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_SEIRVV_PARAMETERS_H
22 : #define MIO_SDE_SEIRVV_PARAMETERS_H
23 :
24 : #include "memilio/utils/uncertain_value.h"
25 : #include "memilio/epidemiology/contact_matrix.h"
26 : #include "memilio/utils/parameter_set.h"
27 :
28 : namespace mio
29 : {
30 : namespace sseirvv
31 : {
32 :
33 : /******************************************
34 : * Define Parameters of the SSEIRVV model *
35 : ******************************************/
36 :
37 : /**
38 : * @brief Probability of getting infected from a contact
39 : * with variant 1.
40 : */
41 : struct TransmissionProbabilityOnContactV1 {
42 : using Type = UncertainValue<>;
43 27 : static Type get_default()
44 : {
45 27 : return Type(1.0);
46 : }
47 : static std::string name()
48 : {
49 : return "TransmissionProbabilityOnContactV1";
50 : }
51 : };
52 :
53 : /**
54 : * @brief Probability of getting infected from a contact
55 : * with variant 2.
56 : */
57 : struct TransmissionProbabilityOnContactV2 {
58 : using Type = UncertainValue<>;
59 27 : static Type get_default()
60 : {
61 27 : return Type(1.0);
62 : }
63 : static std::string name()
64 : {
65 : return "TransmissionProbabilityOnContactV2";
66 : }
67 : };
68 :
69 : /**
70 : * @brief The latent time of variant 1 in days.
71 : */
72 : struct TimeExposedV1 {
73 : using Type = UncertainValue<ScalarType>;
74 27 : static Type get_default()
75 : {
76 27 : return Type(6.0);
77 : }
78 : static std::string name()
79 : {
80 : return "TimeExposedV1";
81 : }
82 : };
83 :
84 : /**
85 : * @brief The latent time of variant 2 in days.
86 : */
87 : struct TimeExposedV2 {
88 : using Type = UncertainValue<ScalarType>;
89 27 : static Type get_default()
90 : {
91 27 : return Type(6.0);
92 : }
93 : static std::string name()
94 : {
95 : return "TimeExposedV2";
96 : }
97 : };
98 :
99 : /**
100 : * @brief The infectious time of variant 1 in days.
101 : */
102 : struct TimeInfectedV1 {
103 : using Type = UncertainValue<ScalarType>;
104 27 : static Type get_default()
105 : {
106 27 : return Type(6.0);
107 : }
108 : static std::string name()
109 : {
110 : return "TimeInfectedV1";
111 : }
112 : };
113 :
114 : /**
115 : * @brief The infectious time of variant 2 in days.
116 : */
117 : struct TimeInfectedV2 {
118 : using Type = UncertainValue<ScalarType>;
119 27 : static Type get_default()
120 : {
121 27 : return Type(6.0);
122 : }
123 : static std::string name()
124 : {
125 : return "TimeInfectedV2";
126 : }
127 : };
128 :
129 : /**
130 : * @brief The contact patterns within the society are modelled using a ContactMatrix.
131 : */
132 : struct ContactPatterns {
133 : using Type = ContactMatrix;
134 27 : static Type get_default()
135 : {
136 27 : return Type{1};
137 : }
138 : static std::string name()
139 : {
140 : return "ContactPatterns";
141 : }
142 : };
143 :
144 : using ParametersBase = ParameterSet<TransmissionProbabilityOnContactV1, TransmissionProbabilityOnContactV2,
145 : TimeExposedV1, TimeExposedV2, TimeInfectedV1, TimeInfectedV2, ContactPatterns>;
146 :
147 : /**
148 : * @brief Parameters of stochastic SEIRVV model.
149 : */
150 : class Parameters : public ParametersBase
151 : {
152 : public:
153 27 : Parameters()
154 27 : : ParametersBase()
155 : {
156 27 : }
157 :
158 : /**
159 : * @brief Checks whether all Parameters satisfy their corresponding constraints and applies them, if they do not.
160 : * Time spans cannot be negative and probabilities can only take values between [0,1].
161 : *
162 : * Attention: This function should be used with care. It is necessary for some test problems to run through quickly,
163 : * but in a manual execution of an example, check_constraints() may be preferred. Note that the apply_constraints()
164 : * function can and will not set Parameters to meaningful values in an epidemiological or virological context,
165 : * as all models are designed to be transferable to multiple diseases. Consequently, only acceptable
166 : * (like 0 or 1 for probabilities or small positive values for time spans) values are set here and a manual adaptation
167 : * may often be necessary to have set meaningful values.
168 : *
169 : * @return Returns true if one ore more constraint were corrected, false otherwise.
