Class Virus¶

template <typename TSeq>

#include <virus-bones.hpp>

Public Functions¶

Type	Name
	EPI_TYPENAME_TRAITS (TSeq, int)
	Virus ()
	Virus (std::string name="unknown virus")
	Virus (std::string name, epiworld_double prevalence, bool as_proportion)
virtual std::unique_ptr< Virus< TSeq > >	clone_ptr () const
void	distribute (Model< TSeq > * model) Get information about the prevalence of the virus.
Agent< TSeq > *	get_agent ()
int	get_date () const
int	get_id () const
epiworld_double	get_incubation (Model< TSeq > * model)
std::string	get_name () const
epiworld_double	get_prob_death (Model< TSeq > * model)
epiworld_double	get_prob_infecting (Model< TSeq > * model)
epiworld_double	get_prob_recovery (Model< TSeq > * model)
void	get_queue (epiworld_fast_int * init, epiworld_fast_int * end, epiworld_fast_int * removed=nullptr) const
void	get_state (epiworld_fast_int * init, epiworld_fast_int * end, epiworld_fast_int * removed=nullptr) const
void	mutate (Model< TSeq > * model)
bool	operator!= (const Virus< TSeq > & other) const
bool	operator== (const Virus< TSeq > & other) const
bool	operator== (const Virus< std::vector< int > > & other) const
void	post_recovery (Model< TSeq > * model)
void	print () const
void	set_agent (Agent< TSeq > * p)
void	set_date (int d)
void	set_distribution (VirusToAgentFun< TSeq > fun)
void	set_id (int idx)
void	set_incubation (std::string param)
void	set_incubation (epiworld_double * prob) = delete
void	set_incubation (epiworld_double prob)
void	set_incubation_fun (VirusFun< TSeq > fun)
void	set_mutation (MutFun< TSeq > fun)
void	set_name (std::string name)
void	set_post_immunity (epiworld_double prob)
void	set_post_immunity (std::string param)
void	set_post_immunity (epiworld_double * prob) = delete
void	set_post_recovery (PostRecoveryFun< TSeq > fun)
void	set_prob_death (std::string param)
void	set_prob_death (epiworld_double * prob) = delete
void	set_prob_death (epiworld_double prob)
void	set_prob_death_fun (VirusFun< TSeq > fun)
void	set_prob_infecting (std::string param)
void	set_prob_infecting (epiworld_double * prob) = delete
void	set_prob_infecting (epiworld_double prob)
void	set_prob_infecting_fun (VirusFun< TSeq > fun)
void	set_prob_recovery (std::string param)
void	set_prob_recovery (epiworld_double * prob) = delete
void	set_prob_recovery (epiworld_double prob)
void	set_prob_recovery_fun (VirusFun< TSeq > fun)
void	set_queue (epiworld_fast_int init, epiworld_fast_int end, epiworld_fast_int removed=-99)
void	set_sequence (TSeq sequence)
void	set_sequence (int sequence)
void	set_state (epiworld_fast_int init, epiworld_fast_int end, epiworld_fast_int removed=-99)
virtual	~Virus () = default

Detailed Description¶

Template parameters:

TSeq

Raw transmisibility of a virus should be a function of its genetic sequence. Nonetheless, transmisibility can be reduced as a result of having one or more tools to fight the virus. Because of this, transmisibility should be a function of the agent.

Public Functions Documentation¶

function EPI_TYPENAME_TRAITS [2/2]¶

Virus::EPI_TYPENAME_TRAITS (
    TSeq,
    int
)

function Virus [1/3]¶

inline Virus::Virus ()

function Virus [2/3]¶

inline Virus::Virus (
    std::string name="unknown virus"
)

function Virus [3/3]¶

inline Virus::Virus (
    std::string name,
    epiworld_double prevalence,
    bool as_proportion
)

function clone_ptr¶

inline virtual std::unique_ptr< Virus < TSeq > > Virus::clone_ptr () const

function distribute¶

Get information about the prevalence of the virus.

