             : template <typename FP = double>
      59             : struct TimeExposed {
      60             :     using Type = CustomIndexArray<UncertainValue<FP>, AgeGroup>;
      61         154 :     static Type get_default(AgeGroup size)
      62             :     {
      63         308 :         return Type(size, 5.2);
      64             :     }
      65             :     static std::string name()
      66             :     {
      67             :         return "TimeExposed";
      68             :     }
      69             : };
      70             : 
      71             : /**
      72             :  * @brief the infectious time in day unit
      73             :  */
      74             : template <typename FP = double>
      75             : struct TimeInfected {
      76             :     using Type = CustomIndexArray<UncertainValue<FP>, AgeGroup>;
      77         154 :     static Type get_default(AgeGroup size)
      78             :     {
      79         308 :         return Type(size, 6.0);
      80             :     }
      81             :     static std::string name()
      82             :     {
      83             :         return "TimeInfected";
      84             :     }
      85             : };
      86             : 
      87             : /**
      88             :  * @brief the contact patterns within the society are modelled using a ContactMatrix
      89             :  */
      90             : template <class FP = ScalarType>
      91             : struct ContactPatterns {
      92             :     using Type = UncertainContactMatrix<FP>;
      93         154 :     static Type get_default(AgeGroup size)
      94             :     {
      95         154 :         return Type(1, static_cast<Eigen::Index>((size_t)size));
      96             :     }
      97             :     static std::string name()
      98             :     {
      99             :         return "ContactPatterns";
     100             :     }
     101             : };
     102             : 
     103             : template <typename FP = double>
     104             : using ParametersBase =
     105             :     ParameterSet<TransmissionProbabilityOnContact<FP>, TimeExposed<FP>, TimeInfected<FP>, ContactPatterns<FP>>;
     106             : 
     107             : /**
     108             :  * @brief Parameters of an age-resolved SECIR/SECIHURD model.
     109             :  */
     110             : template <typename FP = double>
     111             : class Parameters : public ParametersBase<FP>
     112             : {
     113             : public:
     114         154 :     Parameters(AgeGroup num_agegroups)
     115             :         : ParametersBase<FP>(num_agegroups)
     116         154 :         , m_num_groups{num_agegroups}
     117             :     {
     118         154 :     }
     119             : 
     120         324 :     AgeGroup get_num_groups() const
     121             :     {
     122         324 :         return m_num_groups;
     123             :     }
     124             : 
     125             :     /**
     126             :      * @brief Checks whether all Parameters satisfy their corresponding constraints and applies them, if they do not.
     127             :      * Time spans cannot be negative and probabilities can only take values between [0,1]. 
     128             :      *
     129             :      * Attention: This function should be used with care. It is necessary for some test problems to run through quickly,
     130             :      *            but in a manual execution of an example, check_constraints() may be preferred. Note that the apply_constraints()
     131             :      *            function can and will not set Parameters to meaningful values in an epidemiological or virological context,
     132             :      *            as all models are designed to be transferable to multiple diseases. Consequently, only acceptable
     133             :      *            (like 0 or 1 for probabilities or small positive values for time spans) values are set here and a manual adaptation
     134             :      *            may often be necessary to have set meaningful values.
     135             :      *
     136             :      * @return Returns true if one ore more constraint were corrected, false otherwise.  
