# *****************************************************
#
# LTBI screening model
# N Green
# Sept 2017
#
# prep scenario decision tree cost & QALY data
# deterministic sensitivity analysis --------------------------------------
# grid of policy input parameter values
# file_tag <- "_high-low"
file_tag <- "_baseline"
# file_tag <- "_effective"
# file_tag <- "_test"
# file_tag <- "_oneway"
# file_tag <- "_fullfactorial"
# load data ---------------------------------------------------------------
parameter_values_file <- system.file("data", sprintf("scenario-parameter-values%s.xlsx", file_tag),
package = "LTBIscreeningproject")
scenario_parameter_cost <- readxl::read_excel(parameter_values_file,
sheet = "cost", na = c("", NA))#,
# col_types = c('text', 'numeric', 'numeric', 'text', 'numeric'))
scenario_parameter_p <- readxl::read_excel(parameter_values_file,
sheet = "p", na = c("", NA))#,
# col_types = c('numeric', 'numeric', 'numeric', 'numeric'))
scenario_parameter_cost$val_type <- "cost"
if (nrow(scenario_parameter_p) > 0) {
# transform to long format
scenario_parameters_df <-
as.data.frame(scenario_parameter_p) %>%
reshape2::melt(id.vars = "scenario") %>%
plyr::rename(replace = c("variable" = "node",
"value" = "p")) %>%
mutate(val_type = "QALYloss") %>%
dplyr::bind_rows(scenario_parameter_cost, .)
}else{
scenario_parameters_df <- scenario_parameter_cost
}
# split by scenario to lists
scenario_parameters <- split(x = scenario_parameters_df,
f = scenario_parameters_df$scenario)
write.csv(scenario_parameters_df, file = "data/scenario_parameters_df.csv")
save(scenario_parameters, file = "data/scenario_parameters.RData")
# convert to percentages and simplify names
design_matrix <-
scenario_parameter_p %>%
mutate_at(vars(-scenario),
funs(.*100)) %>%
set_names(~sub(' Treatment', '', .x)) %>%
set_names(~sub(' to Screen', '', .x))
save(design_matrix, file = "data/design_matrix.RData")
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