Class DataBase¶

template <typename TSeq>

Statistical data about the process. More...

#include <database-bones.hpp>

Public Functions¶

Type	Name
	DataBase () = delete
	DataBase (Model< TSeq > & m)
	DataBase (const DataBase< TSeq > & db)
void	add_user_data (std::vector< epiworld_double > x)
void	add_user_data (epiworld_fast_uint j, epiworld_double x)
void	get_active_cases (std::vector< int > & date, std::vector< int > & virus_id, std::vector< int > & count) const
void	get_generation_time (std::vector< int > & agent_id, std::vector< int > & virus_id, std::vector< int > & time, std::vector< int > & gentime) const Get the generation time.
void	get_generation_time (std::string fn) const Write the generation time to a file.
void	get_hist_tool (std::vector< int > & date, std::vector< int > & id, std::vector< std::string > & state, std::vector< int > & counts) const
void	get_hist_total (std::vector< int > * date, std::vector< std::string > * state, std::vector< int > * counts) const
void	get_hist_transition_matrix (std::vector< std::string > & state_from, std::vector< std::string > & state_to, std::vector< int > & date, std::vector< int > & counts, bool skip_zeros) const
void	get_hist_virus (std::vector< int > & date, std::vector< int > & id, std::vector< std::string > & state, std::vector< int > & counts) const
void	get_hospitalizations (std::vector< int > & date, std::vector< int > & virus_id, std::vector< int > & tool_id, std::vector< int > & count, std::vector< double > & weight) const Get the full time series of hospitalization data.
Model< TSeq > *	get_model ()
size_t	get_n_tools () const Get the number of tools.
size_t	get_n_viruses () const Get the number of viruses.
const std::vector< int > &	get_nexposed () const
void	get_outbreak_size (std::vector< int > & date, std::vector< int > & virus_id, std::vector< int > & size) const
MapVec_type< int, int >	get_reproductive_number () const Computes the reproductive number of each case.
void	get_reproductive_number (std::string fn) const
const std::vector< TSeq > &	get_sequence () const
int	get_today_total (const std::string & what) const
int	get_today_total (const epiworld_fast_uint & what) const
void	get_today_total (std::vector< std::string > * state=nullptr, std::vector< int > * counts=nullptr) const
void	get_today_transition_matrix (std::vector< int > & counts) const
void	get_today_virus (std::vector< std::string > & state, std::vector< int > & id, std::vector< int > & counts) const
std::vector< epiworld_double >	get_transition_probability (bool print=true, bool normalize=true) const Calculates the transition probabilities.
void	get_transmissions (std::vector< int > & date, std::vector< int > & source, std::vector< int > & target, std::vector< int > & virus, std::vector< int > & source_exposure_date) const Get the transmissions object.
void	get_transmissions (int * date, int * source, int * target, int * virus, int * source_exposure_date) const
UserData< TSeq > &	get_user_data ()
bool	operator!= (const DataBase< TSeq > & other) const
bool	operator== (const DataBase< TSeq > & other) const
bool	operator== (const DataBase< std::vector< int > > & other) const
void	record ()
void	record_hospitalization (Agent< TSeq > & agent) Record a hospitalization event for an agent.
void	record_tool (Tool< TSeq > & t)
void	record_transmission (int i, int j, int virus, int i_expo_date)
void	record_virus (Virus< TSeq > & v) Registering a new variant.
void	reset ()
void	set_seq_hasher (std::function< std::vector< int >(TSeq)> fun)
void	set_user_data (std::vector< std::string > names)
size_t	size () const
void	write_data (std::string fn_virus_info, std::string fn_virus_hist, std::string fn_tool_info, std::string fn_tool_hist, std::string fn_total_hist, std::string fn_transmission, std::string fn_transition, std::string fn_reproductive_number, std::string fn_generation_time, std::string fn_active_cases, std::string fn_outbreak_size, std::string fn_hospitalizations) const

Detailed Description¶

Template parameters:

