
#ifndef EPIWORLD_MODELS_MEASLESMIXINGRISKQUARANTINE_HPP
#define EPIWORLD_MODELS_MEASLESMIXINGRISKQUARANTINE_HPP

#include "../tools/vaccine.hpp"
#include "../model-bones.hpp"

#define COL_MAJOR_POS(i, j, n) \
    (j * n + i)

#if defined(__clang__)
    // Clang
    #define GET_MODEL(model, output) \
        auto * output = dynamic_cast< ModelMeaslesMixingRiskQuarantine<TSeq> * >( (model) ); \
        __builtin_assume((output) != nullptr);
#elif defined(__GNUC__) && __GNUC__ >= 13
    // GCC 13 or later
    #define GET_MODEL(model, output) \
        auto * output = dynamic_cast< ModelMeaslesMixingRiskQuarantine<TSeq> * >( (model) ); \
        [[assume((output) != nullptr)]];
#else
    #define GET_MODEL(model, output) \
        auto * output = dynamic_cast< ModelMeaslesMixingRiskQuarantine<TSeq> * >( (model) ); \
        assert((output) != nullptr); // Use assert for runtime checks
#endif

/**
 * @brief Macro to sample from a list of probabilities
 * @return The index of the sampled probability; and the total length
 * if none is found, returns n.
 */
#define SAMPLE_FROM_PROBS(n, ans) \
    int ans; \
    epiworld_double p_total = m->runif(); \
    for (ans = 0; ans < static_cast<int>(n); ans++) \
    { \
        if (p_total < m->array_double_tmp[ans]) \
            break; \
        m->array_double_tmp[ans + 1] += m->array_double_tmp[ans]; \
    };

/**
 * @file measlesmixingriskquarantine.hpp
 * @brief Template for a Measles model with population mixing and risk-based quarantine
 */

/**
 * @brief Measles model with population mixing and risk-based quarantine strategies
 * 
 * This class extends the Measles epidemiological model to support different
 * quarantine strategies based on exposure risk levels:
 * 
 * - **High Risk**: Unvaccinated agents who share entity membership with the case
 * - **Medium Risk**: Unvaccinated agents who contacted an infected individual but don't share entity membership  
 * - **Low Risk**: Other unvaccinated agents
 * 
 * Each risk level can have different quarantine durations, allowing for targeted 
 * public health interventions. The model also includes enhanced detection during
 * active quarantine periods.
 * 
 * Disease progression follows the same states as ModelMeaslesMixing:
 * Susceptible → Exposed → Prodromal → Rash → Recovered
 * 
 * ![Model Diagram](../assets/img/measlesmixingriskquarantine.png)
 * 
 * @tparam TSeq Type for genetic sequences (default: EPI_DEFAULT_TSEQ)
 * @ingroup disease_specific
 */
template<typename TSeq = EPI_DEFAULT_TSEQ>
class ModelMeaslesMixingRiskQuarantine : public Model<TSeq> 
{
private:
    // Vector of vectors of infected agents (prodromal agents are infectious)
    std::vector< size_t > infectious;

    // Number of infectious agents in each group
    std::vector< size_t > n_infectious_per_group;
    
    // Where the agents start in the `infectious` vector
    std::vector< size_t > infectious_entity_indices;

    double m_get_risk_period(size_t agent_id);

    // Update the list of infectious agents
    void m_update_infectious_list();

    // Vector to hold sampled agents temporarily
    std::vector< size_t > sampled_agents;

    /**
     * @brief Sample infected agents based on contact matrix
     * @param agent Pointer to the agent for whom contacts are being sampled.
     * @param sampled_agents Vector to store the IDs of sampled agents.
     * @return The number of sampled agents.
     */
    size_t sample_infectious_agents(
        Agent<TSeq> * agent,
        std::vector< size_t > & sampled_agents
        );

    std::vector< double > adjusted_contact_rate;

    // Contact matrix (column-major order)
    std::vector< double > contact_matrix;

    #ifdef EPI_DEBUG
    std::vector< int > sampled_sizes;
    #endif

    // Update functions
    static void m_update_susceptible(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_exposed(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_prodromal(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_rash(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_isolated(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_isolated_recovered(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_quarantine_suscep(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_quarantine_exposed(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_quarantine_prodromal(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_quarantine_recovered(Agent<TSeq> * p, Model<TSeq> * m);
    static void m_update_hospitalized(Agent<TSeq> * p, Model<TSeq> * m);

    // Data about the quarantine process
    std::vector< bool > quarantine_willingness; ///< Indicator for quarantine willingness
    std::vector< bool > isolation_willingness;  ///< Indicator for isolation willingness
    std::vector< int > day_flagged;             ///< Either detected or started quarantine
    std::vector< int > day_rash_onset;          ///< Day of rash onset

    std::vector< size_t > agents_triggered_contact_tracing; ///< List of agents that triggered contact tracing
    size_t agents_triggered_contact_tracing_size = 0u;      ///< Number of agents that triggered contact tracing
    std::vector< bool > agents_checked_contact_tracing;     ///< if an agent has been checked for contact tracing

    // Add an agent to the list of those that triggered contact tracing
    void m_add_contact_tracing(size_t agent_id);
    
    std::vector< int > quarantine_risk_level; ///< Risk level assigned to each agent (0=low, 1=medium, 2=high)
    
    void m_quarantine_process(); ///< Overall quarantine process

    static void m_update_model(Model<TSeq> * m);

