#include <odeproblem.h>

Public Member Functions
	odeproblem (Rcpp::List param, Rcpp::NumericVector init, Rcpp::List funs, int n_capture_)
	~odeproblem ()
void	do_init_calc (bool answer)
void	advance (double tfrom, double tto, LSODA &solver)
void	call_derivs (double t, double y, double *ydot)
void	init (int pos, double value)
double	init (int pos)
void	init_call (const double &time)
void	init_call_record (const double &time)
void	init_derivs (double time)
void	y_init (int pos, double value)
void	y_init (Rcpp::NumericVector init)
void	y_add (const unsigned int pos, const double &value)
	add `value` to compartment `pos`
void	table_call ()
	Call `$TABLE` function.
void	table_init_call ()
void	event_call ()
	Call `$EVENT` function.
void	config_call ()
	Call `$PREAMBLE` function.
void	set_d (rec_ptr this_rec)
void	omega (const Rcpp::S4 &mod)
void	sigma (const Rcpp::S4 &mod)
void	copy_sigma_diagonals ()
arma::mat	mv_omega (int n)
arma::mat	mv_sigma (int n)
void	pass_envir (Rcpp::Environment *x)
bool	CFONSTOP ()
const std::vector< double > &	param ()
void	param (int pos, double value)
void	check_data_rate (rec_ptr rec, int cmtn)
void	check_modeled_dur (rec_ptr rec)
void	check_modeled_rate (rec_ptr rec)
void	rate (unsigned int pos, double value)
double	rate (unsigned int pos)
	Get the modeled infusion rate from $MAIN.
void	rate0 (unsigned int pos, double value)
double	rate0 (unsigned int pos)
	Get the functioning infusion rate.
int	rate_count (unsigned int pos)
void	rate_add (unsigned int pos, const double &value)
void	rate_rm (unsigned int pos, const double &value)
void	rate_bump (const unsigned int pos, const double &value)
void	rate_main (rec_ptr rec, int cmtn)
void	rate_reset ()
	Reset all infusion rates.
void	dur (unsigned int pos, double value)
double	dur (unsigned int pos)
	Get the modeled infusion duration from $MAIN.
void	reset_newid (const double id_)
	Reset `odeproblem` object for new individual.
void	eta (int pos, double value)
void	eps (int pos, double value)
unsigned short int	systemoff ()
void	on (unsigned short int cmt)
void	off (unsigned short int cmt)
int	is_on (unsigned int eq_n)
void	fbio (unsigned int pos, double value)
double	fbio (unsigned int pos)
	Get the bioavailability from $MAIN.
double	alag (int cmt)
	Get the lag time from $MAIN.
void	time (double time_)
void	newind (unsigned int newind_)
unsigned int	newind ()
void	advan (int x)
int	advan ()
void	advan2 (const double &tfrom, const double &tto)
void	advan4 (const double &tfrom, const double &tto)
void	advan11 (const double &tfrom, const double &tto)
void	set_eta ()
	set number of `ETAs` in the model
void	set_eps ()
	set number of `EPSs` in the model
int	neta ()
int	neps ()
void	nid (int n)
	sets the number of IDs
void	idn (int n)
	sets the current ID number
void	nrow (int n)
	sets the number of data set rows
void	rown (int n)
	sets the current data set row number
void	inrow (int n)
	sets number of output rows for current ID
void	irown (int n)
	sets the output row number for current ID
dvec &	get_capture ()
double	capture (int i)
void	copy_parin (const Rcpp::List &parin, const Rcpp::S4 &mod)
	copies items passed in through parin into the odeproblem object
void	copy_funs (const Rcpp::List &funs)
bool	any_mtime ()
std::vector< mrgsolve::evdata >	mtimes ()
void	clear_mtime ()
void	y (const int pos, const double value)
double	y (const int pos)
int	istate ()
void	istate (int value)
void	lsoda_init ()
int	npar ()
	returns the number of parameters
int	neq ()
	returns the number of state variables
void	tol (double atol, double rtol)
	sets the absolute and relative tolerances

