scripts/cluster-prep-decisiontree-data-HALT.R

In n8thangreen/LTBIscreeningproject: LTBI screening cost-effectiveness analysis

# LTBI screening model HALT
# N Green
# May 2017
#
# create data in a format to use in DIDE computer cluster functions
# run jobs using network drive Q:\R\cluster--LTBI-decision-tree


devtools::load_all(".")

library(dplyr)
library(plyr)


parameter_values_file <- system.file("data", "scenario-parameter-values_HALT.xlsx",
                                     package = "LTBIscreeningproject")

scenario_parameter_cost <- readxl::read_excel(parameter_values_file,
                                              sheet = "cost")

scenario_parameter_p <- readxl::read_excel(parameter_values_file,
                                           sheet = "p")

# transform probabilities to long format

scenario_parameter_p.melt <-
  as.data.frame(scenario_parameter_p) %>%
  reshape2::melt(id.vars = "scenario") %>%
  plyr::rename(replace = c("variable" = "node",
                           "value" = "p"))

# combine probs and costs in to a single array

scenario_parameter_cost$val_type <- "cost"
scenario_parameter_p.melt$val_type <- "QALYloss"

scenario_parameters <- plyr::rbind.fill(scenario_parameter_cost,
                                        scenario_parameter_p.melt)

# split by scenario to lists
scenario_parameters <- plyr::dlply(scenario_parameters, .(scenario))


#  ------------------------------------------------------------------------

save(scenario_parameters, file = "data/scenario_parameters-HALT.RData")