    // We will limit tracking to up to EPI_MAX_TRACKING
    ContactTracing contact_tracing;

    std::vector< size_t > days_quarantine_triggered; ///< Days when quarantine was triggered

public:

    static constexpr int SUSCEPTIBLE             = 0;
    static constexpr int EXPOSED                 = 1;
    static constexpr int PRODROMAL               = 2;
    static constexpr int RASH                    = 3;
    static constexpr int ISOLATED                = 4;
    static constexpr int ISOLATED_RECOVERED      = 5;
    static constexpr int DETECTED_HOSPITALIZED   = 6;
    static constexpr int QUARANTINED_EXPOSED     = 7;
    static constexpr int QUARANTINED_SUSCEPTIBLE = 8;
    static constexpr int QUARANTINED_PRODROMAL   = 9;
    static constexpr int QUARANTINED_RECOVERED   = 10;
    static constexpr int HOSPITALIZED            = 11;
    static constexpr int RECOVERED               = 12;

    static constexpr size_t QUARANTINE_PROCESS_INACTIVE = 0u;
    static constexpr size_t QUARANTINE_PROCESS_ACTIVE   = 1u;
    static constexpr size_t QUARANTINE_PROCESS_DONE     = 2u;

    // Risk levels for quarantine
    static constexpr int RISK_LOW    = 0;
    static constexpr int RISK_MEDIUM = 1;
    static constexpr int RISK_HIGH   = 2;

    ModelMeaslesMixingRiskQuarantine() {};
    
    /**
     * @brief Constructs a ModelMeaslesMixingRiskQuarantine object.
     *
     * @param model A reference to an existing ModelMeaslesMixingRiskQuarantine object.
     * @param n The number of entities in the model.
     * @param prevalence The initial prevalence of the disease in the model.
     * @param contact_rate The contact rate between entities in the model.
     * @param transmission_rate The transmission rate of the disease in the model.
     * @param vax_efficacy The efficacy of the vaccine.
     * @param incubation_period The incubation period of the disease in the model.
     * @param prodromal_period The prodromal period of the disease in the model.
     * @param rash_period The rash period of the disease in the model.
     * @param contact_matrix The contact matrix between entities in the model. Specified in
     * column-major order.
     * @param hospitalization_rate The rate at which infected individuals are hospitalized.
     * @param hospitalization_period The average duration of hospitalization in days.
     * @param days_undetected The average number of days an infected individual remains undetected.
     * @param quarantine_period_high The duration of quarantine in days for high-risk contacts.
     * @param quarantine_period_medium The duration of quarantine in days for medium-risk contacts.
     * @param quarantine_period_low The duration of quarantine in days for low-risk contacts.
     * @param quarantine_willingness The proportion of individuals willing to comply with quarantine measures.
     * @param isolation_willingness The proportion of individuals willing to self-isolate when detected.
     * @param isolation_period The duration of isolation in days for detected infected individuals.
     * @param prop_vaccinated The proportion of vaccinated agents.
     * @param detection_rate_quarantine The detection rate during active quarantine periods.
     * @param contact_tracing_success_rate The probability of successfully identifying and tracing contacts (default: 1.0).
     * @param contact_tracing_days_prior The number of days prior to detection for which contacts are traced (default: 4).
     */
    ModelMeaslesMixingRiskQuarantine(
        ModelMeaslesMixingRiskQuarantine<TSeq> & model,
        epiworld_fast_uint n,
        epiworld_double prevalence,
        epiworld_double contact_rate,
        epiworld_double transmission_rate,
        epiworld_double vax_efficacy,
        epiworld_double incubation_period,
        epiworld_double prodromal_period,
        epiworld_double rash_period,
        std::vector< double > contact_matrix,
        epiworld_double hospitalization_rate,
        epiworld_double hospitalization_period,
        // Policy parameters
        epiworld_double days_undetected,
        epiworld_fast_int quarantine_period_high,
        epiworld_fast_int quarantine_period_medium,
        epiworld_fast_int quarantine_period_low,
        epiworld_double quarantine_willingness,
        epiworld_double isolation_willingness,
        epiworld_fast_int isolation_period,
        epiworld_double prop_vaccinated,
        epiworld_double detection_rate_quarantine,
        epiworld_double contact_tracing_success_rate = 1.0,
        epiworld_fast_uint contact_tracing_days_prior = 4u
    );
    
    /**
     * @brief Constructs a ModelMeaslesMixingRiskQuarantine object.
     *
     * @param n The number of entities in the model.
     * @param prevalence The initial prevalence of the disease in the model.
     * @param contact_rate The contact rate between entities in the model.
     * @param transmission_rate The transmission rate of the disease in the model.
     * @param vax_efficacy The efficacy of the vaccine.
     * @param incubation_period The incubation period of the disease in the model.
     * @param prodromal_period The prodromal period of the disease in the model.
     * @param rash_period The rash period of the disease in the model.
     * @param contact_matrix The contact matrix between entities in the model.
     * @param hospitalization_rate The rate at which infected individuals are hospitalized.
     * @param hospitalization_period The average duration of hospitalization in days.
     * @param days_undetected The average number of days an infected individual remains undetected.
     * @param quarantine_period_high The duration of quarantine in days for high-risk contacts.
     * @param quarantine_period_medium The duration of quarantine in days for medium-risk contacts.
     * @param quarantine_period_low The duration of quarantine in days for low-risk contacts.
     * @param quarantine_willingness The proportion of individuals willing to comply with quarantine measures.
     * @param isolation_willingness The proportion of individuals willing to self-isolate when detected.
     * @param isolation_period The duration of isolation in days for detected infected individuals.
     * @param prop_vaccinated The proportion of vaccinated agents.
     * @param detection_rate_quarantine The detection rate during active quarantine periods.
     * @param contact_tracing_success_rate The probability of successfully identifying and tracing contacts (default: 1.0).
     * @param contact_tracing_days_prior The number of days prior to detection for which contacts are traced (default: 4).
     */
    ModelMeaslesMixingRiskQuarantine(
        epiworld_fast_uint n,
        epiworld_double prevalence,
        epiworld_double contact_rate,
        epiworld_double transmission_rate,
        epiworld_double vax_efficacy,
        epiworld_double incubation_period,
        epiworld_double prodromal_period,
        epiworld_double rash_period,
        std::vector< double > contact_matrix,
        epiworld_double hospitalization_rate,
        epiworld_double hospitalization_period,
        // Policy parameters
        epiworld_double days_undetected,
        epiworld_fast_int quarantine_period_high,
        epiworld_fast_int quarantine_period_medium,
        epiworld_fast_int quarantine_period_low,
        epiworld_double quarantine_willingness,
        epiworld_double isolation_willingness,
        epiworld_fast_int isolation_period,
        epiworld_double prop_vaccinated,
        epiworld_double detection_rate_quarantine,
        epiworld_double contact_tracing_success_rate = 1.0,
        epiworld_fast_uint contact_tracing_days_prior = 4u
    );

