# *********************************************
#
# LTBI screening
# N Green
#
# create environments for each set of global
# policy parameter values as inputs
policies <- data.frame()
## WHO incidence groups: subsets
incidence_list <- list(c("(0,50]", "(50,150]", "(150,250]", "(250,350]", "(350,1e+05]"),
c("(150,250]", "(250,350]", "(350,1e+05]"),
c("(250,350]", "(350,1e+05]"))
## WHO incidence groups: mutually exclusive
# incidence_list <- list(c("(0,50]", "(50,150]", "(150,250]", "(250,350]", "(350,1e+05]"),
# c("(50,150]"),
# c("(150,250]"),
# c("(250,350]"))
## everyone
# incidence_list <- list(c("(0,50]", "(50,150]", "(150,250]", "(250,350]", "(350,1e+05]"))
endpoints <- c("death", "exit uk")
# LTBI_test <- c("QFT_GIT", "QFT_plus", "TSPOT")
# treatment <- c("LTBI_Tx_3mISORIF", "LTBI_Tx_6mISO")
## test:
# incidence_list <- list(c("(0,50]", "(50,150]", "(150,250]"),
# c("(250,350]", "(350,1e+05]"))
# endpoints <- c("death")
LTBI_test <- c("TSPOT")
treatment <- c("LTBI_Tx_3mISORIF")
# create policies ---------------------------------------------------------
num_policy <- 1
for (min_screen_length_of_stay in 0) {
for (incidence in seq_along(incidence_list)) {
for (endpoint_QALY in seq_along(endpoints)) {
for (endpoint_cost in endpoint_QALY:length(endpoints)) {
for (test in LTBI_test) {
for (treat in treatment) {
policies <- rbind(policies,
cbind(policy = formatC(num_policy, width = 3, format = "d", flag = "0"),
min_screen_length_of_stay,
incid_grps = as.character(incidence_list[incidence]),
treatment = treat,
LTBI_test = test,
endpoint_cost = endpoints[endpoint_cost],
endpoint_QALY = endpoints[endpoint_QALY]))
environ_name <- sprintf("policy_%s",
formatC(num_policy, width = 3, format = "d", flag = "0"))
assign(x = environ_name, value = new.env())
assign(x = "min_screen_length_of_stay", value = min_screen_length_of_stay, envir = eval(parse(text = environ_name)))
assign(x = "incidence_grps_screen", value = incidence_list[[incidence]], envir = eval(parse(text = environ_name)))
assign(x = "ENDPOINT_cost", value = endpoints[endpoint_cost], envir = eval(parse(text = environ_name)))
assign(x = "ENDPOINT_QALY", value = endpoints[endpoint_QALY], envir = eval(parse(text = environ_name)))
assign(x = "treatment", value = treat, envir = eval(parse(text = environ_name)))
assign(x = "LTBI_test", value = test, envir = eval(parse(text = environ_name)))
num_policy %<>% add(1)
}
}
}
}
}
}
global_params <-
policies %>%
split(seq(nrow(.))) %>%
lapply(as.list)
# save --------------------------------------------------------------------
save(global_params, file = "data/global_params.RData")
rm(global_params)
write.csv(policies, file = "data/policies-inputs.csv")
rm(list = ls()[!ls() %in% ls(pattern = "policy_")])
save.image(file = "data/policies.RData")
policies_ls <- ls()
save(policies_ls, file = "data/policies_ls.RData")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.