ode_seir/parameters.h

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/*
* Copyright (C) 2020-2026 MEmilio
*
* Authors: Daniel Abele, Jan Kleinert, Martin J. Kuehn
*
* Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
*
* 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 SEIR_PARAMETERS_H
#define SEIR_PARAMETERS_H
 
#include "memilio/config.h"
#include "memilio/epidemiology/age_group.h"
#include "memilio/epidemiology/uncertain_matrix.h"
#include "memilio/utils/custom_index_array.h"
#include "memilio/utils/uncertain_value.h"
#include "memilio/utils/parameter_set.h"
 
namespace mio
{
namespace oseir
{
 
/***************************************
 * Define Parameters of the SEIR model *
 ***************************************/
 
template <typename FP>
struct TransmissionProbabilityOnContact {
    using Type = CustomIndexArray<UncertainValue<FP>, AgeGroup>;
    static Type get_default(AgeGroup size)
    {
        return Type(size, 1.);
    }
    static std::string name()
    {
        return "TransmissionProbabilityOnContact";
    }
};
 
template <typename FP>
struct TimeExposed {
    using Type = CustomIndexArray<UncertainValue<FP>, AgeGroup>;
    static Type get_default(AgeGroup size)
    {
        return Type(size, 5.2);
    }
    static std::string name()
    {
        return "TimeExposed";
    }
};
 
template <typename FP>
struct TimeInfected {
    using Type = CustomIndexArray<UncertainValue<FP>, AgeGroup>;
    static Type get_default(AgeGroup size)
    {
        return Type(size, 6.0);
    }
    static std::string name()
    {
        return "TimeInfected";
    }
};
 
template <class FP>
struct ContactPatterns {
    using Type = UncertainContactMatrix<FP>;
    static Type get_default(AgeGroup size)
    {
        return Type(1, static_cast<Eigen::Index>((size_t)size));
    }
    static std::string name()
    {
        return "ContactPatterns";
    }
};
 
template <typename FP>
using ParametersBase =
    ParameterSet<TransmissionProbabilityOnContact<FP>, TimeExposed<FP>, TimeInfected<FP>, ContactPatterns<FP>>;
 
template <typename FP>
class Parameters : public ParametersBase<FP>
{
public:
    Parameters(AgeGroup num_agegroups)
        : ParametersBase<FP>(num_agegroups)
        , m_num_groups{num_agegroups}
    {
    }
 
    AgeGroup get_num_groups() const
    {
        return m_num_groups;
    }
 
    bool apply_constraints()
    {
        const FP tol_times = 1e-1;
 
        int corrected = false;
 
        for (auto i = AgeGroup(0); i < AgeGroup(m_num_groups); ++i) {
            if (this->template get<TimeExposed<FP>>()[i] < tol_times) {
                log_warning(
                    "Constraint check: Parameter TimeExposed changed from {} to {}. Please note that "
                    "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
                    "and reset parameters.",
                    this->template get<TimeExposed<FP>>()[i], tol_times);
                this->template get<TimeExposed<FP>>()[i] = tol_times;
                corrected                                = true;
            }
            if (this->template get<TimeInfected<FP>>()[i] < tol_times) {
                log_warning(
                    "Constraint check: Parameter TimeInfected changed from {} to {}. Please note that "
                    "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
                    "and reset parameters.",
                    this->template get<TimeInfected<FP>>()[i], tol_times);
                this->template get<TimeInfected<FP>>()[i] = tol_times;
                corrected                                 = true;
            }
            if (this->template get<TransmissionProbabilityOnContact<FP>>()[i] < 0.0 ||
                this->template get<TransmissionProbabilityOnContact<FP>>()[i] > 1.0) {
                log_warning("Constraint check: Parameter TransmissionProbabilityOnContact changed from {} to {} ",
                            this->template get<TransmissionProbabilityOnContact<FP>>()[i], 0.0);
                this->template get<TransmissionProbabilityOnContact<FP>>()[i] = 0.0;
                corrected                                                     = true;
            }
        }
        return corrected;
    }
 
    bool check_constraints() const
    {
        const FP tol_times = 1e-1;
 
        for (auto i = AgeGroup(0); i < m_num_groups; i++) {
            if (this->template get<TimeExposed<FP>>()[i] < tol_times) {
                log_warning(
                    "Constraint check: Parameter TimeExposed {} smaller or equal {}. Please note that "
                    "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
                    "and reset parameters.",
                    this->template get<TimeExposed<FP>>()[i], tol_times);
                return true;
            }
            if (this->template get<TimeInfected<FP>>()[i] < tol_times) {
                log_warning(
                    "Constraint check: Parameter TimeInfected {} smaller or equal {}. Please note that "
                    "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
                    "and reset parameters.",
                    this->template get<TimeInfected<FP>>()[i], tol_times);
                return true;
            }
            if (this->template get<TransmissionProbabilityOnContact<FP>>()[i] < 0.0 ||
                this->template get<TransmissionProbabilityOnContact<FP>>()[i] > 1.0) {
                log_error("Constraint check: Parameter TransmissionProbabilityOnContact {} smaller {} or "
                          "greater {}",
                          this->template get<TransmissionProbabilityOnContact<FP>>()[i], 0.0, 1.0);
                return true;
            }
        }
        return false;
    }
 
private:
    Parameters(ParametersBase<FP>&& base)
        : ParametersBase<FP>(std::move(base))
        , m_num_groups(this->template get<ContactPatterns<FP>>().get_cont_freq_mat().get_num_groups())
    {
    }
 
public:
    template <class IOContext>
    static IOResult<Parameters> deserialize(IOContext& io)
    {
        BOOST_OUTCOME_TRY(auto&& base, ParametersBase<FP>::deserialize(io));
        return success(Parameters(std::move(base)));
    }
 
private:
    AgeGroup m_num_groups;
};
} // namespace oseir
} // namespace mio
 
#endif // SEIR_PARAMETERS_H