    /**
     * @brief Run the model simulation
     * @param ndays Number of days to simulate
     * @param seed Random seed for reproducibility (default: -1 for random seed)
     * @return Reference to this model instance
     */
    ModelMeaslesMixingRiskQuarantine<TSeq> & run(
        epiworld_fast_uint ndays,
        int seed = -1
    );

    /**
     * @brief Reset the model to initial state
     */
    void reset();

    /**
     * @brief Create a clone of this model
     * @return Pointer to a new model instance with the same configuration
     */
    std::unique_ptr< Model<TSeq> > clone_ptr();

    /**
     * @brief Set the initial states of the model
     * @param proportions_ Double vector with two elements:
     * - [0]: The proportion of initially infected individuals who start in the exposed state.
     * - [1]: The proportion of initially non-infected individuals who have recovered (immune).
     * @param queue_ Optional vector for queuing specifications (default: empty).
     */
    ModelMeaslesMixingRiskQuarantine<TSeq> & initial_states(
        std::vector< double > proportions_,
        std::vector< int > queue_ = {}
    );

    /**
     * @brief Set the contact matrix for population mixing
     * @param cmat Contact matrix specifying interaction rates between groups
     */
    void set_contact_matrix(std::vector< double > cmat)
    {
        contact_matrix = cmat;
        return;
    };

    /**
     * @brief Get the current contact matrix
     * @return Vector representing the contact matrix
     */
    auto get_contact_matrix() const
    {
        return contact_matrix;
    };

    /**
     * @brief Get the quarantine willingness for all agents
     * @return Vector of boolean values indicating each agent's willingness to quarantine
     */
    auto get_quarantine_willingness() const
    {
        return quarantine_willingness;
    };

    /**
     * @brief Get the isolation willingness for all agents
     * @return Vector of boolean values indicating each agent's willingness to self-isolate
     */
    auto get_isolation_willingness() const
    {
        return isolation_willingness;
    };

    /**
     * @brief Get the risk level assigned to each agent for quarantine purposes
     * @return Vector of integers representing risk levels (0=low, 1=medium, 2=high)
     */
    const auto & get_quarantine_risk_level() const
    {
        return quarantine_risk_level;
    };


    /**
     * @brief Get the total number of quarantines that have occurred
     * @return The number of quarantines
     */
    auto get_days_quarantine_triggered() const
    {
        return days_quarantine_triggered;
    };

};

// Implementation starts here

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_model(
    Model<TSeq> * m
)
{
    GET_MODEL(m, model);

    // This will move agents between states
    model->m_quarantine_process();

    // Updating the list of infectious agents. This is needed
    // for the transmission dynamics.
    model->m_update_infectious_list();

    return;
}

template<typename TSeq>
inline double ModelMeaslesMixingRiskQuarantine<TSeq>::m_get_risk_period(size_t agent_id)
{

    double risk_period = 0.0;

    // Getting the risk level
    int risk_level = quarantine_risk_level[agent_id];

    if (risk_level == RISK_HIGH)
        risk_period = this->par("Quarantine period high");
    else if (risk_level == RISK_MEDIUM)
        risk_period = this->par("Quarantine period medium");
    else
        risk_period = this->par("Quarantine period low");

    return risk_period;

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_infectious_list()
{

    // Getting the agents from the model
    auto & agents = Model<TSeq>::get_agents();

    // Resetting the infectious list (no infected agents)
    std::fill(n_infectious_per_group.begin(), n_infectious_per_group.end(), 0u);

    // Resetting the number of available contacts
    adjusted_contact_rate.assign(this->entities.size(), 0.0);
    
    // Looping over agents to find the infectious ones
    for (const auto & a : agents)
    {

        if (a.get_state() == PRODROMAL)
        {
            if (a.get_n_entities() > 0u)
            {
                const auto & entity = a.get_entity(0u, *this);
                infectious[
                    // Position of the group in the `infectious` vector
                    infectious_entity_indices[entity.get_id()] +
                    // Position of the agent in the group
                    n_infectious_per_group[entity.get_id()]++
                ] = a.get_id();

            }
        }

        // Setting how many agents are available for contact
        if (
            ((a.get_state() < RASH) || (a.get_state() == RECOVERED)) &&
            (a.get_n_entities() > 0u)
        )
        {
            adjusted_contact_rate[
                a.get_entity(0u, *this).get_id()
            ] += 1.0;
        }

    }

    // This simplifies calculations later
    for (auto & rate: adjusted_contact_rate)
    {
        if (rate > 0.0)
            rate = Model<TSeq>::get_param("Contact rate") / rate;
        else
            rate = 0.0;  // No available contacts in this group

        if (rate > 1.0)
            rate = 1.0;
    }

    return;

}

template<typename TSeq>
inline size_t ModelMeaslesMixingRiskQuarantine<TSeq>::sample_infectious_agents(
    Agent<TSeq> * agent,
    std::vector< size_t > & sampled_agents
    )
{

