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1132 Rename public members of IDE model #1173

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1132 Rename public members of IDE model #1173

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28d6a77
renaming
annawendler Jan 7, 2025
9a321fc
some adaptations
annawendler Jan 8, 2025
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6 changes: 3 additions & 3 deletions cpp/examples/ide_initialization.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ int main(int argc, char** argv)
init.add_time_point(init.get_last_time() + dt,
Vec::Constant((int)mio::isecir::InfectionTransition::Count, 1. * dt));
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Eventually adapt also the num_transitions in the ide examples and name them num_flows? Also in the tests? On the other hand this is consistent with InfectionTransition.. I dont know

}
model.m_transitions = init;
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Can you adjust in the example ide_secir lines 78+80+123+124 and in example ide_secir_ageres 64 - 69 + 124-125?

model.flows = init;
}
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Please also adapt the README (with m_populations). And maybe transitions to flows.

else {
// Use the real data for initialization.
Expand All @@ -100,8 +100,8 @@ int main(int argc, char** argv)
sim.advance(2.);

// Print results.
sim.get_transitions().print_table({"S->E", "E->C", "C->I", "C->R", "I->H", "I->R", "H->U", "H->R", "U->D", "U->R"},
16, 8);
sim.get_flows().print_table({"S->E", "E->C", "C->I", "C->R", "I->H", "I->R", "H->U", "H->R", "U->D", "U->R"}, 16,
8);

return 0;
}
185 changes: 91 additions & 94 deletions cpp/models/ide_secir/model.cpp
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58 changes: 29 additions & 29 deletions cpp/models/ide_secir/model.h
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Expand Up @@ -42,22 +42,22 @@ class Model
/**
* @brief Constructor to create an IDE-SECIR model.
*
* @param[in, out] init TimeSeries with the initial values of the number of individuals,
* @param[in, out] flows_init TimeSeries with the initial values of the number of individuals,
* which transit within one timestep dt from one compartment to another.
* Possible transitions are specified in #InfectionTransition%s.
* Considered time points should have the distance dt. The last time point determines the start time t0 of the
* simulation.
* The time history must reach a certain point in the past so that the simulation can be performed.
* A warning is displayed if the condition is violated.
* @param[in] N_init A vector, containing the populations of the considered region, for every AgeGroup.
* @param[in] deaths A vector, containing the total number of deaths at time t0, for every AgeGroup.
* @param[in] deaths_init A vector, containing the total number of deaths at time t0, for every AgeGroup.
* @param[in] num_agegroups The number of AgeGroups.
* @param[in] total_confirmed_cases A vector, containing the total confirmed cases at time t0 can be set if it
* @param[in] total_confirmed_cases_init A vector, containing the total confirmed cases at time t0 can be set if it
* should be used for initialization, for every AgeGroup.
*/
Model(TimeSeries<ScalarType>&& init, CustomIndexArray<ScalarType, AgeGroup> N_init,
CustomIndexArray<ScalarType, AgeGroup> deaths, size_t num_agegroups,
CustomIndexArray<ScalarType, AgeGroup> total_confirmed_cases = CustomIndexArray<ScalarType, AgeGroup>());
Model(TimeSeries<ScalarType>&& flows_init, CustomIndexArray<ScalarType, AgeGroup> N_init,
CustomIndexArray<ScalarType, AgeGroup> deaths_init, size_t num_agegroups,
CustomIndexArray<ScalarType, AgeGroup> total_confirmed_cases_init = CustomIndexArray<ScalarType, AgeGroup>());

// ---- Additional functionality such as constraint checking, setters and getters, etc. ----
/**
Expand All @@ -67,10 +67,10 @@ class Model
bool check_constraints(ScalarType dt) const;

/**
* @brief Returns a flat index for the InfectionTransition TimeSeries.
* @brief Returns a flat index for the TimeSeries flows which contains values for the InfectionTransitions.
*
* In the TimeSeries we store a vector for each time point. In this vector we store the different
* #InfectionTransition%s for every AgeGroup.
* In the TimeSeries we store a vector for each time point. In this vector we store values for the different
* InfectionTransitions for every AgeGroup.
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Why not #InfectionTransition%s?

* This function is used to get the right index in this vector for a specific AgeGroup and InfectionTransition.
*
* @param[in] transition_idx Index determining which InfectionTransition we want to evaluate.
Expand All @@ -83,10 +83,10 @@ class Model
}

/**
* @brief Returns a flat index for the InfectionState TimeSeries.
* @brief Returns a flat index for the TimeSeries populations which contains values for the InfectionStates.
*
* In the TimeSeries we store a vector for each time point. In this vector we store the different InfectionStates
* for every AgeGroup.
* In the TimeSeries we store a vector for each time point. In this vector we store values for the
* different InfectionStates for every AgeGroup.
* This function is used to get the right index in this vector for a specific AgeGroup and InfectionState.
*
* @param[in] state_idx Index at which InfectionState we want to evaluate.
Expand Down Expand Up @@ -142,15 +142,15 @@ class Model

// ---- Public parameters. ----
ParameterSet parameters{AgeGroup(m_num_agegroups)}; ///< ParameterSet of Model Parameters.
// Attention: m_populations and m_transitions do not necessarily have the same number of time points due to the
// Attention: populations and flows do not necessarily have the same number of time points due to the
// initialization part.
TimeSeries<ScalarType>
m_transitions; ///< TimeSeries containing points of time and the corresponding number of transitions for every
// AgeGroup.
TimeSeries<ScalarType> m_populations; ///< TimeSeries containing points of time and the corresponding number of
flows; ///< TimeSeries containing points of time and the corresponding number of individuals transitioning from
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flows and InfectionTransitions and Transitiondistributions are no longer linked by name. Do you think that's bad? I dont know how to feel about this.

