#include <ModelContext.hpp>

Public Member Functions
	ModelContext ()

	~ModelContext ()

void	populate (InitData _A0, covariateArgs xArgs, covariateArgs xPrsArgs, double offset, int Y, compartmentArgs S_starArgs, compartmentArgs E_starArgs, compartmentArgs I_starArgs, compartmentArgs R_starArgs, scaledDistanceArgs scaledDistArgs, double rho, double phi, double beta, double gamma_ei, double gamma_ir, double betaPrs, int N, sliceParameters sliceWidths, priorControl *priorInformation, modelConfiguration _config)

void	buildModel ()

void	configureIterationTasks ()

void	calculateS_CPU ()

void	calculateS_CPU (int startLoc, int startTime)

void	calculateS_givenE_CPU ()

void	calculateS_givenE_CPU (int startLoc, int startTime)

void	calculateS_OCL ()

void	calculateE_CPU ()

void	calculateE_CPU (int startLoc, int startTime)

void	calculateE_givenI_CPU ()

void	calculateE_givenI_CPU (int startLoc, int startTime)

void	calculateE_OCL ()

void	calculateI_CPU ()

void	calculateI_CPU (int startLoc, int startTime)

void	calculateI_givenR_CPU ()

void	calculateI_givenR_CPU (int startLoc, int startTime)

void	calculateI_OCL ()

void	calculateR_CPU ()

void	calculateR_CPU (int startLoc, int startTime)

void	calculateR_givenS_CPU ()

void	calculateR_givenS_CPU (int startLoc, int startTime)

void	calculateR_OCL ()

void	calculateGenericCompartment_CPU (CompartmentalModelMatrix comp, int comp0, CompartmentalModelMatrix compStarAdd, CompartmentalModelMatrix compStarSub)

void	calculateGenericCompartment_CPU (CompartmentalModelMatrix comp, int comp0, CompartmentalModelMatrix compStarAdd, CompartmentalModelMatrix compStarSub, int startLoc, int startTime)

void	calculateGenericCompartment_OCL (int comp, int comp0, int compStarAdd, int compStarSub)

int	checkCompartmentBounds ()

void	printFCValues ()

void	setRandomSeed (unsigned int seedValue)

void	simulationIter (bool verbose, bool debug)

void	runSimulation (int nIterations, bool verbose, bool debug)

void	updateSamplingParameters (double desiredRatio, double targetWidth, double proportionChange)

void	setCompartmentSamplingMode (int mode)

int	getCompartmentSamplingMode ()

void	setParameterSamplingMode (int mode)

int	getParameterSamplingMode ()

void	cacheP_SE_Calculation ()

void	calculateP_SE_CPU ()

void	calculateP_SE_CPU (int startLoc, int startTime)

void	calculateP_SE_OCL ()

void	calculateP_EI_CPU ()

void	calculateP_IR_CPU ()

void	calculateP_RS_CPU ()

int	totalS ()

int	totalE ()

int	totalI ()

int	totalR ()

int	totalS (int tpt)

int	totalE (int tpt)

int	totalI (int tpt)

int	totalR (int tpt)

int	totalS_star ()

int	totalE_star ()

int	totalI_star ()

int	totalR_star ()

int	totalS_star (int tpt)

int	totalE_star (int tpt)

int	totalI_star (int tpt)

int	totalR_star (int tpt)

double	avgP_SE ()

double	avgP_RS ()

double	avgP_SE (int tpt)

double	estimateR0 ()

double *	estimateR0 (int t)

double	estimateEffectiveR0 ()

double *	estimateEffectiveR0 (int t)

double *	calculateR0Components (int t)

double *	calculateEffectiveR0Components (int t)

double *	calculateG (int t)

double *	calculateIntegratedG (int t)