Public Attributes
std::vector< double >	Y
	compartment amounts
std::vector< double >	Ydot
	dxdt values
std::vector< double >	Yout
	used to hold Y values during solving
std::vector< double >	Param
	parameter vector
std::vector< double >	Capture
	captured data items
double	Atol
	absolute tolerance used by ODE solver
double	Rtol
	relative tolerance used by ODE solver
double	ssAtol
	absolute tolerance when finding steady state
double	ssRtol
int	Npar
	number of parameters
int	Neq
	number of equations
int	Istate
	istate value
bool	ss_fixed
	If true, then no warning is issued if SS not reached in ss_n doses.
int	ss_n
	Max number of doses during SS advance before warning is issued.
bool	ss_flag
	flag indicating when the system is advancing to SS
bool	system_at_ss
	flag indicating the system was advanced to SS
std::vector< int >	Ss_cmt
	vector of compartments to consider for SS
bool	check_modeled_infusions
std::vector< double >	R0
	acutal current infusion rate
std::vector< unsigned int >	infusion_count
	number of active infusions
std::vector< double >	R
	receive user input for infusion rate
std::vector< double >	D
	receive user input for infusion duration
std::vector< double >	Init_value
	initial conditions
std::vector< double >	Init_dummy
	initial conditions for user input
std::vector< double >	F
	bioavability
std::vector< double >	Alag
	dosing lag time
std::vector< int >	On
	compartment on/off indicator
databox	d
	various data passed to model functions
int	Advan
	simulation mode: 1/2/3/4 (PK models) or 13 (odes)
std::vector< double >	a
	used for advan 1/2/3/4 calculations
std::vector< double >	alpha
	used for advan 1/2/3/4 calculation
mrgsolve::resim	simeta
	functor for resimulating etas
mrgsolve::resim	simeps
	functor for resimulating epsilons
arma::mat	Omega
	variance/covariance matrix for between-subject variability
arma::mat	Sigma
	variance/covariance matrix for within-subject variability
std::vector< double >	pred
	brings clearances, volumes, and & for advan 1/2/3/4
deriv_func	Derivs
	`$ODE` function
init_func	Inits
	`$MAIN` function
table_func	Table
	`$TABLE` function
event_func	Event
	`$EVENT` function
config_func	Config
	`$PREAMBLE` function
bool	Do_Init_Calc
	Flag regulating whether or not initials are taken from `$MAIN`.
int	interrupt
	Check User Interrupt interval (number of simulation records).

Constructor & Destructor Documentation

◆ odeproblem()

odeproblem::odeproblem	(	Rcpp::List	param,
		Rcpp::NumericVector	init,
		Rcpp::List	funs,
		int	n_capture_ )

◆ ~odeproblem()

odeproblem::~odeproblem ( )

inline

Member Function Documentation

◆ advan() [1/2]

int odeproblem::advan ( )

inline

◆ advan() [2/2]

void odeproblem::advan ( int x )

◆ advan11()

void odeproblem::advan11	(	const double &	tfrom,
		const double &	tto )

◆ advan2()

void odeproblem::advan2	(	const double &	tfrom,
		const double &	tto )

◆ advan4()

void odeproblem::advan4	(	const double &	tfrom,
		const double &	tto )

◆ advance()

void odeproblem::advance	(	double	tfrom,
		double	tto,
		LSODA &	solver )

◆ alag()

double odeproblem::alag ( int cmt )

Get the lag time from $MAIN.

◆ any_mtime()

bool odeproblem::any_mtime ( )

inline

◆ call_derivs()

void odeproblem::call_derivs	(	double *	t,
		double *	y,
		double *	ydot )

◆ capture()

double odeproblem::capture ( int i )

inline

◆ CFONSTOP()

bool odeproblem::CFONSTOP ( )

inline

◆ check_data_rate()

void odeproblem::check_data_rate	(	rec_ptr	rec,
		int	cmtn )

◆ check_modeled_dur()

void odeproblem::check_modeled_dur ( rec_ptr rec )

◆ check_modeled_rate()

void odeproblem::check_modeled_rate ( rec_ptr rec )

◆ clear_mtime()

void odeproblem::clear_mtime ( )

inline

◆ config_call()

void odeproblem::config_call ( )

Call $PREAMBLE function.