TSeq

Public Functions Documentation¶

function DataBase [1/3]¶

DataBase::DataBase () = delete

function DataBase [2/3]¶

inline DataBase::DataBase (
    Model < TSeq > & m
)

function DataBase [3/3]¶

inline DataBase::DataBase (
    const DataBase < TSeq > & db
)

function add_user_data [1/2]¶

inline void DataBase::add_user_data (
    std::vector< epiworld_double > x
)

function add_user_data [2/2]¶

inline void DataBase::add_user_data (
    epiworld_fast_uint j,
    epiworld_double x
)

function get_active_cases¶

inline void DataBase::get_active_cases (
    std::vector< int > & date,
    std::vector< int > & virus_id,
    std::vector< int > & count
) const

function get_generation_time [1/2]¶

Get the generation time.

inline void DataBase::get_generation_time (
    std::vector< int > & agent_id,
    std::vector< int > & virus_id,
    std::vector< int > & time,
    std::vector< int > & gentime
) const

Calculates the generating time

Parameters:

agent_id vectors where to save the values

The generation time is the time between the infection of the source and the infection of the target.

function get_generation_time [2/2]¶

Write the generation time to a file.

inline void DataBase::get_generation_time (
    std::string fn
) const

function get_hist_tool¶

inline void DataBase::get_hist_tool (
    std::vector< int > & date,
    std::vector< int > & id,
    std::vector< std::string > & state,
    std::vector< int > & counts
) const

function get_hist_total¶

inline void DataBase::get_hist_total (
    std::vector< int > * date,
    std::vector< std::string > * state,
    std::vector< int > * counts
) const

function get_hist_transition_matrix¶

inline void DataBase::get_hist_transition_matrix (
    std::vector< std::string > & state_from,
    std::vector< std::string > & state_to,
    std::vector< int > & date,
    std::vector< int > & counts,
    bool skip_zeros
) const

function get_hist_virus¶

inline void DataBase::get_hist_virus (
    std::vector< int > & date,
    std::vector< int > & id,
    std::vector< std::string > & state,
    std::vector< int > & counts
) const

function get_hospitalizations¶

Get the full time series of hospitalization data.

inline void DataBase::get_hospitalizations (
    std::vector< int > & date,
    std::vector< int > & virus_id,
    std::vector< int > & tool_id,
    std::vector< int > & count,
    std::vector< double > & weight
) const

Parameters:

date Output vector for dates.
virus_id Output vector for virus IDs.
tool_id Output vector for tool IDs.
count Output vector for counts (number of hospitalized individuals).
weight Output vector for summed weights (fractional contribution based on tool distribution).

Returns the full time series of hospitalization data. For each unique (virus_id, tool_id) combination observed, returns an entry for every day from 0 to ndays-1.

The count vector contains the actual number of individuals hospitalized for that (date, virus_id, tool_id) combination. This is useful for answering questions like "how many total people were hospitalized?" regardless of their tools.

The weight vector contains fractional contributions: if an agent has N tools, each tool gets weight = 1/N. Summing weights across all tool_ids for a given date and virus_id gives the total number of hospitalizations.

function get_model¶

inline Model < TSeq > * DataBase::get_model ()

function get_n_tools¶

Get the number of tools.

inline size_t DataBase::get_n_tools () const

function get_n_viruses¶

Get the number of viruses.

inline size_t DataBase::get_n_viruses () const

function get_nexposed¶

const std::vector< int > & DataBase::get_nexposed () const

function get_outbreak_size¶

inline void DataBase::get_outbreak_size (
    std::vector< int > & date,
    std::vector< int > & virus_id,
    std::vector< int > & size
) const

function get_reproductive_number [1/2]¶

Computes the reproductive number of each case.

inline MapVec_type < int, int > DataBase::get_reproductive_number () const

By definition, whereas it computes R0 (basic reproductive number) or Rt/R (the effective reproductive number) will depend on whether the virus is allowed to circulate naïvely or not, respectively.

Parameters:

fn File where to write out the reproductive number.