Public Attributes
IOProvider *	fileProvider

RandomNumberProvider *	random

OCLProvider *	oclProvider

FC_S0 *	S0_fc

FC_E0 *	E0_fc

FC_I0 *	I0_fc

FC_R0 *	R0_fc

FC_S_Star *	S_star_fc

FC_E_Star *	E_star_fc

FC_R_Star *	R_star_fc

FC_Beta *	beta_fc

FC_Rho *	rho_fc

FC_Beta_P_RS *	betaPrs_fc

FC_Gamma_EI *	gamma_ei_fc

FC_Gamma_IR *	gamma_ir_fc

FC_I_Star_overdispersed *	I_star_overdispersed_fc

FC_Phi *	phi_fc

SetCompartmentSamplingIndicesTask *	setSamplingIndicesTask

PerformHybridSE_EI_UpdateStep *	performHybridSE_EI_UpdateTask

PerformDecorrelationStep *	decorrelationStepTask

int *	Y

CompartmentalModelMatrix *	S

CompartmentalModelMatrix *	E

CompartmentalModelMatrix *	I

CompartmentalModelMatrix *	R

CompartmentalModelMatrix *	S_star

CompartmentalModelMatrix *	E_star

CompartmentalModelMatrix *	I_star

CompartmentalModelMatrix *	R_star

InitData *	A0

CovariateMatrix *	X

CovariateMatrix *	X_pRS

std::vector< DistanceMatrix * > *	scaledDistMatrices

CompartmentalModelMatrix *	tmpContainer

modelConfiguration *	config

std::vector< FullConditional * > *	model

std::vector< IterationTask * > *	iterationTasks

double *	beta

double *	betaPrs

double *	rho

double *	phi

double *	gamma

double *	eta

double *	offset

double *	p_se

double *	p_se_components

double *	compartmentCache

int *	indexLength

int *	indexList

double *	gamma_ei

double *	p_ei

double *	gamma_ir

double *	p_ir

double *	p_rs

int *	N

int *	isPopulated

int *	singleLocation

int *	numIterations

Detailed Description

The model context class provides the central interface of libspatialSEIR. After instantiation, the populate method must be called before any meaningful work can be done. Once populated, ModelContext holds pointers to all of the required FullConditional instances as well as the data they use. In addition, ModelContext provides calculation functions and holds pointers to additional utility classes such as OCLProvider, IOProvider, and RandomNumberProvider.

Constructor & Destructor Documentation

SpatialSEIR::ModelContext::ModelContext ( )

SpatialSEIR::ModelContext::~ModelContext ( )

Member Function Documentation

double SpatialSEIR::ModelContext::avgP_RS ( )

Calculates the average of all components of p_rs.

double SpatialSEIR::ModelContext::avgP_SE ( )

Calculates the average of all components of p_se.

double SpatialSEIR::ModelContext::avgP_SE ( int tpt )

Calculates the average of all components of p_se for a particular time point..

void SpatialSEIR::ModelContext::buildModel ( )

void SpatialSEIR::ModelContext::cacheP_SE_Calculation ( )

cacheP_SE_Calculation places the pre-requisites for calculating p_se in p_se_components. This is useful when partial updates can be performed by calculateP_SE_CPU(int startLoc, int startTime)

void SpatialSEIR::ModelContext::calculateE_CPU ( )

The zero parameter overload of calculateE_CPU calculates the E compartment from A0, I_star, and E_star.

void SpatialSEIR::ModelContext::calculateE_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculateE_CPU again calculates the E compartment from A0, I_star and E_star, but assumes that only values of I_star and E_star at column (location) startLoc and after row (time) startTime have changed since E was last calculated. When applicable, this saves considerable time.

void SpatialSEIR::ModelContext::calculateE_givenI_CPU ( )

The zero parameter overload of calculate E_givenI_CPU takes advantage of the fact that N=S+E+I+R to update E when I changes.

void SpatialSEIR::ModelContext::calculateE_givenI_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculate E_givenI_CPU takes advantage of the fact that N=S+E+I+R to update E when I changes, while assuming that I has only changed for location startLoc and after time point startTime.

void SpatialSEIR::ModelContext::calculateE_OCL ( )

calculateE_OCL works identically to calculateS_CPU using calls to oclProvider to perform computations in parallel.

double * SpatialSEIR::ModelContext::calculateEffectiveR0Components ( int t )

Calculates the location specific components of the effective R0 quantity at time t

double * SpatialSEIR::ModelContext::calculateG ( int t )

Calculates the next generation matrix

void SpatialSEIR::ModelContext::calculateGenericCompartment_CPU	(	CompartmentalModelMatrix *	comp,
		int *	comp0,
		CompartmentalModelMatrix *	compStarAdd,
		CompartmentalModelMatrix *	compStarSub
	)

Parameters

comp	pointer to CompartmentalModelMatrix to be calculated.
comp0	pointer to integer array containing starting values for comp.
compStarAdd	pointer to transition matrix into comp.
compStarSub	pointer to transition CompartmentalModelMatrix out of comp.