inline void Virus::distribute (
    Model < TSeq > * model
)

function get_agent¶

inline Agent < TSeq > * Virus::get_agent ()

function get_date¶

inline int Virus::get_date () const

function get_id¶

inline int Virus::get_id () const

function get_incubation¶

inline epiworld_double Virus::get_incubation (
    Model < TSeq > * model
)

function get_name¶

inline std::string Virus::get_name () const

function get_prob_death¶

inline epiworld_double Virus::get_prob_death (
    Model < TSeq > * model
)

function get_prob_infecting¶

inline epiworld_double Virus::get_prob_infecting (
    Model < TSeq > * model
)

function get_prob_recovery¶

inline epiworld_double Virus::get_prob_recovery (
    Model < TSeq > * model
)

function get_queue¶

inline void Virus::get_queue (
    epiworld_fast_int * init,
    epiworld_fast_int * end,
    epiworld_fast_int * removed=nullptr
) const

function get_state¶

inline void Virus::get_state (
    epiworld_fast_int * init,
    epiworld_fast_int * end,
    epiworld_fast_int * removed=nullptr
) const

function mutate¶

inline void Virus::mutate (
    Model < TSeq > * model
)

function operator!=¶

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

function operator==¶

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

function operator==¶

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

function post_recovery¶

inline void Virus::post_recovery (
    Model < TSeq > * model
)

function print¶

inline void Virus::print () const

function set_agent¶

inline void Virus::set_agent (
    Agent < TSeq > * p
)

function set_date¶

inline void Virus::set_date (
    int d
)

function set_distribution¶

inline void Virus::set_distribution (
    VirusToAgentFun < TSeq > fun
)

function set_id¶

inline void Virus::set_id (
    int idx
)

function set_incubation [1/3]¶

inline void Virus::set_incubation (
    std::string param
)

function set_incubation [2/3]¶

void Virus::set_incubation (
    epiworld_double * prob
) = delete

function set_incubation [3/3]¶

inline void Virus::set_incubation (
    epiworld_double prob
)

function set_incubation_fun¶

inline void Virus::set_incubation_fun (
    VirusFun < TSeq > fun
)

function set_mutation¶

inline void Virus::set_mutation (
    MutFun < TSeq > fun
)

function set_name¶

inline void Virus::set_name (
    std::string name
)

function set_post_immunity [1/3]¶

inline void Virus::set_post_immunity (
    epiworld_double prob
)

function set_post_immunity [2/3]¶

inline void Virus::set_post_immunity (
    std::string param
)

function set_post_immunity [3/3]¶

void Virus::set_post_immunity (
    epiworld_double * prob
) = delete

function set_post_recovery¶

inline void Virus::set_post_recovery (
    PostRecoveryFun < TSeq > fun
)

function set_prob_death [1/3]¶

inline void Virus::set_prob_death (
    std::string param
)

function set_prob_death [2/3]¶

void Virus::set_prob_death (
    epiworld_double * prob
) = delete

function set_prob_death [3/3]¶

inline void Virus::set_prob_death (
    epiworld_double prob
)

function set_prob_death_fun¶

inline void Virus::set_prob_death_fun (
    VirusFun < TSeq > fun
)

function set_prob_infecting [1/3]¶

inline void Virus::set_prob_infecting (
    std::string param
)

function set_prob_infecting [2/3]¶

void Virus::set_prob_infecting (
    epiworld_double * prob
) = delete

function set_prob_infecting [3/3]¶

inline void Virus::set_prob_infecting (
    epiworld_double prob
)

function set_prob_infecting_fun¶

inline void Virus::set_prob_infecting_fun (
    VirusFun < TSeq > fun
)

function set_prob_recovery [1/3]¶

inline void Virus::set_prob_recovery (
    std::string param
)

function set_prob_recovery [2/3]¶

void Virus::set_prob_recovery (
    epiworld_double * prob
) = delete

function set_prob_recovery [3/3]¶

inline void Virus::set_prob_recovery (
    epiworld_double prob
)

function set_prob_recovery_fun¶

inline void Virus::set_prob_recovery_fun (
    VirusFun < TSeq > fun
)

function set_queue¶

inline void Virus::set_queue (
    epiworld_fast_int init,
    epiworld_fast_int end,
    epiworld_fast_int removed=-99
)

function set_sequence [1/2]¶

inline void Virus::set_sequence (
    TSeq sequence
)

function set_sequence [2/2]¶

inline void Virus::set_sequence (
    int sequence
)

function set_state¶

inline void Virus::set_state (
    epiworld_fast_int init,
    epiworld_fast_int end,
    epiworld_fast_int removed=-99
)

function ~Virus¶

virtual Virus::~Virus () = default

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