#
# VANTDET:
# create input parameter lists
# new_test_params.R
# N Green
#########
# costs #
#########
# staff time @ RA:
# http://www.imperial.ac.uk/media/imperial-college/administration-and-support-services/hr/public/salaries/job-families/AR---London-SP-Rates---2017-18.pdf
staff_per_hr <- 24.20
IGRA_staff_hrs <- list(distn = "unif",
params = c(min = 6, max = 8)) #0.25-0.33 days
# load("C:/Users/ngreen1/Dropbox/TB/IDEA/R/packages/IDEAdectree/data/COSTdistns_allerror.RData")
data("COSTdistns_allerror", package = "IDEAdectree")
costs <- COST.distns.allerror
costs$transcriptomic <-
IGRA_staff_hrs %>%
modify_at(.at = "params",
.f = function(x) x*staff_per_hr + 16.5)
costs$proteomic_SELDI <-
IGRA_staff_hrs %>%
modify_at(.at = "params",
.f = function(x) x*staff_per_hr + 36)
costs$flow_cytometry <-
IGRA_staff_hrs %>%
modify_at(.at = "params",
.f = function(x) x*staff_per_hr + 150) #55-350
##TODO:nested sampling
costs$molecular <- list(distn = "unif",
params = 7*staff_per_hr + c(min = 27, max = 35))
costs$visit1 <- list(distn = "gamma",
params = c(shape = 53.3, scale = 4.52))
costs$visit2 <- list(distn = "gamma",
params = c(shape = 18.78, scale = 7.62))
#########
# times #
#########
time_res <- list(transcriptomic =
list(distn = "unif",
params = c(min = 1, max = 1.5)), #24-36 hours
proteomic_SELDI =
list(distn = "unif",
params = c(min = 0.5, max = 2)),
flow_cytometry =
list(distn = "unif",
params = c(min = 2, max = 7)),
molecular =
list(distn = "unif",
params = c(min = 2, max = 5)),
IGRA =
list(distn = "unif",
params = c(min = 2, max = 7)))
####################
# test performance #
####################
performance <- list(transcriptomic_rulein =
list(sens =
list(distn = "unif", #0.902
params = c(min = 0.865, max = 0.932)),
spec =
list(distn = "unif", #0.552
params = c(min = 0.493, max = 0.609))),
transcriptomic_ruleout =
list(sens =
list(distn = "unif", #0.294
params = c(min = 0.245, max = 0.346)),
spec =
list(distn = "unif", #0.95
params = c(min = 0.919, max = 0.972))),
proteomic_SELDI_rulein =
list(sens =
list(distn = "unif",
params = c(min = NA, max = NA)),
spec =
list(distn = "unif",
params = c(min = NA, max = NA))),
proteomic_SELDI_ruleout =
list(sens =
list(distn = "unif",
params = c(min = NA, max = NA)),
spec =
list(distn = "unif",
params = c(min = NA, max = NA))),
flow_cytometry_HIVneg =
list(sens =
list(distn = "unif", #66.7
params = c(min = 0.548, max = 0.771)),
spec =
list(distn = "unif", #92.1
params = c(min = 0.836, max = 0.971))),
molecular =
list(sens =
list(distn = "unif", #0.97
params = c(min = 0.85, max = 1.0)),
spec =
list(distn = "unif", #0.2
params = c(min = 0.057, max = 0.44))),
# QFT-GIT all patients from IDEA
##TODO:use separate HIV negative estimates
##TODO:beta distn
IGRA =
list(sens =
list(distn = "unif",
params = c(min = 0.673, max = 0.721)),
spec =
list(distn = "unif",
params = c(min = 0.761, max = 0.841))))
# save --------------------------------------------------------------------
save(costs, file = "data/costs.RData")
save(time_res, file = "data/time_res.RData")
save(performance, file = "data/performance.RData")
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