DEN.spatial.UCT: Simulate an urban cluster trial of dengue prophylactic drugs

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

Description

Provide basic information on the UCT and the number of stochastic runs over which model runs should be averaged

Usage

DEN.spatial.UCT(weekdates, fitdat, pastdat, unipix, pixdistmat, UCTinfo,
  nruns, paramsList = NULL)

Arguments

weekdates	Two element vector of the start and end weeks of the simulation over which the mdoel 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
UCTinfo	A data frame including details on Urban Cluster Trial tart time, delay between enrollment and followup, number of treatment and control clustes and drug effective coverage
nruns	integer, number of stochastic runs of the model over which results should be averaged
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

runs "nruns" number of stochastic simulations and enrolls treatment or control clusters once the trail has begun then stops enrolling once the target number of clusters has been reached. Returns the normal DEN.spatial sumamry results but with "treatlog" and "contlog" which detail which patches were enrolled into treatment or control arms at which point

Examples

data(sgdat)
data(sgpop)
sgpop <- pop.process(sgpop, agg = 10)
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)

UCTinfo <- list(Tstart = 50,
               Tfollowup = 28,
               ntreat = 30,
               ncontrol = 30,
               DrugEfficacy = 0.9)

denmod_UCT = DEN.spatial.UCT(weekdates, sgdat, sgdat, unipix, pixdistmat, UCTinfo, nruns = 10)
effectiveness <- UCT.Eff.calc(denmod_UCT, unipix)

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