     137             :      */
     138          54 :     bool apply_constraints()
     139             :     {
     140          54 :         const double tol_times = 1e-1;
     141             : 
     142          54 :         int corrected = false;
     143             : 
     144         108 :         for (auto i = AgeGroup(0); i < AgeGroup(m_num_groups); ++i) {
     145          54 :             if (this->template get<TimeExposed<FP>>()[i] < tol_times) {
     146          18 :                 log_warning(
     147             :                     "Constraint check: Parameter TimeExposed changed from {:.4f} to {:.4f}. Please note that "
     148             :                     "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
     149             :                     "and reset parameters.",
     150           9 :                     this->template get<TimeExposed<FP>>()[i], tol_times);
     151           9 :                 this->template get<TimeExposed<FP>>()[i] = tol_times;
     152           9 :                 corrected                                = true;
     153             :             }
     154          54 :             if (this->template get<TimeInfected<FP>>()[i] < tol_times) {
     155          18 :                 log_warning(
     156             :                     "Constraint check: Parameter TimeInfected changed from {:.4f} to {:.4f}. Please note that "
     157             :                     "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
     158             :                     "and reset parameters.",
     159           9 :                     this->template get<TimeInfected<FP>>()[i], tol_times);
     160           9 :                 this->template get<TimeInfected<FP>>()[i] = tol_times;
     161           9 :                 corrected                                 = true;
     162             :             }
     163         108 :             if (this->template get<TransmissionProbabilityOnContact<FP>>()[i] < 0.0 ||
     164          54 :                 this->template get<TransmissionProbabilityOnContact<FP>>()[i] > 1.0) {
     165          18 :                 log_warning(
     166             :                     "Constraint check: Parameter TransmissionProbabilityOnContact changed from {:0.4f} to {:d} ",
     167          18 :                     this->template get<TransmissionProbabilityOnContact<FP>>()[i], 0.0);
     168           9 :                 this->template get<TransmissionProbabilityOnContact<FP>>()[i] = 0.0;
     169           9 :                 corrected                                                     = true;
     170             :             }
     171             :         }
     172          54 :         return corrected;
     173             :     }
     174             : 
     175             :     /**
     176             :      * @brief Checks whether all Parameters satisfy their corresponding constraints and logs an error 
     177             :      * if constraints are not satisfied.
     178             :      * @return Returns true if one constraint is not satisfied, otherwise false.   
     179             :      */
     180         143 :     bool check_constraints() const
     181             :     {
     182         143 :         const double tol_times = 1e-1;
     183             : 
     184         259 :         for (auto i = AgeGroup(0); i < m_num_groups; i++) {
     185         143 :             if (this->template get<TimeExposed<FP>>()[i] < tol_times) {
     186          18 :                 log_error(
     187             :                     "Constraint check: Parameter TimeExposed {:.4f} smaller or equal {:.4f}. Please note that "
     188             :                     "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
     189             :                     "and reset parameters.",
     190          18 :                     this->template get<TimeExposed<FP>>()[i], 0.0);
     191           9 :                 return true;
     192             :             }
     193         134 :             if (this->template get<TimeInfected<FP>>()[i] < tol_times) {
     194          18 :                 log_error(
     195             :                     "Constraint check: Parameter TimeInfected {:.4f} smaller or equal {:.4f}. Please note that "
     196             :                     "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
     197             :                     "and reset parameters.",
     198          18 :                     this->template get<TimeInfected<FP>>()[i], 0.0);
     199           9 :                 return true;
     200             :             }
     201         250 :             if (this->template get<TransmissionProbabilityOnContact<FP>>()[i] < 0.0 ||
     202         125 :                 this->template get<TransmissionProbabilityOnContact<FP>>()[i] > 1.0) {
     203          18 :                 log_error("Constraint check: Parameter TransmissionProbabilityOnContact {:.4f} smaller {:.4f} or "
     204             :                           "greater {:.4f}",
     205          18 :                           this->template get<TransmissionProbabilityOnContact<FP>>()[i], 0.0, 1.0);
     206           9 :                 return true;
     207             :             }
     208             :         }
     209         116 :         return false;
     210             :     }
     211             : 
     212             : private:
     213             :     Parameters(ParametersBase<FP>&& base)
     214             :         : ParametersBase<FP>(std::move(base))
     215             :         , m_num_groups(this->template get<ContactPatterns<FP>>().get_cont_freq_mat().get_num_groups())
     216             :     {
     217             :     }
     218             : 
     219             : public:
     220             :     /**
     221             :      * deserialize an object of this class.
     222             :      * @see mio::deserialize
     223             :      */
     224             :     template <class IOContext>
     225             :     static IOResult<Parameters> deserialize(IOContext& io)
     226             :     {
     227             :         BOOST_OUTCOME_TRY(auto&& base, ParametersBase<FP>::deserialize(io));
     228             :         return success(Parameters(std::move(base)));
     229             :     }
     230             : 
     231             : private:
     232             :     AgeGroup m_num_groups;
     233             : };
     234             : } // namespace oseir
     235             : } // namespace mio
     236             : 
     237             : #endif // SEIR_PARAMETERS_H