scripts/output_ruleout.R

In n8thangreen/VANTDET: Cost-Effectiveness Decision Tree

#
# VANTDET:
# output table of key cost-effectiveness statistics for rule-out test
# output_ruleout.R
# N Green


# HIV?

source(file = "scripts/define-decision-tree.R")

dat <- list()

dat[['transcript']] <- dectree(
  data = data,
  name.newtest = "transcript",
  costDistns = costs,
  performance = list(performance$transcript_ruleout),
  time_res = list(time_res$transcript),
  drug = drug,
  QALYloss = QALYloss,
  terminal_cost = terminal_cost_ruleout,
  terminal_health = terminal_health_ruleout)

dat[['proteomic_SELDI']] <- dectree(
  data = data,
  name.newtest = "proteomic_SELDI",
  costDistns = costs,
  performance = list(performance$proteomic_SELDI_ruleout),
  time_res = list(time_res$proteomic_SELDI),
  drug = drug,
  QALYloss = QALYloss,
  terminal_cost = terminal_cost_ruleout,
  terminal_health = terminal_health_ruleout)


# dat[['microscopy']] <- dectree(
#   data = data,
#   name.newtest = "microscopy",
#   costDistns = costs,
#   performance = list(performance$microscopy),
#   time_res = list(time_res$microscopy),
#   drug = drug,
#   QALYloss = QALYloss,
#   terminal_cost = terminal_cost_ruleout,
#   terminal_health = terminal_health_ruleout)


e_df <- do.call(cbind, purrr::map(dat, 'e'))
c_df <- do.call(cbind, purrr::map(dat, 'c'))

evens <- seq(from = 2, to = 2*length(dat), 2)
odds <- evens - 1
QALYgain <- as.matrix(data.frame(0, e_df[ ,odds] - e_df[ ,evens]))
cost_incur <- as.matrix(data.frame(0, c_df[ ,evens] - c_df[ ,odds]))

res_bcea <- bcea(e = -QALYgain,
                 c = -cost_incur,
                 interventions = c("status-quo", names(dat)))

##########
# output #
##########

contour2(res_bcea, graph = "ggplot2")

my_contour2(res_bcea, graph = "ggplot2", CONTOUR_PC = '5%') +
  coord_cartesian(xlim = c(-0.002, 0.002)) +
  theme(legend.position = "none")

my_contour2_facet(dat)

cost_effectiveness_table(dat)
result_tab <- cost_effectiveness_table(res_bcea)


write.csv(x = result_tab,
          file = "output/ICERtable_ruleout.csv")