DEN.spatial.seasonal: Run a single realisation of the spatial dengue model

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

Description

Main wrapper function for running a single realisation of the dengue spatial model, may take a while to run depending on specification

Usage

DEN.spatial.seasonal(weekdates, fitdat, pastdat, sgpop, unipix, pixdistmat,
  steprun, seasonal_vector, seasonal_start, paramsList = NULL)

Arguments

weekdates	Two element vector of the start and end weeks of the simulation over which the model will be evaluated over
fitdat	Data frame of the locations, numbers and timings (in weeks) of cases to fit the model to, see ?sgdat
pastdat	Data frame of the locations, numbers and timings (in weeks) of all cases in the dataset (is used to generate the starting immunity profile), see ?sgdat
unipix	Universal pixel lookup table, see ?make.unipix
pixdistmat	A patch distance matrix, see example
steprun	integer, number of days for which the simulation should run, excluding burn in period
seasonal_vector	A vector of multipliers to change human-mosquito contact rate, for each day of the year, to account for seasonality
seasonal_start	Day in the year for the start of the model
paramsList	Optional parameter list. If not supplied returns to defaults, see tutorial for full parameter list, see ?model.run for full list and explanation of parameters

Details

This function undertakes three main processes: i) fills in parameters with default options if not supplied, ii) generates a human movement matrix between patches, ii) runs the model simulation. within "paramsList()". Missing parameters will return to their default values. This function returns a outputs in a three element list giving: i) daily counts of each model state (S, I, R, etc) sumed across the whole landscape, ii) daily counts of each model state for every patch, iii) A treatment log (of length = number of steps) detailing which patches were treated each day

Examples

data(sgdat)
data(sgpop)
data(seasonal_vector)
data(sero)
sgpop <- pop.process(sgpop, agg = 10)
sero <-aggregate(sero, 10, fun = mean)
unipix <- make.unipix(sgpop)
pixdistmat <- distm(cbind(unipix$x, unipix$y))
sgdat <- data.frame(sgdat, patchID = apply(cbind(sgdat[, 3:2]), 1, pix.id.find, unipix))
weekdates <- c(40, 92)
# model run with default parameters
denmod_sim <- DEN.spatial.seasonal(weekdates, 
                                   fitdat = sgdat, 
                                   pastdat = sgdat, 
                                   sgpop, 
                                   unipix, 
                                   pixdistmat, 
                                   steprun = 365, 
                                   seasonal_vector, 
                                   seasonal_start = 1)

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