model.run: Run a model simulation (workhorse function)

In obrady/SpatialDengue: Fits and simulates a spatial model of the vector-borne disease dengue

Description

Directly implements the daily simulation of the dengue spatial model, usually used nested within a wrapper function, see ?DENSpatial

Usage

model.run(sing_S, sing_I, sing_R, sing_Rt, mos_S, mos_E, mos_I, betaEnv,
  mm_list2, mm_list_cum, pdetec, func_IIP, func_EIP, mospdeath,
  drugtreat_Eff, drugtreat_Dur, drugtreat_Rad, vectreat_Eff, vectreat_Dur,
  vectreat_Rad, steps = 365, unipix, pixdistmat, StopCriteria)

Arguments

sing_S	vector, Susceptible human individuals in each pixel
sing_I	matrix, Infectious human individuals in each pixel, rows = day of infection
sing_R	vector, Recovered human individuals in each pixel
sing_Rt	matrix, Recovered (temporary) human individuals in each pixel, rows = day of protection
mos_S	vector, Susceptible mosquitoes in each pixel
mos_E	matrix, Exposed but not yet infectious mosquitoes in each pixel, rows = day since infection
mos_I	vector, Infectious mosquitoes in each pixel
betaEnv	Starting human <-> mosquito contact rate landscape, see ?betaEnv.generate
mm_list2	List of human movement matrices adjusted by the hometime parameter, see ?move.matrix.gene and ?DEN.spatial
mm_list_cum	Matrix of patch effective population size (including both resident population and those who move there during the day)
pdetec	Function for sampling probability of detecting a denge ifected individual (by passive surveillance), beta distributied probability
func_IIP	Function for probability of completing human Intrinsic Incubation Period (time between infection and becoming symptomatic), a funciton of time since infection
func_EIP	Function for probability of completing mosquito Extrinsic Incubation Period (time between mosquito becoming infected and becoming infectious), a function of time since infection
mospdeath	Function for daily probability of death of a mosquito, beta distributed hazard, exponential distributed survival
drugtreat_Eff	Effective coverage of prophylactic drug
drugtreat_Dur	Duration of prophylactic drug effectiveness
drugtreat_Rad	Radius of deployment around an index case of prophylactic drug
vectreat_Eff	Effective coverage of vector control
vectreat_Dur	Not used
vectreat_Rad	Radius of deployment around an index case of vector control
steps	Number of days for which the simulation shoudl run, defaults to 365
unipix	Universal pixel lookup table, see ?make.unipix
pixdistmat	A patch distance matrix, see example in ?DENspatial
StopCriteria	Single numeric value, if the model predicts reported cases exceed this value at any point during the simulation, simulation is terminated and "NA" is returned
mos_S	vector, Susceptible mosquitoes in each pixel
drugtreat_Del	Delay in days between detection of a dengue case and treatment of target population with drugs
vectreat_Del	Delay in days between detection of a dengue case and treatment of target population with vector control
vectreat	three element vector of details governing routine reactive vector control, see tutorial

Details

Implements a stochastic daily timestep model predictign the spatial spread of dengue across Singapore. As long as "StopCriteria" are not exceeded, will return a list of final values of each of the main stages of the model and three summaries: i) "totals" - population wide totals for each model state and ii) detailed_totals- pixel-specific totals for each model state, iii) treatlog - log of length "steps" detailing which patches were treated with drugs or vector control on each day

Examples

See tutorial

obrady/SpatialDengue documentation built on Nov. 27, 2020, 12:13 p.m.