void SpatialSEIR::ModelContext::calculateGenericCompartment_CPU	(	CompartmentalModelMatrix *	comp,
		int *	comp0,
		CompartmentalModelMatrix *	compStarAdd,
		CompartmentalModelMatrix *	compStarSub,
		int	startLoc,
		int	startTime
	)

The six parameter overload of calculateGenericCompartment_CPU takes advantege of the common calculation pattern for S,E,I, and R to provide a single function mapping starting and transition values to the filan CompartmentalModelMatrix values, assuming that only location startLoc and time points after startTime need be considered.

Parameters

comp	pointer to CompartmentalModelMatrix to be calculated
comp0	pointer to integer array containing starting values for comp
compStarAdd	pointer to transition matrix into comp
compStarSub	pointer to transition CompartmentalModelMatrix out of comp
startLoc	location to update
startTime	time after which update is needed

void SpatialSEIR::ModelContext::calculateGenericCompartment_OCL	(	int *	comp,
		int *	comp0,
		int *	compStarAdd,
		int *	compStarSub
	)

calculateGenericCompartment_OCL works identically to calculateGenericCompartment_CPU while using calls to oclProvider to perform calculations in parallel.

Parameters

comp	pointer to CompartmentalModelMatrix to be calculated
comp0	pointer to integer array containing starting values for comp
compStarAdd	pointer to transition matrix into comp
compStarSub	pointer to transition CompartmentalModelMatrix out of comp

void SpatialSEIR::ModelContext::calculateI_CPU ( )

The zero parameter overload of calculateI_CPU calculates the I compartment from A0, I_star, and R_star.

void SpatialSEIR::ModelContext::calculateI_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculateI_CPU again calculates the I compartment from A0, I_star and R_star, but assumes that only values of I_star and R_star at column (location) startLoc and after row (time) startTime have changed since I was last calculated. When applicable, this saves considerable time.

void SpatialSEIR::ModelContext::calculateI_givenR_CPU ( )

The zero parameter overload of calculate I_givenR_CPU takes advantage of the fact that N=S+E+I+R to update I when R changes.

void SpatialSEIR::ModelContext::calculateI_givenR_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculate I_givenR_CPU takes advantage of the fact that N=S+E+I+R to update I when R changes, while assuming that R has only changed for location startLoc and after time point startTime.

void SpatialSEIR::ModelContext::calculateI_OCL ( )

calculateI_OCL works identically to calculateI_CPU using calls to oclProvider to perform computations in parallel.

double * SpatialSEIR::ModelContext::calculateIntegratedG ( int t )

Calculates the next generation matrix, integrated forward in time.

void SpatialSEIR::ModelContext::calculateP_EI_CPU ( )

calculateP_EI_CPU calculates the E to I transition probability vector p_ei

void SpatialSEIR::ModelContext::calculateP_IR_CPU ( )

calculateP_IR_CPU calculates the I to R transition probability vector p_ir

void SpatialSEIR::ModelContext::calculateP_RS_CPU ( )

calculateP_RS_CPU calculates the reinfection probability p_rs.

void SpatialSEIR::ModelContext::calculateP_SE_CPU ( )

The zero parameter overload of calculateP_SE_CPU calculates the exposure probability p_se.

void SpatialSEIR::ModelContext::calculateP_SE_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculateP_SE_CPU calculates the exposure probability starting at startLoc and startTime. cacheP_SE_Calculation must be called first.

void SpatialSEIR::ModelContext::calculateP_SE_OCL ( )

calculateP_SE_OCL works identically to calculateP_SE_CPU, while making calls to oclProvider to perform calculations in parallel.

double * SpatialSEIR::ModelContext::calculateR0Components ( int t )

Calculates the location specific components of the effective R0 quantity at time t

void SpatialSEIR::ModelContext::calculateR_CPU ( )

The zero parameter overload of calculateR_CPU calculates the R compartment from A0, R_star, and S_star.

void SpatialSEIR::ModelContext::calculateR_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculateR_CPU again calculates the R compartment from A0, R_star and S_star, but assumes that only values of R_star and S_star at column (location) startLoc and after row (time) startTime have changed since I was last calculated. When applicable, this saves considerable time.

void SpatialSEIR::ModelContext::calculateR_givenS_CPU ( )