// one InfectionState to another as defined in InfectionTransitions for every AgeGroup.
TimeSeries<ScalarType> populations; ///< TimeSeries containing points of time and the corresponding number of
// people in defined #InfectionState%s for every AgeGroup.
CustomIndexArray<ScalarType, AgeGroup>
m_total_confirmed_cases; ///< CustomIndexArray that contains the total number of confirmed cases at time t0 for every AgeGroup.
total_confirmed_cases; ///< CustomIndexArray that contains the total number of confirmed cases at time t0 for every AgeGroup.

private:
// ---- Functionality to calculate the sizes of the compartments for time t0. ----
Expand All @@ -165,7 +165,7 @@ class Model
* @param[in] dt Time discretization step size.
* @param[in] idx_InfectionState Specifies the considered #InfectionState
* @param[in] group The AgeGroup for which we want to compute.
* @param[in] idx_IncomingFlow Specifies the index of the incoming flow to #InfectionState in m_transitions.
* @param[in] idx_IncomingFlow Specifies the index of the incoming flow to #InfectionState in flows.
* @param[in] idx_TransitionDistribution1 Specifies the index of the first relevant TransitionDistribution,
* related to a flow from the considered #InfectionState to any other #InfectionState.
* This index is also used for related probability.
Expand All @@ -185,7 +185,7 @@ class Model
*
* The values for the compartments Exposed, InfectedNoSymptoms, InfectedSymptoms, InfectedSevere and
* InfectedCritical for time t_0 are calculated using the initial data in form of flows.
* Calculated values are stored in m_populations.
* Calculated values are stored in populations.
*
* @param[in] dt Time discretization step size.
*/
Expand Down Expand Up @@ -214,10 +214,10 @@ class Model

// ---- Functionality for the iterations of a simulation. ----
/**
* @brief Computes number of Susceptible%s for the current last time in m_populations.
* @brief Computes number of Susceptible%s for the current last time in populations.
*
* Number is computed using previous number of Susceptible%s and the force of infection (also from previous timestep).
* Number is stored at the matching index in m_populations.
* Number is stored at the matching index in populations.
* @param[in] dt Time discretization step size.
*/
void compute_susceptibles(ScalarType dt);
Expand All @@ -240,10 +240,10 @@ class Model
Eigen::Index current_time_index, AgeGroup group);

/**
* @brief Computes size of a flow for the current last time value in m_transitions.
* @brief Computes size of a flow for the current last time value in flows.
*
* Computes size of one flow from #InfectionTransition, specified in idx_InfectionTransitions, for the current
* last time value in m_transitions.
* last time value in flows.
*
* @param[in] idx_InfectionTransitions Specifies the considered flow from #InfectionTransition.
* @param[in] idx_IncomingFlow Index of the flow in #InfectionTransition, which goes to the considered starting
Expand All @@ -256,9 +256,9 @@ class Model
AgeGroup group);

/**
* @brief Sets all required flows for the current last timestep in m_transitions.
* @brief Sets all required flows for the current last timestep in flows.
*
* New values are stored in m_transitions. Most values are computed via the function compute_flow().
* New values are stored in flows. Most values are computed via the function compute_flow().
*
* @param[in] dt Time step.
*/
Expand All @@ -267,7 +267,7 @@ class Model
/**
* @brief Updates the values of one compartment using flows.
*
* New value is stored in m_populations. The value is calculated using the compartment size in the previous
* New value is stored in populations. The value is calculated using the compartment size in the previous
* time step and the related flows of the current time step.
* Therefore the flows of the current time step should be calculated before using this function.
*/
Expand All @@ -278,22 +278,22 @@ class Model
/**
* @brief Updates the values of all compartments except Susceptible at initialization.
*
* New values are stored in m_populations. The values are calculated using the compartment size in the previous
* New values are stored in populations. The values are calculated using the compartment size in the previous
* time step and the related flows of the current time step.
* Therefore the flows of the current time step should be calculated before using this function.
*
*/
void update_compartments();

/**
* @brief Computes force of infection for the current last time in m_transitions.
* @brief Computes force of infection for the current last time in flows.
*
* Computed value is stored in m_forceofinfection.
*
* @param[in] dt Time discretization step size.
* @param[in] initialization If true we are in the case of the initialization of the model.
* For this we need forceofinfection at time point t0-dt and not at the current last time
* (given by m_transitions) as in the other time steps.
* (given by flows) as in the other time steps.
*/
void compute_forceofinfection(ScalarType dt, bool initialization = false);

Expand Down
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