◆ copy_funs()

void odeproblem::copy_funs ( const Rcpp::List & funs )

◆ copy_parin()

void odeproblem::copy_parin	(	const Rcpp::List &	parin,
		const Rcpp::S4 &	mod )

copies items passed in through parin into the odeproblem object

◆ copy_sigma_diagonals()

void odeproblem::copy_sigma_diagonals ( )

◆ do_init_calc()

void odeproblem::do_init_calc ( bool answer )

inline

◆ dur() [1/2]

double odeproblem::dur ( unsigned int pos )

Get the modeled infusion duration from $MAIN.

◆ dur() [2/2]

void odeproblem::dur	(	unsigned int	pos,
		double	value )

inline

◆ eps()

void odeproblem::eps	(	int	pos,
		double	value )

inline

◆ eta()

void odeproblem::eta	(	int	pos,
		double	value )

inline

◆ event_call()

void odeproblem::event_call ( )

Call $EVENT function.

◆ fbio() [1/2]

double odeproblem::fbio ( unsigned int pos )

Get the bioavailability from $MAIN.

◆ fbio() [2/2]

void odeproblem::fbio	(	unsigned int	pos,
		double	value )

inline

◆ get_capture()

dvec & odeproblem::get_capture ( )

inline

◆ idn()

void odeproblem::idn ( int n )

inline

sets the current ID number

◆ init() [1/2]

double odeproblem::init ( int pos )

inline

◆ init() [2/2]

void odeproblem::init	(	int	pos,
		double	value )

inline

◆ init_call()

void odeproblem::init_call ( const double & time )

Call $MAIN to get the initial conditions.

Parameters

time	the time to assume for the calculation

◆ init_call_record()

void odeproblem::init_call_record ( const double & time )

Call $MAIN with the dummy initial condition vector.

Parameters

time	the time to assume when making the call.

◆ init_derivs()

void odeproblem::init_derivs ( double time )

◆ inrow()

void odeproblem::inrow ( int n )

inline

sets number of output rows for current ID

◆ irown()

void odeproblem::irown ( int n )

inline

sets the output row number for current ID

◆ is_on()

int odeproblem::is_on ( unsigned int eq_n )

inline

◆ istate() [1/2]

int odeproblem::istate ( )

inline

◆ istate() [2/2]

void odeproblem::istate ( int value )

inline

◆ lsoda_init()

void odeproblem::lsoda_init ( )

inline

◆ mtimes()

std::vector< mrgsolve::evdata > odeproblem::mtimes ( )

inline

◆ mv_omega()

arma::mat odeproblem::mv_omega ( int n )

◆ mv_sigma()

arma::mat odeproblem::mv_sigma ( int n )

◆ neps()

int odeproblem::neps ( )

inline

◆ neq()

int odeproblem::neq ( )

inline

returns the number of state variables

◆ neta()

int odeproblem::neta ( )

inline

◆ newind() [1/2]

unsigned int odeproblem::newind ( )

inline

◆ newind() [2/2]

void odeproblem::newind ( unsigned int newind_ )

inline

◆ nid()

void odeproblem::nid ( int n )

inline

sets the number of IDs

◆ npar()

int odeproblem::npar ( )

inline

returns the number of parameters

◆ nrow()

void odeproblem::nrow ( int n )

inline

sets the number of data set rows

◆ off()

void odeproblem::off ( unsigned short int cmt )

◆ omega()

void odeproblem::omega ( const Rcpp::S4 & mod )

◆ on()

void odeproblem::on ( unsigned short int cmt )

◆ param() [1/2]

const std::vector< double > & odeproblem::param ( )

inline

◆ param() [2/2]

void odeproblem::param	(	int	pos,
		double	value )

inline

◆ pass_envir()

void odeproblem::pass_envir ( Rcpp::Environment * x )

inline

◆ rate() [1/2]

double odeproblem::rate ( unsigned int pos )

Get the modeled infusion rate from $MAIN.

