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1133 Change member functions in Model class from public to private in IDE model #1166

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1133 Change member functions in Model class from public to private in IDE model #1166

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@annawendler annawendler commented Dec 19, 2024 •
edited by lenaploetzke
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Changes and Information

  • Make member functions that are required for simulating private
  • Define Simulation class and set_initial_flows() as friends

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Closes #1133

@annawendler annawendler linked an issue Dec 19, 2024 that may be closed by this pull request
Change member functions in Model class from public to private in IDE model #1133
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lenaploetzke
lenaploetzke reviewed Jan 2, 2025
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Nice PR, I guess this really prevents the model functions from being misused. :) I just have a few comments. Please also tick the boxes of the checks by author.

cpp/models/ide_secir/model.h
@@ -61,6 +61,67 @@ class Model
CustomIndexArray<ScalarType, AgeGroup> deaths, size_t num_agegroups,
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Just a side note: Can you remove the second #include here? And what is the header cstddef needed for?

cpp/models/ide_secir/model.h
* @brief Checks constraints on model parameters and initial data.
* @return Returns true if one (or more) constraint(s) are not satisfied, otherwise false.
*/
bool check_constraints(ScalarType dt) const
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Can we maybe move the implementation of the function in the cpp file? This got a little long. If you want to keep it in place, we should include the logging.h file.

cpp/models/ide_secir/model.h
@@ -61,6 +61,67 @@ class Model
CustomIndexArray<ScalarType, AgeGroup> deaths, size_t num_agegroups,
CustomIndexArray<ScalarType, AgeGroup> total_confirmed_cases = CustomIndexArray<ScalarType, AgeGroup>());
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We have a typo in lines 54+55: containg instead of containing

cpp/models/ide_secir/model.h
*
* @return Index representing the initialization method.
*/
int get_initialization_method_compartments()
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Can you add the const keyword here?

cpp/models/ide_secir/model.h
CustomIndexArray<ScalarType, AgeGroup>
m_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. ----
/**
* @brief Compute the compartment specified in idx_InfectionState at the current time -- only using historic flow
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In line 224 there is also a typo: infoming instead of incoming.

cpp/models/ide_secir/model.h
@@ -406,6 +407,11 @@ class Model
m_transitiondistributions_in_forceofinfection; ///< CustomIndexArray
// of Type AgeGroup containing a Vector containing the weighted TransitionDistributions for all necessary time
// points in the force of infection term.

// ---- Friend classes/functions. ----
friend class Simulation;
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Maybe you can add some small comments why these friends are necessary.

lenaploetzke
lenaploetzke reviewed Jan 2, 2025
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cpp/models/ide_secir/model.h
// Attention: m_populations and m_transitions 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
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Btw: Actually, m_ is only used for private variables. I dont know if you want to change this,

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Change member functions in Model class from public to private in IDE model
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@annawendler @lenaploetzke