The zero parameter overload of calculate R_givenS_CPU takes advantage of the fact that N=S+E+I+R to update R when S changes.

void SpatialSEIR::ModelContext::calculateR_givenS_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculate R_givenS_CPU takes advantage of the fact that N=S+E+I+R to update R when S changes, while assuming that S has only changed for location startLoc and after time point startTime.

void SpatialSEIR::ModelContext::calculateR_OCL ( )

calculateR_OCL works identically to calculateR_CPU using calls to oclProvider to perform computations in parallel. The four parameter overload of calculateGenericCompartment_CPU takes advantege of the common calculation pattern for S,E,I, and R to provide a single function mapping starting and transition values to the filan CompartmentalModelMatrix values.

void SpatialSEIR::ModelContext::calculateS_CPU ( )

The zero parameter overload of calculateS_CPU calculates the S compartment from A0, S_star, and E_star.

void SpatialSEIR::ModelContext::calculateS_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculateS_CPU again calculates the S compartment from A0, S_star and E_star, but assumes that only values of S_star and E_star at column (location) startLoc and after row (time) startTime have changed since S was last calculated. When applicable, this saves considerable time.

void SpatialSEIR::ModelContext::calculateS_givenE_CPU ( )

The zero parameter overload of calculate S_givenE_CPU takes advantage of the fact that N=S+E+I+R to update S when E changes.

void SpatialSEIR::ModelContext::calculateS_givenE_CPU	(	int	startLoc,
		int	startTime
	)

The two parameter overload of calculate S_givenE_CPU takes advantage of the fact that N=S+E+I+R to update S when E changes, while assuming that E has only changed for location startLoc and after time point startTime.

void SpatialSEIR::ModelContext::calculateS_OCL ( )

calculateS_OCL works identically to calculateS_CPU using calls to oclProvider to perform computations in parallel.

int SpatialSEIR::ModelContext::checkCompartmentBounds ( )

checkCompartmentBounds is a debug mode function which checks for impossible compartment values and prints errors accordingly.

void SpatialSEIR::ModelContext::configureIterationTasks ( )

configureIterationTasks determines whether there are any conditions which require additional logical tasks to be performed during MCMC sampling.

double SpatialSEIR::ModelContext::estimateEffectiveR0 ( )

Estimates the effective reproductive rate across all time periods and spatial locations

double * SpatialSEIR::ModelContext::estimateEffectiveR0 ( int t )

Estimates the effective reproductive rate at time t.

double SpatialSEIR::ModelContext::estimateR0 ( )

Estimates the average basic reproductive number across all time periods and spatial locations.

double * SpatialSEIR::ModelContext::estimateR0 ( int t )

Estimates the basic reproductive number for time point t

int SpatialSEIR::ModelContext::getCompartmentSamplingMode ( )

getCompartmentSamplingMode returns the current sampling mode as an integer

int SpatialSEIR::ModelContext::getParameterSamplingMode ( )

getParameterSamplingMode returns the current sampling mode for non-compartment parameters as an integer

void SpatialSEIR::ModelContext::populate	(	InitData *	_A0,
		covariateArgs *	xArgs,
		covariateArgs *	xPrsArgs,
		double *	offset,
		int *	Y,
		compartmentArgs *	S_starArgs,
		compartmentArgs *	E_starArgs,
		compartmentArgs *	I_starArgs,
		compartmentArgs *	R_starArgs,
		scaledDistanceArgs *	scaledDistArgs,
		double *	rho,
		double *	phi,
		double *	beta,
		double *	gamma_ei,
		double *	gamma_ir,
		double *	betaPrs,
		int *	N,
		sliceParameters *	sliceWidths,
		priorControl *	priorInformation,
		modelConfiguration	_config
	)

The populate method is the entry point to working with spatial SEIR models in libspatialSEIR.