In the case of MapVec_type<int,int>, the key is a vector of 3 integers: * Virus id * Source id * Date when the source was infected

function get_reproductive_number [2/2]¶

inline void DataBase::get_reproductive_number (
    std::string fn
) const

function get_sequence¶

inline const std::vector< TSeq > & DataBase::get_sequence () const

function get_today_total [1/3]¶

inline int DataBase::get_today_total (
    const std::string & what
) const

function get_today_total [2/3]¶

int DataBase::get_today_total (
    const epiworld_fast_uint & what
) const

function get_today_total [3/3]¶

inline void DataBase::get_today_total (
    std::vector< std::string > * state=nullptr,
    std::vector< int > * counts=nullptr
) const

function get_today_transition_matrix¶

inline void DataBase::get_today_transition_matrix (
    std::vector< int > & counts
) const

function get_today_virus¶

inline void DataBase::get_today_virus (
    std::vector< std::string > & state,
    std::vector< int > & id,
    std::vector< int > & counts
) const

function get_transition_probability¶

Calculates the transition probabilities.

inline std::vector< epiworld_double > DataBase::get_transition_probability (
    bool print=true,
    bool normalize=true
) const

Parameters:

print Print the transition matrix.
normalize Normalize the transition matrix. Otherwise, it returns raw counts.

The transition matrix is the matrix of the counts of transitions from one state to another. So the ij-th element of the matrix is the number of transitions from state i to state j (when not normalized), or the probability of transitioning from state i to state j (when normalized).

Returns:

std::vector< epiworld_double >

function get_transmissions [1/2]¶

Get the transmissions object.

inline void DataBase::get_transmissions (
    std::vector< int > & date,
    std::vector< int > & source,
    std::vector< int > & target,
    std::vector< int > & virus,
    std::vector< int > & source_exposure_date
) const

Parameters:

date
source
target
virus
source_exposure_date

function get_transmissions [2/2]¶

inline void DataBase::get_transmissions (
    int * date,
    int * source,
    int * target,
    int * virus,
    int * source_exposure_date
) const

function get_user_data¶

inline UserData < TSeq > & DataBase::get_user_data ()

function operator!=¶

inline bool DataBase::operator!= (
    const DataBase < TSeq > & other
) const

function operator==¶

inline bool DataBase::operator== (
    const DataBase < TSeq > & other
) const

function operator==¶

inline bool DataBase::operator== (
    const DataBase < std::vector< int > > & other
) const

function record¶

inline void DataBase::record ()

function record_hospitalization¶

Record a hospitalization event for an agent.

inline void DataBase::record_hospitalization (
    Agent < TSeq > & agent
)

Parameters:

agent Reference to the agent being hospitalized.

For each hospitalization, the method records: * The current date from the model * The virus ID from the agent's virus * For each tool the agent has, a separate record with weight = 1/N where N is the number of tools * If the agent has no tools, a single record with tool_id = -1 and weight = 1.0

function record_tool¶

inline void DataBase::record_tool (
    Tool < TSeq > & t
)

function record_transmission¶

inline void DataBase::record_transmission (
    int i,
    int j,
    int virus,
    int i_expo_date
)

function record_virus¶

Registering a new variant.

inline void DataBase::record_virus (
    Virus < TSeq > & v
)

Parameters:

v Pointer to the new virus. Since viruses are originated in the agent, the numbers simply move around. From the parent virus to the new virus. And the total number of infected does not change.

function reset¶

inline void DataBase::reset ()

function set_seq_hasher¶

void DataBase::set_seq_hasher (
    std::function< std::vector< int >(TSeq)> fun
)

function set_user_data¶

inline void DataBase::set_user_data (
    std::vector< std::string > names
)

function size¶

inline size_t DataBase::size () const

function write_data¶

inline void DataBase::write_data (
    std::string fn_virus_info,
    std::string fn_virus_hist,
    std::string fn_tool_info,
    std::string fn_tool_hist,
    std::string fn_total_hist,
    std::string fn_transmission,
    std::string fn_transition,
    std::string fn_reproductive_number,
    std::string fn_generation_time,
    std::string fn_active_cases,
    std::string fn_outbreak_size,
    std::string fn_hospitalizations
) const

The documentation for this class was generated from the following file epiworld-src/include/epiworld/database-bones.hpp