◆ rate() [2/2]

void odeproblem::rate	(	unsigned int	pos,
		double	value )

inline

◆ rate0() [1/2]

double odeproblem::rate0 ( unsigned int pos )

Get the functioning infusion rate.

◆ rate0() [2/2]

void odeproblem::rate0	(	unsigned int	pos,
		double	value )

inline

◆ rate_add()

void odeproblem::rate_add	(	unsigned int	pos,
		const double &	value )

◆ rate_bump()

void odeproblem::rate_bump	(	const unsigned int	pos,
		const double &	value )

◆ rate_count()

int odeproblem::rate_count ( unsigned int pos )

inline

◆ rate_main()

void odeproblem::rate_main	(	rec_ptr	rec,
		int	cmtn )

◆ rate_reset()

void odeproblem::rate_reset ( )

Reset all infusion rates.

◆ rate_rm()

void odeproblem::rate_rm	(	unsigned int	pos,
		const double &	value )

◆ reset_newid()

void odeproblem::reset_newid ( const double id_ )

Reset odeproblem object for new individual.

◆ rown()

void odeproblem::rown ( int n )

inline

sets the current data set row number

◆ set_d()

void odeproblem::set_d ( rec_ptr this_rec )

◆ set_eps()

void odeproblem::set_eps ( )

set number of EPSs in the model

◆ set_eta()

void odeproblem::set_eta ( )

set number of ETAs in the model

◆ sigma()

void odeproblem::sigma ( const Rcpp::S4 & mod )

◆ systemoff()

unsigned short int odeproblem::systemoff ( )

inline

◆ table_call()

void odeproblem::table_call ( )

Call $TABLE function.

◆ table_init_call()

void odeproblem::table_init_call ( )

◆ time()

void odeproblem::time ( double time_ )

inline

◆ tol()

void odeproblem::tol	(	double	atol,
		double	rtol )

sets the absolute and relative tolerances

◆ y() [1/2]

double odeproblem::y ( const int pos )

inline

◆ y() [2/2]

void odeproblem::y	(	const int	pos,
		const double	value )

inline

◆ y_add()

void odeproblem::y_add	(	const unsigned int	pos,
		const double &	value )

add value to compartment pos

◆ y_init() [1/2]

void odeproblem::y_init	(	int	pos,
		double	value )

Assigns values to both the compartment and the vector of initial conditions.

Parameters

pos	the compartment number (C++ indexing)
value	the value for the compartment

◆ y_init() [2/2]

void odeproblem::y_init ( Rcpp::NumericVector init )

Member Data Documentation

◆ a

std::vector<double> odeproblem::a

used for advan 1/2/3/4 calculations

◆ Advan

int odeproblem::Advan

simulation mode: 1/2/3/4 (PK models) or 13 (odes)

◆ Alag

std::vector<double> odeproblem::Alag

dosing lag time

◆ alpha

std::vector<double> odeproblem::alpha

used for advan 1/2/3/4 calculation

◆ Atol

double odeproblem::Atol

absolute tolerance used by ODE solver

◆ Capture

std::vector<double> odeproblem::Capture

captured data items

◆ check_modeled_infusions

bool odeproblem::check_modeled_infusions

◆ Config

config_func odeproblem::Config

$PREAMBLE function

◆ D

std::vector<double> odeproblem::D

receive user input for infusion duration

◆ d

databox odeproblem::d

various data passed to model functions

◆ Derivs

deriv_func odeproblem::Derivs

$ODE function

◆ Do_Init_Calc

bool odeproblem::Do_Init_Calc

Flag regulating whether or not initials are taken from $MAIN.

◆ Event

event_func odeproblem::Event

$EVENT function

◆ F

std::vector<double> odeproblem::F

bioavability

◆ infusion_count

std::vector<unsigned int> odeproblem::infusion_count

number of active infusions

◆ Init_dummy

std::vector<double> odeproblem::Init_dummy

initial conditions for user input

◆ Init_value

std::vector<double> odeproblem::Init_value

initial conditions

◆ Inits

init_func odeproblem::Inits

$MAIN function

◆ interrupt

int odeproblem::interrupt

Check User Interrupt interval (number of simulation records).