Parameters

_A0	A0 must be an instance of InitData, which contains the starting values of S0, E0, I0, R0
xArgs	xArgs is an instance of covariateArgs which contains the dimensions of the fixed and time varying covariate matrices driving the exposure process.
xPrsArgs	xPrsArgs is an instance of covariateArgs which contains the dimensions of the fixed and time varying covariate matrices driving the reinfection process.
offset	Offset allows irregular spacing between time points.
Y	Y is the actual observed data vector. It must be of the same dimension as the rest of the Compartments. In the default data model, Y is exactly equal to I_star.
S_starArgs	S_starArgs is an instance of compartmentArgs containing the dimensions and data for S_star, along with the steadyStateConstraintPrecision parameter.
E_starArgs	E_starArgs is an instance of compartmentArgs containing the dimensions and data for E_star, along with the steadyStateConstraintPrecision parameter.
I_starArgs	I_starArgs is an instance of compartmentArgs containing the dimensions and data for I_star, along with the steadyStateConstraintPrecision parameter.
R_starArgs	R_starArgs is an instance of compartmentArgs containing the dimensions and data for R_star, along with the steadyStateConstraintPrecision parameter.
scaledDistArgs	scaledDistArgs is the scaledDistanceArgs struct containing the data and dimension of the unscaled distance matrices.
rho	rho gives the starting value of the spatial dependence parameter
phi	starting value for overdispersion precision
beta	beta gives the starting vector of regression parameters driving the exposure process.
gamma_ei	p_ei is the starting value of the parameter driving the exposed to infectious transition probability.
gamma_ir	p_ir is the starting value of the parameter driving the infectious to removed/recovered transition probability.
betaPrs	betaPrs is the starting vector of regression parameters driving the reinfection process.
N	N is the matrix of population sizes, corresponding in dimension to the CompartmentalModelMatrix instances.
sliceWidths	sliceWidths is an instance of sliceParameters which gives the slice sampling widths/ Metropolis-Hastings tuning parameters for the various FullConditional distributions.
priorInformation	The priorControl struct gives the prior precisions for the regression parameters, and the prior alpha and beta parameters for the p_ei and p_ir distributions.
_config	The modelConfiguration struct gives the reinfection mode (SEIRS, SEIR, SSEIR) and the MCMC sampling mode. MCMC sampling modes are under very active development.

void SpatialSEIR::ModelContext::printFCValues ( )

printFCValues is a semi-depricated debug mode function which displays the current full conditional likelihood values of the model parameters.

void SpatialSEIR::ModelContext::runSimulation	(	int	nIterations,
		bool	verbose = `false`,
		bool	debug = `false`
	)

runSimulation runs nIterations MCMC updates given the current model state. Optionally, verbose and debug level output is available.

void SpatialSEIR::ModelContext::setCompartmentSamplingMode ( int mode )

setCompartmentSamplingMode sets the sampling mode for the disease compartments. This part of the API is in flux.

void SpatialSEIR::ModelContext::setParameterSamplingMode ( int mode )

setParameterSamplingMode sets the sampling mode for non compartment parameters. This part of the API is in flux.

void SpatialSEIR::ModelContext::setRandomSeed ( unsigned int seedValue )

setRandomSeed sets the seed used by the pseudorandom number generator provided by RandomNumberProvider

void SpatialSEIR::ModelContext::simulationIter	(	bool	verbose = `false`,
		bool	debug = `false`
	)

simulationIter runs a single MCMC update given the current model state. Optionally, verbose and debug level output is available.

int SpatialSEIR::ModelContext::totalE ( )

Calculates the sum of all components of E.

int SpatialSEIR::ModelContext::totalE ( int tpt )

Calculates the sum of all components of E.

int SpatialSEIR::ModelContext::totalE_star ( )

Calculates the sum of all components of E_star.

int SpatialSEIR::ModelContext::totalE_star ( int tpt )

Calculates the sum of all components of E_star.

int SpatialSEIR::ModelContext::totalI ( )

Calculates the sum of all components of I.

int SpatialSEIR::ModelContext::totalI ( int tpt )

Calculates the sum of all components of I.

int SpatialSEIR::ModelContext::totalI_star ( )

Calculates the sum of all components of I_star.

int SpatialSEIR::ModelContext::totalI_star ( int tpt )

Calculates the sum of all components of I_star.

int SpatialSEIR::ModelContext::totalR ( )

Calculates the sum of all components of R.

int SpatialSEIR::ModelContext::totalR ( int tpt )

Calculates the sum of all components of R.

int SpatialSEIR::ModelContext::totalR_star ( )

Calculates the sum of all components of R_star.

int SpatialSEIR::ModelContext::totalR_star ( int tpt )

Calculates the sum of all components of R_star.

int SpatialSEIR::ModelContext::totalS ( )

Calculates the sum of all components of S.

int SpatialSEIR::ModelContext::totalS ( int tpt )

Calculates the sum of all components of S.

int SpatialSEIR::ModelContext::totalS_star ( )

Calculates the sum of all components of S_star.

int SpatialSEIR::ModelContext::totalS_star ( int tpt )

Calculates the sum of all components of S_star.

void SpatialSEIR::ModelContext::updateSamplingParameters	(	double	desiredRatio,
		double	targetWidth,
		double	proportionChange
	)

updateSamplingParameters moves the various slice sampling widths / Metropolis-Hastings tuning parameters up or down depending on the current acceptance rate, and re-sets the acceptance counters.