    // If agent has no entities, then we return 0
    if (agent->get_n_entities() == 0u)
        return 0u;

    size_t agent_group_id = agent->get_entity(0u, *this).get_id();
    size_t ngroups = this->entities.size();

    int samp_id = 0;
    for (size_t g = 0; g < ngroups; ++g)
    {

        size_t group_size = n_infectious_per_group[g];

        if (group_size == 0u)
            continue;

        // How many from this entity?
        int nsamples = Model<TSeq>::rbinom(
            group_size,
            adjusted_contact_rate[g] * contact_matrix[
                COL_MAJOR_POS(agent_group_id, g, ngroups)
            ]
        );

        if (nsamples == 0)
            continue;

        // Sampling from the entity
        for (int s = 0; s < nsamples; ++s)
        {

            // Randomly selecting an agent
            int which = Model<TSeq>::runif() * group_size;

            // Correcting overflow error
            if (which >= static_cast<int>(group_size))
                which = static_cast<int>(group_size) - 1;

            #ifdef EPI_DEBUG
            auto & a = this->population.at(
                infectious.at(infectious_entity_indices[g] + which)
            );
            #else
            const auto & a = this->get_agent(
                infectious[infectious_entity_indices[g] + which]
            );
            #endif

            #ifdef EPI_DEBUG
            if (a.get_state() != PRODROMAL)
                throw std::logic_error(
                    "The agent is not in prodromal state, but it should be."
                );
            #endif

            // Can't sample itself
            if (a.get_id() == agent->get_id())
                continue;

            sampled_agents[samp_id++] = a.get_id();
            
        }

    }
    
    return samp_id;

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_susceptible(
    Agent<TSeq> * p, Model<TSeq> * m
) {

    // If the agent has no entities, then it can't be infected
    // (e.g., isolated agents)
    if (p->get_n_entities() == 0)
        return;

    // Downcasting to retrieve the sampler attached to the
    // class
    GET_MODEL(m, m_down);
    
    // Sampling infected agents
    size_t ndraws = m_down->sample_infectious_agents(p, m_down->sampled_agents);

    #ifdef EPI_DEBUG
    m_down->sampled_sizes.push_back(static_cast<int>(ndraws));
    #endif

    if (ndraws == 0u)
        return;
    
    // Drawing from the set
    int nviruses_tmp = 0;
    auto & m_ref = *m;
    for (size_t n = 0u; n < ndraws; ++n)
    {

        // Getting the neighbor and its virus
        auto & neighbor = m->get_agent(m_down->sampled_agents[n]);
        auto & v = neighbor.get_virus();

        #ifdef EPI_DEBUG
        if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
            throw std::logic_error(
                "Trying to add an extra element to a temporal array outside of the range."
            );
        #endif

        // Adding the current agent to the tracked interactions
        // In this case, the infected neighbor is the one
        // who interacts with the susceptible agent
        m_down->contact_tracing.add_contact(neighbor.get_id(), p->get_id(), m->today());
            
        /* And it is a function of susceptibility_reduction as well */ 
        m->array_double_tmp[nviruses_tmp] =
            (1.0 - p->get_susceptibility_reduction(v, m_ref)) *
            v->get_prob_infecting(m) *
            (1.0 - neighbor.get_transmission_reduction(v, m_ref)) 
            ; 
    
        m->array_virus_tmp[nviruses_tmp++] = &(*v);

    }

    // Running the roulette
    int which = roulette(nviruses_tmp, m);

    if (which < 0)
        return;

    p->set_virus(*m, *m->array_virus_tmp[which], EXPOSED);

    return;

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_exposed(
    Agent<TSeq> * p, Model<TSeq> * m
) {

    // Getting the virus
    auto & v = p->get_virus();

    // Does the agent become prodromal (infectious)?
    if (m->runif() < 1.0/(v->get_incubation(m)))
    {
        p->change_state(*m, PRODROMAL);
    }

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_prodromal(
    Agent<TSeq> * p, Model<TSeq> * m
) {
    
    GET_MODEL(m, model);

    // Does the agent transition to rash?
    if (m->runif() < 1.0/m->par("Prodromal period"))
    {
        // Check for detection during active quarantine
        bool detect_it = (model->get_days_quarantine_triggered().size() > 0u) &&
            (m->runif() < m->par("Detection rate quarantine"));

        model->day_rash_onset[p->get_id()] = m->today();
        p->change_state(*m, detect_it ? ISOLATED : RASH);

        if (detect_it)
            model->m_add_contact_tracing(p->get_id());
        
    }

    return ;

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_rash(
    Agent<TSeq> * p, Model<TSeq> * m
) {

    GET_MODEL(m, model);

    // Checking if the agent will be detected or not
    bool detected = false;
    if (
        (m->par("Isolation period") >= 0) &&
        (m->runif() < 1.0/m->par("Days undetected"))
    )
    {
        model->m_add_contact_tracing(p->get_id());
        detected = true;
        model->day_flagged[p->get_id()] = m->today();
    }

    // Computing probabilities for state change
    m->array_double_tmp[0] = 1.0/m->par("Rash period"); // Recovery
    m->array_double_tmp[1] = m->par("Hospitalization rate"); // Hospitalization
        
    SAMPLE_FROM_PROBS(2, which);
    
    if (which == 0) // Recovers (probability 1/rash_period)
    {
        p->rm_virus(*m, detected ? ISOLATED_RECOVERED: RECOVERED);
    }
    else if (which == 1) // Hospitalized
    {
        m->record_hospitalization(*p);
        p->change_state(*m, detected ? DETECTED_HOSPITALIZED : HOSPITALIZED);
    }
    else if (which > 2)
    {
        throw std::logic_error("The roulette returned an unexpected value.");
    }
    else if (detected)
    {
        p->change_state(*m, ISOLATED);
    }
    
    return ;

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_isolated(
    Agent<TSeq> * p, Model<TSeq> * m
) {

    GET_MODEL(m, model);

