inst/doc/Bias_adjustment.R

In drugdevelopR: Utility-Based Optimal Phase II/III Drug Development Planning

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## -----------------------------------------------------------------------------
library(drugdevelopR)

## ----eval = FALSE-------------------------------------------------------------
#  res <- optimal_bias(w = 0.3,                                 # define parameters for prior
#     hr1 = 0.75, hr2 = 0.8, id1 = 210, id2 = 420,              # (https://web.imbi.uni-heidelberg.de/prior/)
#     d2min = 20, d2max = 400, stepd2 = 5,                      # define optimization set for d2
#     adj = "both",                                             # choose both adjustment methods
#     lambdamin = 0.7, lambdamax = 1, steplambda = 0.05,        # optimization set for multiplicative adjustment
#     alphaCImin = 0.1, alphaCImax = 0.5, stepalphaCI = 0.05,   # optimization set for additive adjustment
#     hrgomin = 0.7, hrgomax = 0.9, stephrgo = 0.01,            # define optimization set for HRgo
#     alpha = 0.025, beta = 0.1, xi2 = 0.7, xi3 = 0.7,          # drug development planning parameters
#     c2 = 0.75, c3 = 1, c02 = 100, c03 = 150,                  # define fixed and variable costs
#     K = Inf, N = Inf, S = -Inf,                               # set constraints
#     steps1 = 1,  stepm1 = 0.95, stepl1 = 0.85,                # define boundary for  effect size categories
#     b1 = 1000, b2 = 2000, b3 = 3000,                          # define expected benefits
#     fixed = TRUE,                                             # choose if  effects are fixed or random
#     num_cl = 1)

## ----eval=TRUE, include=FALSE-------------------------------------------------
# res <- optimal_bias(w = 0.3,                                 # define parameters for prior
#   hr1 = 0.75, hr2 = 0.8, id1 = 210, id2 = 420,              # (https://web.imbi.uni-heidelberg.de/prior/)
#   d2min = 20, d2max = 400, stepd2 = 5,                      # define optimization set for d2
#   adj = "both",                                             # choose both adjustment methods
#   lambdamin = 0.7, lambdamax = 1, steplambda = 0.05,        # optimization set for multiplicative adjustment
#   alphaCImin = 0.1, alphaCImax = 0.5, stepalphaCI = 0.05,   # optimization set for additive adjustment
#   hrgomin = 0.7, hrgomax = 0.9, stephrgo = 0.01,            # define optimization set for HRgo
#   alpha = 0.025, beta = 0.1, xi2 = 0.7, xi3 = 0.7,           # drug development planning parameters
#   c2 = 0.75, c3 = 1, c02 = 100, c03 = 150,                  # define fixed and variable costs
#   K = Inf, N = Inf, S = -Inf,                               # set constraints
#   steps1 = 1,  stepm1 = 0.95, stepl1 = 0.85,                # define boundary for  effect size categories
#   b1 = 1000, b2 = 2000, b3 = 3000,                          # define expected benefits
#   fixed = TRUE,                                             # choose if  effects are fixed or random
#   num_cl = 1)
# saveRDS(res, file="optimal_bias_adjustment.RDS")

## ----eval=TRUE, include=FALSE-------------------------------------------------
res <- readRDS(file="optimal_bias_adjustment.RDS")

## -----------------------------------------------------------------------------
res