optimal_bias_binary: Optimal phase II/III drug development planning when...

In Sterniii3/drugdevelopR: Utility-Based Optimal Phase II/III Drug Development Planning

Optimal phase II/III drug development planning when discounting phase II results with binary endpoint

Description

The function optimal_bias_binary of the drugdevelopR package enables planning of phase II/III drug development programs with optimal sample size allocation and go/no-go decision rules including methods for discounting of phase II results for binary endpoints (Preussler et. al, 2020). The discounting may be necessary as programs that proceed to phase III can be overoptimistic about the treatment effect (i.e. they are biased). The assumed true treatment effects can be assumed fixed or modelled by a prior distribution. The R Shiny application prior visualizes the prior distributions used in this package. Fast computing is enabled by parallel programming.

Usage

optimal_bias_binary(
  w,
  p0,
  p11,
  p12,
  in1,
  in2,
  n2min,
  n2max,
  stepn2,
  rrgomin,
  rrgomax,
  steprrgo,
  adj = "both",
  lambdamin = NULL,
  lambdamax = NULL,
  steplambda = NULL,
  alphaCImin = NULL,
  alphaCImax = NULL,
  stepalphaCI = NULL,
  alpha,
  beta,
  c2,
  c3,
  c02,
  c03,
  K = Inf,
  N = Inf,
  S = -Inf,
  steps1 = 1,
  stepm1 = 0.95,
  stepl1 = 0.85,
  b1,
  b2,
  b3,
  fixed = FALSE,
  num_cl = 1
)

Arguments

w	weight for mixture prior distribution
p0	assumed true rate of control group, see here for details
p11	assumed true rate of treatment group, see here for details
p12	assumed true rate of treatment group, see here for details
in1	amount of information for p11 in terms of sample size, see here for details
in2	amount of information for p12 in terms of sample size, see here for details
n2min	minimal total sample size for phase II; must be an even number
n2max	maximal total sample size for phase II, must be an even number
stepn2	step size for the optimization over n2; must be an even number
rrgomin	minimal threshold value for the go/no-go decision rule
rrgomax	maximal threshold value for the go/no-go decision rule
steprrgo	step size for the optimization over RRgo
adj	choose type of adjustment: "multiplicative", "additive", "both" or "all". When using "both", res[1,] contains the results using the multiplicative method and res[2,] contains the results using the additive method. When using "all", there are also res[3,] and res[4,], containing the results of a multiplicative and an additive method which do not only adjust the treatment effect but also the threshold value for the decision rule.
lambdamin	minimal multiplicative adjustment parameter lambda (i.e. use estimate with a retention factor)
lambdamax	maximal multiplicative adjustment parameter lambda (i.e. use estimate with a retention factor)
steplambda	stepsize for the adjustment parameter lambda
alphaCImin	minimal additive adjustment parameter alphaCI (i.e. adjust the lower bound of the one-sided confidence interval)
alphaCImax	maximal additive adjustment parameter alphaCI (i.e. adjust the lower bound of the one-sided confidence interval)
stepalphaCI	stepsize for alphaCI
alpha	one-sided significance level
beta	type II error rate; i.e. 1 - beta is the power for calculation of the number of events for phase III
c2	variable per-patient cost for phase II in 10^5 $
c3	variable per-patient cost for phase III in 10^5 $
c02	fixed cost for phase II in 10^5 $
c03	fixed cost for phase III in 10^5 $
K	constraint on the costs of the program, default: Inf, e.g. no constraint
N	constraint on the total expected sample size of the program, default: Inf, e.g. no constraint
S	constraint on the expected probability of a successful program, default: -Inf, e.g. no constraint
steps1	lower boundary for effect size category "small" in RR scale, default: 1
stepm1	lower boundary for effect size category "medium" in RR scale = upper boundary for effect size category "small" in RR scale, default: 0.95
stepl1	lower boundary for effect size category "large" in RR scale = upper boundary for effect size category "medium" in RR scale, default: 0.85
b1	expected gain for effect size category "small"
b2	expected gain for effect size category "medium"
b3	expected gain for effect size category "large"
fixed	choose if true treatment effects are fixed or random, if TRUE p11 is used as fixed effect for p1
num_cl	number of clusters used for parallel computing, default: 1

Value

The output of the function is a data.frame object containing the optimization results:

Method

Type of adjustment: "multipl." (multiplicative adjustment of effect size), "add." (additive adjustment of effect size), "multipl2." (multiplicative adjustment of effect size and threshold), "add2." (additive adjustment of effect size and threshold)

Adj

optimal adjustment parameter (lambda or alphaCI according to Method)

u

maximal expected utility under the optimization constraints, i.e. the expected utility of the optimal sample size and threshold value

RRgo

optimal threshold value for the decision rule to go to phase III

n2

total sample size for phase II; rounded to the next even natural number

n3

total sample size for phase III; rounded to the next even natural number

n

total sample size in the program; n = n2 + n3

K

maximal costs of the program (i.e. the cost constraint, if it is set or the sum K2+K3 if no cost constraint is set)

pgo

probability to go to phase III

sProg

probability of a successful program

sProg1

probability of a successful program with "small" treatment effect in phase III

sProg2

probability of a successful program with "medium" treatment effect in phase III

sProg3

probability of a successful program with "large" treatment effect in phase III

K2

expected costs for phase II

K3

expected costs for phase III

and further input parameters. Taking cat(comment()) of the data frame lists the used optimization sequences, start and finish date of the optimization procedure.

References

IQWiG (2016). Allgemeine Methoden. Version 5.0, 10.07.2016, Technical Report. Available at https://www.iqwig.de/ueber-uns/methoden/methodenpapier/, assessed last 15.05.19.

Examples

# Activate progress bar (optional)
## Not run: progressr::handlers(global = TRUE)
# Optimize

optimal_bias_binary(w = 0.3,                 # define parameters for prior
  p0 = 0.6, p11 =  0.3, p12 = 0.5,
  in1 = 30, in2 = 60,                                 # (https://web.imbi.uni-heidelberg.de/prior/)
  n2min = 20, n2max = 100, stepn2 = 10,               # define optimization set for n2
  rrgomin = 0.7, rrgomax = 0.9, steprrgo = 0.05,      # define optimization set for RRgo
  adj = "both",                                       # choose type of adjustment
  alpha = 0.025, beta = 0.1,                          # drug development planning parameters
  lambdamin = 0.2, lambdamax = 1, steplambda = 0.05,  # define optimization set for lambda
  alphaCImin = 0.025, alphaCImax = 0.5,
  stepalphaCI = 0.025,                                # define optimization set for alphaCI
  c2 = 0.75, c3 = 1, c02 = 100, c03 = 150,            # fixed and variable costs for phase II/III
  K = Inf, N = Inf, S = -Inf,                         # set constraints
  steps1 = 1,                                         # define lower boundary for "small"
  stepm1 = 0.95,                                      # "medium"
  stepl1 = 0.85,                                      # and "large" effect size categories
  b1 = 1000, b2 = 2000, b3 = 3000,                    # define expected benefits
  fixed = TRUE,                                       # true treatment effects are fixed/random
  num_cl = 1)                                         # number of cores for parallelized computing
  

Sterniii3/drugdevelopR documentation built on Jan. 26, 2024, 6:17 a.m.