    // Figuring out if the agent can be released from isolation
    // if the isolation period is over.
    int days_since = m->today() - model->day_rash_onset[p->get_id()];

    bool unisolate =
        (m->par("Isolation period") <= days_since) ?
        true: false;

    // Probability of staying in the rash period vs becoming
    // hospitalized
    m->array_double_tmp[0] = 1.0/m->par("Rash period");
    m->array_double_tmp[1] = m->par("Hospitalization rate");

    // Sampling from the probabilities
    SAMPLE_FROM_PROBS(2, which);

    // Recovers (which == 0 fires with probability 1/rash_period)
    if (which == 0u)
    {
        p->rm_virus(*m, unisolate ? RECOVERED : ISOLATED_RECOVERED);
    }
    // Moves to hospitalized
    else if (which == 1u)
    {
        m->record_hospitalization(*p);
        p->change_state(*m, DETECTED_HOSPITALIZED);
    }
    // Stays in rash, may or may not be released from isolation
    else if (unisolate)
    {
        p->change_state(*m, RASH);
    }


}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_isolated_recovered(
    Agent<TSeq> * p,
    Model<TSeq> * m
) {

    GET_MODEL(m, model);

    // Figuring out if the agent can be released from isolation
    // if the isolation period is over.
    int days_since = m->today() - model->day_rash_onset[p->get_id()];

    if (m->par("Isolation period") <= days_since)
        p->change_state(*m, RECOVERED);

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_quarantine_suscep(
    Agent<TSeq> * p,
    Model<TSeq> * m
) {

    GET_MODEL(m, model);

    // Get the appropriate quarantine period based on risk level
    auto quarantine_period = model->m_get_risk_period(p->get_id());

    // Figuring out if the agent can be released from quarantine
    int days_since = m->today() - model->day_flagged[p->get_id()];

    if (quarantine_period <= days_since)
        p->change_state(*m, SUSCEPTIBLE);

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_quarantine_exposed(
    Agent<TSeq> * p,
    Model<TSeq> * m
) {

    GET_MODEL(m, model);

    // Get the appropriate quarantine period based on risk level
    auto quarantine_period = model->m_get_risk_period(p->get_id());

    // Figuring out if the agent can be released from quarantine
    int days_since = m->today() - model->day_flagged[p->get_id()];

    // Probability of moving to prodromal
    if (m->runif() < 1.0/(p->get_virus()->get_incubation(m)))
    {

        // If the agent is unquarantined, it becomes prodromal
        p->change_state(*m, 
            (quarantine_period <= days_since) ?
            PRODROMAL : QUARANTINED_PRODROMAL
        );
        

    }
    else if (quarantine_period <= days_since)
    {
        p->change_state(*m, EXPOSED);
    }

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_quarantine_prodromal(
    Agent<TSeq> * p,
    Model<TSeq> * m
) {

    GET_MODEL(m, model);

    // Get the appropriate quarantine period based on risk level
    auto quarantine_period = model->m_get_risk_period(p->get_id());

    // Figuring out if the agent can be released from quarantine
    int days_since = m->today() - model->day_flagged[p->get_id()];

    // Develops rash?
    if (m->runif() < (1.0/m->par("Prodromal period")))
    {
        
        // Developing Rash automatically triggers contact tracing
        model->m_add_contact_tracing(p->get_id());
        
        model->day_rash_onset[p->get_id()] = m->today();
        p->change_state(*m, ISOLATED);
        
    }
    else if (quarantine_period <= days_since)
    {
        p->change_state(*m, PRODROMAL);

    }

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_quarantine_recovered(
    Agent<TSeq> * p,
    Model<TSeq> * m
) {

    GET_MODEL(m, model);

    // Get the appropriate quarantine period based on risk level
    auto quarantine_period = model->m_get_risk_period(p->get_id());

    // Figuring out if the agent can be released from quarantine
    int days_since = m->today() - model->day_flagged[p->get_id()];

    if (quarantine_period <= days_since)
        p->change_state(*m, RECOVERED);

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_update_hospitalized(
    Agent<TSeq> * p,
    Model<TSeq> * m
) {

    // The agent is removed from the system
    if (m->runif() < 1.0/m->par("Hospitalization period"))
        p->rm_virus(*m, RECOVERED);

};

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_add_contact_tracing(size_t agent_id) {

    this->agents_triggered_contact_tracing[
        this->agents_triggered_contact_tracing_size++
    ] = agent_id;

    return;

}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::m_quarantine_process() {

    // If no agents triggered contact tracing, then we skip
    if (agents_triggered_contact_tracing_size == 0u)
        return;

    // We increase the number of quarantines
    days_quarantine_triggered.push_back(Model<TSeq>::today());

    // This vector indicates whether an agent can be quarantined
    // (i.e., is not already in quarantine or isolation)
    std::vector< bool > can_quarantine(
        Model<TSeq>::size(), false
    );

    // Assigning all individuals who are not currently in quarantine/isolation
    // a low level
    for (auto & agent: Model<TSeq>::get_agents())
    {

        auto state = agent.get_state();

        if (
            (state == SUSCEPTIBLE) ||
            (state == EXPOSED) ||
            (state == PRODROMAL) ||
            (state == RASH)
        )
        {
            quarantine_risk_level[agent.get_id()] = RISK_LOW;
            can_quarantine[agent.get_id()] = true;
        }

    }

    #ifdef EPI_DEBUG
    std::map< std::pair<size_t, size_t>, bool> success_contact;
    #endif

    // Checking the risk levels
    double param_days_prior = Model<TSeq>::par("Contact tracing days prior");
    for (size_t i = 0u; i < agents_triggered_contact_tracing_size; ++i)
    {

        size_t agent_i_idx = agents_triggered_contact_tracing[i];
        auto & agent_i = Model<TSeq>::get_agent(agent_i_idx);