Parameters

desiredRatio	desired MCMC acceptance ratio
targetWidth	target ratio tolerance (how close is close enough)
proportionChange	proportion to change the sampling parameters by

Member Data Documentation

InitData* SpatialSEIR::ModelContext::A0

Pointer to InitData instance containing the data for the initial compartment sizes.

double* SpatialSEIR::ModelContext::beta

Storage for the regression parameters beta

FC_Beta* SpatialSEIR::ModelContext::beta_fc

Pointer to FullConditional distribution for the regression parameters beta

double* SpatialSEIR::ModelContext::betaPrs

Storage for the regression parameters betaP_RS

FC_Beta_P_RS* SpatialSEIR::ModelContext::betaPrs_fc

Pointer to FullConditional distribution for the regression parameters betaP_RS

double* SpatialSEIR::ModelContext::compartmentCache

ComparmentalModelMatrix sized cache of doubles.

modelConfiguration* SpatialSEIR::ModelContext::config

Pointer to modelConfiguration instance.

PerformDecorrelationStep* SpatialSEIR::ModelContext::decorrelationStepTask

Pointer to the decorrelation step task

CompartmentalModelMatrix* SpatialSEIR::ModelContext::E

Pointer to the CompartmentalModelMatrix data structure storing the E compartment.

FC_E0* SpatialSEIR::ModelContext::E0_fc

Pointer to FullConditional distribution for the initial exposed population - not used

CompartmentalModelMatrix* SpatialSEIR::ModelContext::E_star

Pointer to the CompartmentalModelMatrix data structure storing the E_star compartment.

FC_E_Star* SpatialSEIR::ModelContext::E_star_fc

Pointer to FullConditional distribution for the transition matrix E_star

double* SpatialSEIR::ModelContext::eta

Storage for the linear predictor, eta

IOProvider* SpatialSEIR::ModelContext::fileProvider

pointer to an IOProvider instance which writes selected sampler output to a comma delimited text file.

double* SpatialSEIR::ModelContext::gamma

Storage for the external infection parameters gamma (DEPRICATED)

double* SpatialSEIR::ModelContext::gamma_ei

Parameter controlling transition probability vector p_ei

FC_Gamma_EI* SpatialSEIR::ModelContext::gamma_ei_fc

Pointer to FullConditional distribution for the parameter transition probability p_ei

double* SpatialSEIR::ModelContext::gamma_ir

Parameter controlling transition probability vector p_ir

FC_Gamma_IR* SpatialSEIR::ModelContext::gamma_ir_fc

Pointer to FullConditional distribution for the parameter controlling transition probability p_ir

CompartmentalModelMatrix* SpatialSEIR::ModelContext::I

Pointer to the CompartmentalModelMatrix data structure storing the I compartment.

FC_I0* SpatialSEIR::ModelContext::I0_fc

Pointer to FullConditional distribution for the initial infectious population

CompartmentalModelMatrix* SpatialSEIR::ModelContext::I_star

Pointer to the CompartmentalModelMatrix data structure storing the I_star compartment.

FC_I_Star_overdispersed* SpatialSEIR::ModelContext::I_star_overdispersed_fc

Pointer to FullConditional distribution for the I_star transition matrix under overdispersion

int* SpatialSEIR::ModelContext::indexLength

Length of the indexList array.

int* SpatialSEIR::ModelContext::indexList

List of indices, used by some sampling functions.

int* SpatialSEIR::ModelContext::isPopulated

Indicator that ModelContext instance is ready for use.

std::vector<IterationTask*>* SpatialSEIR::ModelContext::iterationTasks

Iteration tasks are bits of logical code that need to execute periodically during MCMC sampling, but don't fall into the usual FullConditional framework.

std::vector<FullConditional*>* SpatialSEIR::ModelContext::model

A model in libspatialSEIR is a collection of full conditional distributions which must be sampled from. This collection is assembled during ModelContext.populate based on the reinfection mode, data model (not yet implemented), and the detection of special cases such as the single location case.

int* SpatialSEIR::ModelContext::N

Matrix of population sizes

int* SpatialSEIR::ModelContext::numIterations

Number of MCMC samples so far.