170 : */
171 72 : bool apply_constraints()
172 : {
173 72 : double tol_times = 1e-1;
174 :
175 72 : int corrected = false;
176 72 : if (this->get<TimeExposedV1>() < tol_times) {
177 18 : log_warning("Constraint check: Parameter TimeExposedV1 changed from {:.4f} to {:.4f}. Please note that "
178 : "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
179 : "and reset parameters.",
180 9 : this->get<TimeExposedV1>(), tol_times);
181 9 : this->get<TimeExposedV1>() = tol_times;
182 9 : corrected = true;
183 : }
184 72 : if (this->get<TimeExposedV2>() < tol_times) {
185 36 : log_warning("Constraint check: Parameter TimeExposedV2 changed from {:.4f} to {:.4f}. Please note that "
186 : "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
187 : "and reset parameters.",
188 18 : this->get<TimeExposedV2>(), tol_times);
189 18 : this->get<TimeExposedV2>() = tol_times;
190 18 : corrected = true;
191 : }
192 72 : if (this->get<TimeInfectedV1>() < tol_times) {
193 18 : log_warning("Constraint check: Parameter TimeInfectedV1 changed from {:.4f} to {:.4f}. Please note that "
194 : "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
195 : "and reset parameters.",
196 9 : this->get<TimeInfectedV1>(), tol_times);
197 9 : this->get<TimeInfectedV1>() = tol_times;
198 9 : corrected = true;
199 : }
200 72 : if (this->get<TimeInfectedV2>() < tol_times) {
201 18 : log_warning("Constraint check: Parameter TimeInfectedV2 changed from {:.4f} to {:.4f}. Please note that "
202 : "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
203 : "and reset parameters.",
204 9 : this->get<TimeInfectedV2>(), tol_times);
205 9 : this->get<TimeInfectedV2>() = tol_times;
206 9 : corrected = true;
207 : }
208 144 : if (this->get<TransmissionProbabilityOnContactV1>() < 0.0 ||
209 72 : this->get<TransmissionProbabilityOnContactV1>() > 1.0) {
210 18 : log_warning("Constraint check: Parameter TransmissionProbabilityOnContactV1 changed from {:0.4f} to {:d} ",
211 18 : this->get<TransmissionProbabilityOnContactV1>(), 0.0);
212 9 : this->get<TransmissionProbabilityOnContactV1>() = 0.0;
213 9 : corrected = true;
214 : }
215 144 : if (this->get<TransmissionProbabilityOnContactV2>() < 0.0 ||
216 72 : this->get<TransmissionProbabilityOnContactV2>() > 1.0) {
217 18 : log_warning("Constraint check: Parameter TransmissionProbabilityOnContactV2 changed from {:0.4f} to {:d} ",
218 18 : this->get<TransmissionProbabilityOnContactV2>(), 0.0);
219 9 : this->get<TransmissionProbabilityOnContactV2>() = 0.0;
220 9 : corrected = true;
221 : }
222 72 : return corrected;
223 : }
224 :
225 : /**
226 : * @brief Checks whether all Parameters satisfy their corresponding constraints and logs an error
227 : * if constraints are not satisfied.
228 : * @return Returns true if one constraint is not satisfied, otherwise false.
229 : */
230 63 : bool check_constraints() const
231 : {
232 63 : ScalarType tol_times = 1e-1;
233 :
234 63 : if (this->get<TimeExposedV1>() < tol_times) {
235 18 : log_error("Constraint check: Parameter TimeExposedV1 {:.4f} smaller or equal {:.4f}. Please note that "
236 : "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
237 : "and reset parameters.",
238 18 : this->get<TimeExposedV1>(), 0.0);
239 9 : return true;
240 : }
241 54 : if (this->get<TimeExposedV2>() < tol_times) {
242 18 : log_error("Constraint check: Parameter TimeExposedV2 {:.4f} smaller or equal {:.4f}. Please note that "
243 : "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
244 : "and reset parameters.",
245 18 : this->get<TimeExposedV2>(), 0.0);
246 9 : return true;
247 : }
248 45 : if (this->get<TimeInfectedV1>() < tol_times) {
249 18 : log_error("Constraint check: Parameter TimeInfectedV1 {:.4f} smaller or equal {:.4f}. Please note that "
250 : "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
251 : "and reset parameters.",
252 18 : this->get<TimeInfectedV1>(), 0.0);
253 9 : return true;
254 : }
255 36 : if (this->get<TimeInfectedV2>() < tol_times) {
256 18 : log_error("Constraint check: Parameter TimeInfectedV2 {:.4f} smaller or equal {:.4f}. Please note that "
257 : "unreasonably small compartment stays lead to massively increased run time. Consider to cancel "
258 : "and reset parameters.",
259 18 : this->get<TimeInfectedV2>(), 0.0);
260 9 : return true;
261 : }
262 54 : if (this->get<TransmissionProbabilityOnContactV1>() < 0.0 ||
263 27 : this->get<TransmissionProbabilityOnContactV1>() > 1.0) {
264 18 : log_error(
265 : "Constraint check: Parameter TransmissionProbabilityOnContactV1 {:.4f} smaller {:.4f} or greater {:.4f}",
266 18 : this->get<TransmissionProbabilityOnContactV1>(), 0.0, 1.0);
267 9 : return true;
268 : }
269 36 : if (this->get<TransmissionProbabilityOnContactV2>() < 0.0 ||
270 18 : this->get<TransmissionProbabilityOnContactV2>() > 1.0) {
271 18 : log_error(
272 : "Constraint check: Parameter TransmissionProbabilityOnContactV2 {:.4f} smaller {:.4f} or greater {:.4f}",
273 18 : this->get<TransmissionProbabilityOnContactV2>(), 0.0, 1.0);
274 9 : return true;
275 : }
276 9 : return false;
277 : }
278 :
279 : private:
280 : Parameters(ParametersBase&& base)
281 : : ParametersBase(std::move(base))
282 : {
283 : }
284 :
285 : public:
286 : /**
287 : * Deserialize an object of this class.
288 : * @see mio::deserialize
289 : */
290 : template <class IOContext>
291 : static IOResult<Parameters> deserialize(IOContext& io)
292 : {
293 : BOOST_OUTCOME_TRY(auto&& base, ParametersBase::deserialize(io));
294 : return success(Parameters(std::move(base)));
295 : }
296 : };
297 :
298 : } // namespace sseirvv
299 : } // namespace mio
300 :
301 : #endif // MIO_SDE_SEIRVV_PARAMETERS_H
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