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[Hotfix] Eigen Refs #139

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Merged
MJC598 merged 1 commit into from
Jun 26, 2026
Merged

[Hotfix] Eigen Refs #139

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14 changes: 8 additions & 6 deletions include/respond/cost_effectiveness.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2025-08-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2025-2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -27,7 +27,7 @@ namespace respond {
/// @param N Number of weeks to discount over.
/// @param isDiscrete Whether the discount is a discrete or continuous discount.
/// @return A matrix with the discounted data.
inline Eigen::VectorXd Discount(const Eigen::VectorXd &data,
inline Eigen::VectorXd Discount(const Eigen::Ref<const Eigen::VectorXd> &data,
double discount_rate, int week,
bool is_discrete = true,
double total_weeks = 52.0) {
Expand All @@ -41,17 +41,19 @@ inline Eigen::VectorXd Discount(const Eigen::VectorXd &data,
/// @param state The state matrix.
/// @param multiplier The multiplying matrix.
/// @return state cwise multiplied by the multiplying matrix.
inline Eigen::VectorXd CwiseProduct(const Eigen::VectorXd &state,
const Eigen::VectorXd &multiplier) {
inline Eigen::VectorXd
CwiseProduct(const Eigen::Ref<const Eigen::VectorXd> &state,
const Eigen::Ref<const Eigen::VectorXd> &multiplier) {
return state.cwiseProduct(multiplier);
}

/// @brief A cwise minimizer. This is used for min utility.
/// @param state The state matrix.
/// @param multiplier The multiplying matrix.
/// @return state cwise multiplied by the multiplying matrix.
inline Eigen::VectorXd CwiseMin(const Eigen::VectorXd &state,
const Eigen::VectorXd &multiplier) {
inline Eigen::VectorXd
CwiseMin(const Eigen::Ref<const Eigen::VectorXd> &state,
const Eigen::Ref<const Eigen::VectorXd> &multiplier) {
return state.cwiseMin(multiplier);
}

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10 changes: 6 additions & 4 deletions include/respond/history.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-05-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand Down Expand Up @@ -206,7 +206,8 @@ class History {
/// automatic next timestep). If timestep is negative, the next sequential
/// timestep is used automatically. If timestep already exists, it is
/// considered invalid but is currently overwritten.
void AddState(const Eigen::VectorXd &state, int timestep = -1) {
void AddState(const Eigen::Ref<const Eigen::VectorXd> &state,
int timestep = -1) {
if (timestep < 0) {
timestep = GetNextTimestep();
}
Expand All @@ -227,13 +228,14 @@ class History {
/// @brief Records a snapshot value at a concrete timestep.
/// @param state The snapshot value to record.
/// @param timestep The simulation timestep for this snapshot.
void RecordSnapshot(const Eigen::VectorXd &state, int timestep) {
void RecordSnapshot(const Eigen::Ref<const Eigen::VectorXd> &state,
int timestep) {
AddState(state, timestep);
}

/// @brief Adds a contribution to an accumulated history.
/// @param state The per-step contribution to accumulate.
void AccumulateState(const Eigen::VectorXd &state) {
void AccumulateState(const Eigen::Ref<const Eigen::VectorXd> &state) {
if (_mode != HistoryMode::Accumulated) {
AddState(state);
return;
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4 changes: 2 additions & 2 deletions include/respond/model.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-12 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand Down Expand Up @@ -33,7 +33,7 @@ class Model {

/// @brief Sets the current state of the model.
/// @param state The state vector to set. A copy is made internally.
virtual void SetState(const Eigen::VectorXd &state) = 0;
virtual void SetState(const Eigen::Ref<const Eigen::VectorXd> &state) = 0;

/// @brief Retrieves the current state of the model.
/// @return A copy of the current state vector (limited to observation).
Expand Down
7 changes: 4 additions & 3 deletions include/respond/transition.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-02 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-09 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand Down Expand Up @@ -40,13 +40,14 @@ class Transition {
/// transition).
/// @return The resulting state vector after applying this transition.
virtual Eigen::VectorXd
Execute(const Eigen::VectorXd &s,
Execute(const Eigen::Ref<const Eigen::VectorXd> &s,
std::map<std::string, History> &h) const = 0;

/// @brief Adds a transformation matrix to this transition.
/// The matrix is stored for use during Execute() calls.
/// @param m The transition matrix to add (not modified by this transition).
virtual void AddTransitionMatrix(const Eigen::MatrixXd &m) = 0;
virtual void
AddTransitionMatrix(const Eigen::Ref<const Eigen::MatrixXd> &m) = 0;

/// @brief Retrieves the name/type of this transition.
/// @return The transition's identifier as a string.
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4 changes: 2 additions & 2 deletions src/background.cpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-12 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -20,7 +20,7 @@

namespace respond {
Eigen::VectorXd
BackgroundDeath::Execute(const Eigen::VectorXd &state,
BackgroundDeath::Execute(const Eigen::Ref<const Eigen::VectorXd> &state,
std::map<std::string, History> &h) const {
if (GetTransitionMatrices().size() != 1) {
std::string error_msg =
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7 changes: 4 additions & 3 deletions src/behavior.cpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-05 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -19,8 +19,9 @@
#include <spdlog/spdlog.h>

namespace respond {
Eigen::VectorXd Behavior::Execute(const Eigen::VectorXd &state,
std::map<std::string, History> &h) const {
Eigen::VectorXd
Behavior::Execute(const Eigen::Ref<const Eigen::VectorXd> &state,
std::map<std::string, History> &h) const {
if (GetTransitionMatrices().size() != 1) {
std::string error_msg =
"Behavior error: Expected 1 transition matrix, got " +
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4 changes: 2 additions & 2 deletions src/internals/background.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -25,7 +25,7 @@ class BackgroundDeath : public virtual TransitionBase {
// Run the execute function and return the final state. Do not edit the
// parameter state, but do edit the history provided. Nothing in the
// Transition object should change.
Eigen::VectorXd Execute(const Eigen::VectorXd &s,
Eigen::VectorXd Execute(const Eigen::Ref<const Eigen::VectorXd> &s,
std::map<std::string, History> &h) const override;