◆ Istate

int odeproblem::Istate

istate value

◆ Neq

int odeproblem::Neq

number of equations

◆ Npar

int odeproblem::Npar

number of parameters

◆ Omega

arma::mat odeproblem::Omega

variance/covariance matrix for between-subject variability

◆ On

std::vector<int> odeproblem::On

compartment on/off indicator

◆ Param

std::vector<double> odeproblem::Param

parameter vector

◆ pred

std::vector<double> odeproblem::pred

brings clearances, volumes, and & for advan 1/2/3/4

◆ R

std::vector<double> odeproblem::R

receive user input for infusion rate

◆ R0

std::vector<double> odeproblem::R0

acutal current infusion rate

◆ Rtol

double odeproblem::Rtol

relative tolerance used by ODE solver

◆ Sigma

arma::mat odeproblem::Sigma

variance/covariance matrix for within-subject variability

◆ simeps

mrgsolve::resim odeproblem::simeps

functor for resimulating epsilons

◆ simeta

mrgsolve::resim odeproblem::simeta

functor for resimulating etas

◆ Ss_cmt

std::vector<int> odeproblem::Ss_cmt

vector of compartments to consider for SS

◆ ss_fixed

bool odeproblem::ss_fixed

If true, then no warning is issued if SS not reached in ss_n doses.

◆ ss_flag

bool odeproblem::ss_flag

flag indicating when the system is advancing to SS

◆ ss_n

int odeproblem::ss_n

Max number of doses during SS advance before warning is issued.

◆ ssAtol

double odeproblem::ssAtol

absolute tolerance when finding steady state

◆ ssRtol

double odeproblem::ssRtol

◆ system_at_ss

bool odeproblem::system_at_ss

flag indicating the system was advanced to SS

◆ Table

table_func odeproblem::Table

$TABLE function

◆ Y

std::vector<double> odeproblem::Y

compartment amounts

◆ Ydot

std::vector<double> odeproblem::Ydot

dxdt values

◆ Yout

std::vector<double> odeproblem::Yout

used to hold Y values during solving

The documentation for this class was generated from the following files:

inst/include/odeproblem.h
src/odeproblem.cpp

Public Member Functions

Public Attributes

Constructor & Destructor Documentation

◆ odeproblem()

◆ ~odeproblem()

Member Function Documentation

◆ advan() [1/2]

◆ advan() [2/2]

◆ advan11()

◆ advan2()

◆ advan4()

◆ advance()

◆ alag()

◆ any_mtime()

◆ call_derivs()

◆ capture()

◆ CFONSTOP()

◆ check_data_rate()

◆ check_modeled_dur()

◆ check_modeled_rate()

◆ clear_mtime()

◆ config_call()

◆ copy_funs()

◆ copy_parin()

◆ copy_sigma_diagonals()

◆ do_init_calc()

◆ dur() [1/2]

◆ dur() [2/2]

◆ eps()

◆ eta()

◆ event_call()

◆ fbio() [1/2]

◆ fbio() [2/2]

◆ get_capture()

◆ idn()

◆ init() [1/2]

◆ init() [2/2]

◆ init_call()

◆ init_call_record()

◆ init_derivs()

◆ inrow()

◆ irown()

◆ is_on()

◆ istate() [1/2]

◆ istate() [2/2]

◆ lsoda_init()

◆ mtimes()

◆ mv_omega()

◆ mv_sigma()

◆ neps()

◆ neq()

◆ neta()

◆ newind() [1/2]

◆ newind() [2/2]

◆ nid()

◆ npar()

◆ nrow()

◆ off()

◆ omega()

◆ on()

◆ param() [1/2]

◆ param() [2/2]

◆ pass_envir()

◆ rate() [1/2]

◆ rate() [2/2]

◆ rate0() [1/2]

◆ rate0() [2/2]

◆ rate_add()

◆ rate_bump()

◆ rate_count()

◆ rate_main()

◆ rate_reset()

◆ rate_rm()

◆ reset_newid()

◆ rown()

◆ set_d()

◆ set_eps()

◆ set_eta()

◆ sigma()

◆ systemoff()