Sample.size.calc: Updating sample size calculations for trial design

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

Description

Updating sample size calculations for trial design

Usage

Sample.size.calc(modresult, radi, pixdistmat, adultsonly = FALSE,
  foi = 0.1, agedist = NA, dly = 0)

Arguments

modresult	a Spatial dengue model object returned from DEN.spatial
radi	radius around the index patch that infections / cases are observed within
pixdistmat	A patch distance matrix, see example
adultsonly	logical, will the trial only include adults (= TRUE), or all ages (= FALSE)
foi	single values range 0-1, long term average force of infection in the area concerned, usually estimated from age-stratified seroprevalence surveys, optional, defaults to 0.1 ~ an endemic setting, only required if adultsonly = TRUE
agedist	optional vector of counts of individuals in 1 year age bands in years 0-100, defaults to an exponential age distribution otherwise
dly	single value, Days between observign symptomatic case and visiting index case's home, defaults to 0 (day of becoming symptomatic)

Details

returns four plots showing: i) total people within the specified radius of each index cases, ii) total seronegative people within the specified radius of each index case, iii) infection incidence within the radius of each index case in the 28 days following the visit, iv) symptomatic disease incidence in the radius of the index case in the 28 days following the visit Each of these measures are plotted over time over the course of the outbreak with red splines showing the estimated median value. A data.frame is also returned summarising these distributions over the course of the experiment

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)
# model run with default parameters
denmod_sim <- DEN.spatial(weekdates, sgdat, unipix, pixdistmat)
set.seed(123)
Sample.size.calc(denmod_sim, radi = 1000, pixdistmat, adultsonly = FALSE)
# now just adults only
set.seed(123)
Sample.size.calc(denmod_sim, radi = 1000, pixdistmat, adultsonly = TRUE, foi = 0.12)

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