Nothing
suppressPackageStartupMessages({
require(denvax); require(data.table); require(jsonlite)
})
#' expected to be called with three arguments
#' first: reference rds with digested life history proportions
#' second: json file with
#' (1) keys for each of the countries to compare
#' (2) that point to objects with costs for
#' secondary infection (S), testing (T), a vaccination (V)
#' last: target rds file name to store resulting ROIs
#' command line invocation from the published usage gives:
#' @example
#' .args <- c(
#' "results/proportions.rds",
#' "pub/malaysia_v_peru.json",
#' "results/example-rois.rds"
#' )
.args <- commandArgs(trailingOnly = T)
proportions <- readRDS(.args[1])
tarCountries <- jsonlite::read_json(.args[2])
outputfile <- tail(.args, 1)
pars <- lapply(
tarCountries, # change the input parameters...
function(pars) list( # into their dimensionless versions
nu = pars$V / pars$S,
tau = pars$T / pars$S
)
)
rcs <- proportions[
Country %in% names(pars), # for only the countries of interest...
denvax::ROIcoeffs(.SD), # compute the ROI surface coefficients
by = Country # n.b., this uses the default age, test limits
]
# using those coefficients and the proposed cost fractions
# compute the ROI surfaces
rois <- rcs[,
denvax::ROI(.SD,
nus = pars[[Country[1]]]$nu,
taus = pars[[Country[1]]]$tau
), by = Country
]
saveRDS(rois, file = tail(.args, 1))
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