OCLProvider* SpatialSEIR::ModelContext::oclProvider

pointer to an instance of OCLProvider which supplies an interface for selecting active OpenCL devices as well as parallelized computations required for various FullConditional distributions.

double* SpatialSEIR::ModelContext::offset

Storage for the vector of offsets.

double* SpatialSEIR::ModelContext::p_ei

Transition probability vector p_ei

double* SpatialSEIR::ModelContext::p_ir

Transition probability vector p_ir

double* SpatialSEIR::ModelContext::p_rs

Transition probability vector p_rs

double* SpatialSEIR::ModelContext::p_se

Storage for the exposure probability matrix, p_se

double* SpatialSEIR::ModelContext::p_se_components

Storage for cacheable portions of the p_se calculation

PerformHybridSE_EI_UpdateStep* SpatialSEIR::ModelContext::performHybridSE_EI_UpdateTask

Pointer to the beta+gamma_ei hybrid sampling task.

double* SpatialSEIR::ModelContext::phi

Storage for the overdispersion parameter

FC_Phi* SpatialSEIR::ModelContext::phi_fc

Pointer to FullConditional distribution for the overdispersion parameter for I_star

CompartmentalModelMatrix* SpatialSEIR::ModelContext::R

Pointer to the CompartmentalModelMatrix data structure storing the R compartment.

FC_R0* SpatialSEIR::ModelContext::R0_fc

Pointer to FullConditional distribution for the initial recovered population - not used

CompartmentalModelMatrix* SpatialSEIR::ModelContext::R_star

Pointer to the CompartmentalModelMatrix data structure storing the R_star compartment.

FC_R_Star* SpatialSEIR::ModelContext::R_star_fc

Pointer to FullConditional distribution for the transition matrix R_star

RandomNumberProvider* SpatialSEIR::ModelContext::random

pointer to a RandomNumberProvider instance which provides random numbers from various distributions as well implementations of several probability density functions.

double* SpatialSEIR::ModelContext::rho

Storage for the vector of spatial dependence parameters, rho

FC_Rho* SpatialSEIR::ModelContext::rho_fc

Pointer to FullConditional distribution for the spatial depenence parameter rho

CompartmentalModelMatrix* SpatialSEIR::ModelContext::S

Pointer to the CompartmentalModelMatrix data structure storing the S compartment.

FC_S0* SpatialSEIR::ModelContext::S0_fc

Pointer to FullConditional distribution for the initial suscptible population.

CompartmentalModelMatrix* SpatialSEIR::ModelContext::S_star

Pointer to the CompartmentalModelMatrix data structure storing the S_star compartment.

FC_S_Star* SpatialSEIR::ModelContext::S_star_fc

Pointer to FullConditional distribution for the transition matrix S_star

std::vector<DistanceMatrix*>* SpatialSEIR::ModelContext::scaledDistMatrices

Pointer to vector of scaled DistanceMatrix objects.

SetCompartmentSamplingIndicesTask* SpatialSEIR::ModelContext::setSamplingIndicesTask

Pointer to the sampling indices task.

int* SpatialSEIR::ModelContext::singleLocation

Indicator that ModelContext is operating in the single location special case.

CompartmentalModelMatrix* SpatialSEIR::ModelContext::tmpContainer

Extra compartment storage for caching integer computations

CovariateMatrix* SpatialSEIR::ModelContext::X

Pointer to CovariateMatrix instance containing covariate informating driving the exposure process.

CovariateMatrix* SpatialSEIR::ModelContext::X_pRS

Pointer to CovariateMatrix instance containing covariate informating driving the reinfection process.

int* SpatialSEIR::ModelContext::Y

Pointer to the actual data vector: Y. Y is related by a data model to I_star.

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

libSpatialSEIR/include/ModelContext.hpp
libSpatialSEIR/src/ModelContext.cpp
libSpatialSEIR/src/ModelContextSummaryFunctions.cpp

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