## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  cache.path = "single-arm-cache/"
)
set.seed(3081)

## ----setup, message=FALSE-----------------------------------------------------
library(goldilocks)

## ----design-------------------------------------------------------------------
end_of_study <- 24
benchmark <- 0.30                       # external standard-of-care failure rate
target    <- 0.20                       # rate we hope the new therapy achieves

# Convert the target failure rate into a constant hazard (so we can simulate)
ht <- prop_to_haz(probs = target, endtime = end_of_study)
ht

## ----run, cache=TRUE----------------------------------------------------------
out <- survival_adapt(
  hazard_treatment = ht,
  hazard_control   = NULL,              # single-arm
  cutpoints        = NULL,
  N_total          = 80,
  lambda           = 5,                 # enrollments per month (constant)
  lambda_time      = NULL,
  interim_look     = 50,
  end_of_study     = end_of_study,
  prior_surv            = c(0.1, 0.1),       # Gamma(0.1, 0.1) on the hazard
  prop_loss        = 0.05,
  alternative      = "less",
  h0               = benchmark,         # benchmark failure probability
  Fn               = 0.05,
  Sn               = 0.95,
  prob_ha          = 0.95,
  N_impute         = 50,
  N_mcmc           = 2000,
  method           = "bayes-surv")

out

## ----oc, eval=FALSE-----------------------------------------------------------
# # Power: simulate under the alternative (true rate = 0.20)
# out_power <- sim_trials(
#   N_trials         = 1000,
#   hazard_treatment = ht,
#   hazard_control   = NULL,
#   cutpoints        = NULL,
#   N_total          = 80,
#   lambda           = 5,
#   lambda_time      = NULL,
#   interim_look     = 50,
#   end_of_study     = end_of_study,
#   prior_surv            = c(0.1, 0.1),
#   prop_loss        = 0.05,
#   alternative      = "less",
#   h0               = benchmark,
#   Fn               = 0.05,
#   Sn               = 0.95,
#   prob_ha          = 0.95,
#   N_impute         = 50,
#   N_mcmc           = 2000,
#   method           = "bayes-surv",
#   return_trace     = TRUE,
#   seed             = 3082)
# 
# # Type I error: simulate under the null (true rate = benchmark/PG/OPC = 0.30)
# ht_null <- prop_to_haz(probs = benchmark, endtime = end_of_study)
# out_t1error <- sim_trials(
#   N_trials         = 1000,
#   hazard_treatment = ht_null,
#   hazard_control   = NULL,
#   cutpoints        = NULL,
#   N_total          = 80,
#   lambda           = 5,
#   lambda_time      = NULL,
#   interim_look     = 50,
#   end_of_study     = end_of_study,
#   prior_surv            = c(0.1, 0.1),
#   prop_loss        = 0.05,
#   alternative      = "less",
#   h0               = benchmark,
#   Fn               = 0.05,
#   Sn               = 0.95,
#   prob_ha          = 0.95,
#   N_impute         = 50,
#   N_mcmc           = 2000,
#   method           = "bayes-surv",
#   seed             = 3083)
# 
# oc <- summarise_sims(list(
#   "target event probability" = out_power$sims,
#   "benchmark event probability" = out_t1error$sims
# ))
# oc$true_event_probability <- c(target, benchmark)
# 
# oc
# plot_sim_ocs(
#   oc,
#   effect = "true_event_probability",
#   xlab = "True treatment event probability"
# )
# plot_sim_stopping(out_power)
# plot_sim_decisions(out_power)