Line data    Source code

       1             : /* 
       2             : * Copyright (C) 2020-2024 MEmilio
       3             : *
       4             : * Authors: Nils Wassmuth, Rene Schmieding, 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 MIO_SDE_SIR_PARAMETERS_H
      22             : #define MIO_SDE_SIR_PARAMETERS_H
      23             : 
      24             : #include "memilio/epidemiology/contact_matrix.h"
      25             : #include "memilio/utils/parameter_set.h"
      26             : #include "memilio/utils/uncertain_value.h"
      27             : 
      28             : namespace mio
      29             : {
      30             : namespace ssir
      31             : {
      32             : 
      33             : /*******************************************
      34             :  * Define Parameters of the SIR model *
      35             :  *******************************************/
      36             : 
      37             : /**
      38             :  * @brief probability of getting infected from a contact
      39             :  */
      40             : struct TransmissionProbabilityOnContact {
      41             :     using Type = UncertainValue<>;
      42          27 :     static Type get_default()
      43             :     {
      44          27 :         return Type(1.0);
      45             :     }
      46             :     static std::string name()
      47             :     {
      48             :         return "TransmissionProbabilityOnContact";
      49             :     }
      50             : };
      51             : 
      52             : /**
      53             :  * @brief the infectious time in day unit
      54             :  */
      55             : struct TimeInfected {
      56             :     using Type = UncertainValue<ScalarType>;
      57          27 :     static Type get_default()
      58             :     {
      59          27 :         return Type(6.0);
      60             :     }
      61             :     static std::string name()
      62             :     {
      63             :         return "TimeInfected";
      64             :     }
      65             : };
      66             : 
      67             : /**
      68             :  * @brief the contact patterns within the society are modelled using a ContactMatrix
      69             :  */
      70             : struct ContactPatterns {
      71             :     using Type = ContactMatrix;
      72          27 :     static Type get_default()
      73             :     {
      74          27 :         return Type{1};
      75             :     }
      76             :     static std::string name()
      77             :     {
      78             :         return "ContactPatterns";
      79             :     }
      80             : };
      81             : 
      82             : using ParametersBase = ParameterSet<TransmissionProbabilityOnContact, TimeInfected, ContactPatterns>;
      83             : 
      84             : /**
      85             :  * @brief Parameters of SIR model.
      86             :  */
      87             : class Parameters : public ParametersBase
      88             : {
      89             : public:
      90          27 :     Parameters()
      91          27 :         : ParametersBase()
      92             :     {
      93          27 :     }
      94             : 
      95             :     /**
      96             :      * @brief Checks whether all Parameters satisfy their corresponding constraints and applies them, if they do not.
      97             :      * Time spans cannot be negative and probabilities can only take values between [0,1]. 
      98             :      *
      99             :      * Attention: This function should be used with care. It is necessary for some test problems to run through quickly,
     100             :      *            but in a manual execution of an example, check_constraints() may be preferred. Note that the apply_constraints()
     101             :      *            function can and will not set Parameters to meaningful values in an epidemiological or virological context,
     102             :      *            as all models are designed to be transferable to multiple diseases. Consequently, only acceptable
     103             :      *            (like 0 or 1 for probabilities or small positive values for time spans) values are set here and a manual adaptation
     104             :      *            may often be necessary to have set meaningful values.
     105             :      *
     106             :      * @return Returns true if one ore more constraint were corrected, false otherwise.  
     107             :      */
     108          27 :     bool apply_constraints()
     109             :     {
     110          27 :         ScalarType tol_times = 1e-1;
     111             : 
     112          27 :         int corrected = false;
     113          27 :         if (this->get<TimeInfected>() < tol_times) {
     114          18 :             log_warning("Constraint check: Parameter TimeInfected changed from {:.4f} to {:.4f}. Please note that "
     115             :                         "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
     116             :                         "and reset parameters.",
     117           9 :                         this->get<TimeInfected>(), tol_times);
     118           9 :             this->get<TimeInfected>() = tol_times;
     119           9 :             corrected                 = true;
     120             :         }
     121          54 :         if (this->get<TransmissionProbabilityOnContact>() < 0.0 ||
     122          27 :             this->get<TransmissionProbabilityOnContact>() > 1.0) {
     123          18 :             log_warning("Constraint check: Parameter TransmissionProbabilityOnContact changed from {:0.4f} to {:d} ",
     124          18 :                         this->get<TransmissionProbabilityOnContact>(), 0.0);
     125           9 :             this->get<TransmissionProbabilityOnContact>() = 0.0;
     126           9 :             corrected                                     = true;
     127             :         }
     128          27 :         return corrected;
     129             :     }
     130             : 
     131             :     /**
     132             :      * @brief Checks whether all Parameters satisfy their corresponding constraints and logs an error 
     133             :      * if constraints are not satisfied.
     134             :      * @return Returns true if one constraint is not satisfied, otherwise false.   
     135             :      */
     136          27 :     bool check_constraints() const
     137             :     {
     138          27 :         ScalarType tol_times = 1e-1;
     139             : 
     140          27 :         if (this->get<TimeInfected>() < tol_times) {
     141          18 :             log_error("Constraint check: Parameter TimeInfected {:.4f} smaller or equal {:.4f}. Please note that "
     142             :                       "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
     143             :                       "and reset parameters.",
     144          18 :                       this->get<TimeInfected>(), 0.0);
     145           9 :             return true;
     146             :         }
     147          36 :         if (this->get<TransmissionProbabilityOnContact>() < 0.0 ||
     148          18 :             this->get<TransmissionProbabilityOnContact>() > 1.0) {
     149          18 :             log_error(
     150             :                 "Constraint check: Parameter TransmissionProbabilityOnContact {:.4f} smaller {:.4f} or greater {:.4f}",
     151          18 :                 this->get<TransmissionProbabilityOnContact>(), 0.0, 1.0);
     152           9 :             return true;
     153             :         }
     154           9 :         return false;
     155             :     }
     156             : 
     157             : private:
     158             :     Parameters(ParametersBase&& base)
     159             :         : ParametersBase(std::move(base))
     160             :     {
     161             :     }
     162             : 
     163             : public:
     164             :     /**
     165             :      * deserialize an object of this class.
     166             :      * @see mio::deserialize
     167             :      */
     168             :     template <class IOContext>
     169             :     static IOResult<Parameters> deserialize(IOContext& io)
     170             :     {
     171             :         BOOST_OUTCOME_TRY(auto&& base, ParametersBase::deserialize(io));
     172             :         return success(Parameters(std::move(base)));
     173             :     }
     174             : };
     175             : 
     176             : } // namespace ssir
     177             : } // namespace mio
     178             : 
     179             : #endif // MIO_SDE_SIR_PARAMETERS_H