        // (A) Checking entity first
        // It doesn't matter if the agent doesn't have a tool; we will
        // check that later
        if (agent_i.get_n_entities() != 0u)
        {
            for (size_t agent_j_idx: agent_i.get_entity(0, *this))
            {

                #ifdef EPI_DEBUG
                auto & agent_j = Model<TSeq>::get_agent(agent_j_idx);
                if (
                    agent_j.get_entity(0u, *this).get_id() !=
                    agent_i.get_entity(0u, *this).get_id()
                )
                    throw std::logic_error(
                        "An agent in a group has a different group id."
                    );
                #endif


                // Only if not already checked we set to high risk
                if (can_quarantine[agent_j_idx])
                    quarantine_risk_level[agent_j_idx] = RISK_HIGH;


            }
        }

        // (B) Checking the contacts
        size_t n_contacts = contact_tracing.get_n_contacts(agent_i_idx);
        if (n_contacts > EPI_MAX_TRACKING)
            n_contacts = EPI_MAX_TRACKING;

        for (size_t contact_j_idx = 0u; contact_j_idx < n_contacts; ++contact_j_idx)
        {

            // Getting the location in the matrix
            auto [contact_id, contact_date] = contact_tracing.get_contact(
                agent_i_idx, contact_j_idx
            );

            // Checked agents should not be considered
            if (!can_quarantine[contact_id])
                continue;

            // Will we detect the contact?
            if (
                Model<TSeq>::runif() >
                Model<TSeq>::par("Contact tracing success rate")
            )
                continue;

            // How many days since they contacted relative to the rash onset?
            // (recall that, in this model, the rash period is not infectious)
            double days_since_contact =
                static_cast<double>(this->day_rash_onset[agent_i_idx]) -
                static_cast<double>(contact_date);

            // If the contact is outside of the tracing window, we skip it
            if (days_since_contact > param_days_prior)
                continue;

            #ifdef EPI_DEBUG
            auto pair = std::make_pair(agent_i_idx, contact_id);
            success_contact[pair] = true;
            #endif

            // Setting the risk level to medium if not already high
            if (quarantine_risk_level[contact_id] < RISK_HIGH)
                quarantine_risk_level[contact_id] = RISK_MEDIUM;
            
        }

    }

    // Proceeding to quarantine/isolating agents
    for (auto & agent: Model<TSeq>::get_agents())
    {

        // Only if not already checked
        if (!can_quarantine[agent.get_id()])
            continue;

        // If has a tool, then skip (is vaxxed)
        if (agent.get_n_tools() != 0u)
            continue;

        if (quarantine_willingness[agent.get_id()] == false)
            continue;

        // Setting the day flagged to today
        day_flagged[agent.get_id()] = Model<TSeq>::today();

        auto state = agent.get_state();
        if (state == SUSCEPTIBLE)
            agent.change_state(*this, QUARANTINED_SUSCEPTIBLE);
        else if (state == EXPOSED)
            agent.change_state(*this, QUARANTINED_EXPOSED);
        else if (state == PRODROMAL)
            agent.change_state(*this, QUARANTINED_PRODROMAL);
        else if (state == RASH)
        {
            if (isolation_willingness[agent.get_id()])
                agent.change_state(*this, ISOLATED);
        }
        else
            throw std::logic_error(
                "An agent in an unexpected state is being quarantined."
            );
    }

    #ifdef EPI_DEBUG
    // Agents in groups that triggered the quarantine level, who are not
    // quarantined should be in RISK_HIGH
    std::set< size_t > groups_ids;
    std::set< size_t > contacted_agents;
    for (size_t i = 0u; i < agents_triggered_contact_tracing_size; ++i)
    {

        auto agent_i_idx = agents_triggered_contact_tracing[i];

        auto & agent_i = Model<TSeq>::get_agent(agent_i_idx);

        // We also check who are the contacted agents
        size_t n_contacts = contact_tracing.get_n_contacts(agent_i_idx);
        if (n_contacts >= EPI_MAX_TRACKING)
            n_contacts = EPI_MAX_TRACKING;

        for (size_t contact_j_idx = 0u; contact_j_idx < n_contacts; ++contact_j_idx)
        {

            // Getting the location in the matrix
            auto [contact_id, contact_date] = contact_tracing.get_contact(
                agent_i_idx, contact_j_idx
            );

            // Was the contact successful?
            auto pair = std::make_pair(agent_i_idx, contact_id);
            if (!success_contact[pair])
                continue;

            contacted_agents.insert(contact_id);
        }

        if (agent_i.get_n_entities() == 0u)
            continue;

        groups_ids.insert(agent_i.get_entity(0u, *this).get_id());
        
    }

    // Iterating over the agents in those groups, if they in the states
    // SUSCEPTIBLE, EXPOSED, PRODROMAL, or RASH, they should be in
    // RISK_HIGH
    for (auto & group: groups_ids)
    {
        for (auto & agent_i_idx: Model<TSeq>::get_entity(group))
        {

            auto & agent_i = Model<TSeq>::get_agent(agent_i_idx);
            auto state = agent_i.get_state();

            // If not in any of these states, we skip
            if (
                (state != SUSCEPTIBLE) &&
                (state != EXPOSED) &&
                (state != PRODROMAL) &&
                (state != RASH)
            )
                continue;

            // If has a tool, then skip (is vaxxed)
            if (agent_i.get_n_tools() != 0u)
                continue;

            if (quarantine_risk_level[agent_i_idx] != RISK_HIGH)
                throw std::logic_error(
                    "An agent in a group that triggered contact tracing is not in RISK_HIGH."
                );

        }
    }

    // Now, agents who were not members of the groups that triggered
    // contact tracing, but were contacted by them should be at least
    // in RISK_MEDIUM
    for (auto & agent_i_idx: contacted_agents)
    {
        auto & agent_i = Model<TSeq>::get_agent(agent_i_idx);
        auto state = agent_i.get_state();