// Clone
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4 changes: 2 additions & 2 deletions src/internals/behavior.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -25,7 +25,7 @@ class Behavior : public virtual TransitionBase {
// Run the execute function and return the final state. Do not edit the
// parameter state, but do edit the history provided. Nothing in the
// Transition object should change.
Eigen::VectorXd Execute(const Eigen::VectorXd &s,
Eigen::VectorXd Execute(const Eigen::Ref<const Eigen::VectorXd> &s,
std::map<std::string, History> &h) const override;

// Clone
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4 changes: 2 additions & 2 deletions src/internals/intervention.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -25,7 +25,7 @@ class Intervention : public virtual TransitionBase {
// Run the execute function and return the final state. Do not edit the
// parameter state, but do edit the history provided. Nothing in the
// Transition object should change.
Eigen::VectorXd Execute(const Eigen::VectorXd &s,
Eigen::VectorXd Execute(const Eigen::Ref<const Eigen::VectorXd> &s,
std::map<std::string, History> &h) const override;

// Clone
Expand Down
6 changes: 4 additions & 2 deletions src/internals/markov.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-05-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand Down Expand Up @@ -78,7 +78,9 @@ class Markov : public virtual Model {
}

// anticipate making a copy of the vector
void SetState(const Eigen::VectorXd &s) override { _state = s; }
void SetState(const Eigen::Ref<const Eigen::VectorXd> &s) override {
_state = s;
}
// return const & to limit to observation of the state
Eigen::VectorXd GetState() const override { return _state; }
// return the transitions
Expand Down
4 changes: 2 additions & 2 deletions src/internals/migration.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -25,7 +25,7 @@ class Migration : public virtual TransitionBase {
// Run the execute function and return the final state. Do not edit the
// parameter state, but do edit the history provided. Nothing in the
// Transition object should change.
Eigen::VectorXd Execute(const Eigen::VectorXd &s,
Eigen::VectorXd Execute(const Eigen::Ref<const Eigen::VectorXd> &s,
std::map<std::string, History> &h) const override;

// Clone
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4 changes: 2 additions & 2 deletions src/internals/overdose.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -25,7 +25,7 @@ class Overdose : public virtual TransitionBase {
// Run the execute function and return the final state. Do not edit the
// parameter state, but do edit the history provided. Nothing in the
// Transition object should change.
Eigen::VectorXd Execute(const Eigen::VectorXd &s,
Eigen::VectorXd Execute(const Eigen::Ref<const Eigen::VectorXd> &s,
std::map<std::string, History> &h) const override;

// Clone
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5 changes: 3 additions & 2 deletions src/internals/transition_base.hpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-06 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -24,7 +24,8 @@ class TransitionBase : public virtual Transition {
// Add a Transition Matrix to the set. We have no need to edit it once it's
// been added, just use it. Thus, we don't need full ownership (reference)
// and can accept the const type.
void AddTransitionMatrix(const Eigen::MatrixXd &m) override {
void
AddTransitionMatrix(const Eigen::Ref<const Eigen::MatrixXd> &m) override {
_transition_matrices.push_back(m);
}
// Get the name of the Transition. No need to edit the object and do not
Expand Down
7 changes: 4 additions & 3 deletions src/intervention.cpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-05 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -19,8 +19,9 @@
#include <spdlog/spdlog.h>

namespace respond {
Eigen::VectorXd Intervention::Execute(const Eigen::VectorXd &state,
std::map<std::string, History> &h) const {
Eigen::VectorXd
Intervention::Execute(const Eigen::Ref<const Eigen::VectorXd> &state,
std::map<std::string, History> &h) const {
if (GetTransitionMatrices().size() != 1) {
std::string error_msg =
"Intervention error: Expected 1 transition matrix, got " +
Expand Down
7 changes: 4 additions & 3 deletions src/migration.cpp
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Expand Up @@ -4,7 +4,7 @@
// Created Date: 2026-02-05 //
// Author: Matthew Carroll //
// ----- //
// Last Modified: 2026-02-12 //
// Last Modified: 2026-06-25 //
// Modified By: Matthew Carroll //
// ----- //
// Copyright (c) 2026 Syndemics Lab at Boston Medical Center //
Expand All @@ -19,8 +19,9 @@
#include <spdlog/spdlog.h>

namespace respond {
Eigen::VectorXd Migration::Execute(const Eigen::VectorXd &state,
std::map<std::string, History> &h) const {
Eigen::VectorXd
Migration::Execute(const Eigen::Ref<const Eigen::VectorXd> &state,
std::map<std::string, History> &h) const {
if (GetTransitionMatrices().size() != 1) {
std::string error_msg =
"Migration error: Expected 1 transition matrix, got " +
Expand Down
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