        // If has a tool, then skip (is vaxxed)
        if (agent_i.get_n_tools() != 0u)
            continue;

        // Checking the agent is not in a group that triggered
        // contact tracing
        if (agent_i.get_n_entities() != 0u)
        {
            size_t group_id = agent_i.get_entity(0u, *m).get_id();
            if (groups_ids.find(group_id) != groups_ids.end())
                continue;
        }

        if (quarantine_risk_level[agent_i_idx] != RISK_MEDIUM)
            throw std::logic_error(
                "An agent who was contacted by an infectious agent is not in at least RISK_MEDIUM."
            );
    }

    // Tabulating the number of agents per group
    std::vector< size_t > n_agents_per_group(Model<TSeq>::entities.size(), 0u);
    for (auto i: quarantine_risk_level)
        n_agents_per_group[i]++;

    #endif
    
    // Applying the changes and resetting the number of agents
    // who triggered contact tracing
    Model<TSeq>::events_run();
    agents_triggered_contact_tracing_size = 0u; 

    return;
}

template<typename TSeq>
inline ModelMeaslesMixingRiskQuarantine<TSeq>::ModelMeaslesMixingRiskQuarantine(
    ModelMeaslesMixingRiskQuarantine<TSeq> & model,
    epiworld_fast_uint n,
    epiworld_double prevalence,
    epiworld_double contact_rate,
    epiworld_double transmission_rate,
    epiworld_double vax_efficacy,
    epiworld_double incubation_period,
    epiworld_double prodromal_period,
    epiworld_double rash_period,
    std::vector< double > contact_matrix,
    epiworld_double hospitalization_rate,
    epiworld_double hospitalization_period,
    // Policy parameters
    epiworld_double days_undetected,
    epiworld_fast_int quarantine_period_high,
    epiworld_fast_int quarantine_period_medium,
    epiworld_fast_int quarantine_period_low,
    epiworld_double quarantine_willingness,
    epiworld_double isolation_willingness,
    epiworld_fast_int isolation_period,
    epiworld_double prop_vaccinated,
    epiworld_double detection_rate_quarantine,
    epiworld_double contact_tracing_success_rate,
    epiworld_fast_uint contact_tracing_days_prior
    )
{

    // Setting up the contact matrix
    this->contact_matrix = contact_matrix;

    // Setting up parameters
    model.add_param(contact_rate, "Contact rate");
    model.add_param(transmission_rate, "Transmission rate");
    model.add_param(incubation_period, "Incubation period");
    model.add_param(prodromal_period, "Prodromal period");
    model.add_param(rash_period, "Rash period");
    model.add_param(hospitalization_rate, "Hospitalization rate");
    model.add_param(hospitalization_period, "Hospitalization period");
    model.add_param(days_undetected, "Days undetected");
    model.add_param(quarantine_period_high, "Quarantine period high");
    model.add_param(quarantine_period_medium, "Quarantine period medium");
    model.add_param(quarantine_period_low, "Quarantine period low");
    model.add_param(
        quarantine_willingness, "Quarantine willingness"
    );
    model.add_param(
        isolation_willingness, "Isolation willingness"
    );
    model.add_param(isolation_period, "Isolation period");
    model.add_param(detection_rate_quarantine, "Detection rate quarantine");
    model.add_param(
        contact_tracing_success_rate, "Contact tracing success rate"
    );
    model.add_param(
        contact_tracing_days_prior, "Contact tracing days prior"
    );
    model.add_param(prop_vaccinated, "Vaccination rate");
    model.add_param(vax_efficacy, "Vax efficacy");
    
    // state
    model.add_state("Susceptible", m_update_susceptible);
    model.add_state("Exposed", m_update_exposed);
    model.add_state("Prodromal", m_update_prodromal);
    model.add_state("Rash", m_update_rash);
    model.add_state("Isolated", m_update_isolated);
    model.add_state("Isolated Recovered", m_update_isolated_recovered);
    model.add_state("Detected Hospitalized", m_update_hospitalized);
    model.add_state("Quarantined Exposed", m_update_quarantine_exposed);
    model.add_state("Quarantined Susceptible", m_update_quarantine_suscep);
    model.add_state("Quarantined Prodromal", m_update_quarantine_prodromal);
    model.add_state("Quarantined Recovered", m_update_quarantine_recovered);
    model.add_state("Hospitalized", m_update_hospitalized);
    model.add_state("Recovered");

    // Global function
    model.add_globalevent(this->m_update_model, "Update infected individuals");
    model.queuing_off();

    // Preparing the virus -------------------------------------------
    Virus<TSeq> virus("Measles", prevalence, true);
    virus.set_state(
        ModelMeaslesMixingRiskQuarantine<TSeq>::EXPOSED,
        ModelMeaslesMixingRiskQuarantine<TSeq>::RECOVERED,
        ModelMeaslesMixingRiskQuarantine<TSeq>::RECOVERED
        );

    virus.set_prob_infecting(&model("Transmission rate"));
    virus.set_prob_recovery(&model("Rash period"));
    virus.set_incubation(&model("Incubation period"));

    model.add_virus(virus);

    // Designing the vaccine
    ToolVaccine<TSeq> vaccine(
        std::string("MMR ") +
        std::to_string(model("Vax efficacy"))
    );
    
    vaccine.set_susceptibility_reduction(model("Vax efficacy"));

    vaccine.set_distribution(
        distribute_tool_randomly(prop_vaccinated, true)
    );

    model.add_tool(vaccine);

    model.queuing_off(); // No queuing need

    // Adding the empty population
    model.agents_empty_graph(n);

    model.set_name("Measles with Mixing and Risk-based Quarantine");

    return;

}

template<typename TSeq>
inline ModelMeaslesMixingRiskQuarantine<TSeq>::ModelMeaslesMixingRiskQuarantine(
    epiworld_fast_uint n,
    epiworld_double prevalence,
    epiworld_double contact_rate,
    epiworld_double transmission_rate,
    epiworld_double vax_efficacy,
    epiworld_double incubation_period,
    epiworld_double prodromal_period,
    epiworld_double rash_period,
    std::vector< double > contact_matrix,
    epiworld_double hospitalization_rate,
    epiworld_double hospitalization_period,
    // Policy parameters
    epiworld_double days_undetected,
    epiworld_fast_int quarantine_period_high,
    epiworld_fast_int quarantine_period_medium,
    epiworld_fast_int quarantine_period_low,
    epiworld_double quarantine_willingness,
    epiworld_double isolation_willingness,
    epiworld_fast_int isolation_period,
    epiworld_double prop_vaccinated,
    epiworld_double detection_rate_quarantine,
    epiworld_double contact_tracing_success_rate,
    epiworld_fast_uint contact_tracing_days_prior
    ) : ModelMeaslesMixingRiskQuarantine<TSeq>(
        *this,
        n,
        prevalence,
        contact_rate,
        transmission_rate,
        vax_efficacy,
        incubation_period,
        prodromal_period,
        rash_period,
        contact_matrix,
        hospitalization_rate,
        hospitalization_period,
        // Policy parameters
        days_undetected,
        quarantine_period_high,
        quarantine_period_medium,
        quarantine_period_low,
        quarantine_willingness,
        isolation_willingness,
        isolation_period,
        prop_vaccinated,
        detection_rate_quarantine,
        contact_tracing_success_rate,
        contact_tracing_days_prior
    ) {};

template<typename TSeq>
inline ModelMeaslesMixingRiskQuarantine<TSeq> & ModelMeaslesMixingRiskQuarantine<TSeq>::run(
    epiworld_fast_uint ndays,
    int seed
)
{
    Model<TSeq>::run(ndays, seed);
    return *this;
}

template<typename TSeq>
inline void ModelMeaslesMixingRiskQuarantine<TSeq>::reset()
{

    Model<TSeq>::reset();

    // Checking contact matrix's rows add to one
    size_t nentities = this->entities.size();
    if (this->contact_matrix.size() !=  nentities*nentities)
        throw std::length_error(
            std::string("The contact matrix must be a square matrix of size ") +
            std::string("nentities x nentities. ") +
            std::to_string(this->contact_matrix.size()) +
            std::string(" != ") + std::to_string(nentities*nentities) +
            std::string(".")
            );

    for (size_t i = 0u; i < this->entities.size(); ++i)
    {
        double sum = 0.0;
        for (size_t j = 0u; j < this->entities.size(); ++j)
        {
            if (this->contact_matrix[COL_MAJOR_POS(i, j, nentities)] < 0.0)
                throw std::range_error(
                    std::string("The contact matrix must be non-negative. ") +
                    std::to_string(this->contact_matrix[COL_MAJOR_POS(i, j, nentities)]) +
                    std::string(" < 0.")
                    );
            sum += this->contact_matrix[COL_MAJOR_POS(i, j, nentities)];
        }
        if (sum < 0.999 || sum > 1.001)
            throw std::range_error(
                std::string("The contact matrix must have rows that add to one. ") +
                std::to_string(sum) +
                std::string(" != 1.")
                );
    }

    // Do it the first time only
    sampled_agents.resize(Model<TSeq>::size());

    // We only do it once
    n_infectious_per_group.assign(this->entities.size(), 0u);

    // We are assuming one agent per entity
    infectious.assign(Model<TSeq>::size(), 0u);

    // This will say when do the groups start in the `infectious` vector
    infectious_entity_indices.assign(this->entities.size(), 0u);
    for (size_t i = 1u; i < this->entities.size(); ++i)
    {

        infectious_entity_indices[i] +=
            this->entities[i - 1].size() +
            infectious_entity_indices[i - 1]
            ;

    }

    this->m_update_infectious_list();

    // Setting up the quarantine parameters
    quarantine_willingness.resize(this->size(), false);
    isolation_willingness.resize(this->size(), false);
    for (size_t idx = 0; idx < quarantine_willingness.size(); ++idx)
    {
        quarantine_willingness[idx] =
            Model<TSeq>::runif() < this->par("Quarantine willingness");
        isolation_willingness[idx] =
            Model<TSeq>::runif() < this->par("Isolation willingness");
    }

    day_flagged.assign(this->size(), 0);
    day_rash_onset.assign(this->size(), 0);

    // Variables about contact tracing
    agents_triggered_contact_tracing.assign(Model<TSeq>::size(), 0u);
    agents_triggered_contact_tracing_size = 0u;
    agents_checked_contact_tracing.assign(this->size(), false);

    quarantine_risk_level.assign(this->size(), RISK_LOW);

    // Setting up contact tracking matrix
    contact_tracing.reset(
        this->size(),
        EPI_MAX_TRACKING
    );
    
    // Resetting the number of quarantines
    days_quarantine_triggered.clear();

    return;

}

template<typename TSeq>
inline std::unique_ptr<Model<TSeq>> ModelMeaslesMixingRiskQuarantine<TSeq>::clone_ptr()
{
    
    return std::make_unique<ModelMeaslesMixingRiskQuarantine<TSeq>>(*this);

}

template<typename TSeq>
inline ModelMeaslesMixingRiskQuarantine<TSeq> & ModelMeaslesMixingRiskQuarantine<TSeq>::initial_states(
    std::vector< double > proportions_,
    std::vector< int > /* queue_ */
)
{

    Model<TSeq>::initial_states_fun =
        create_init_function_seir<TSeq>(proportions_)
        ;

    return *this;

}

#undef SAMPLE_FROM_PROBS
#undef GET_MODEL

#endif
