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README.Rmd
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---
output: github_document
bibliography: paper/bibfile.bib
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%",
cache = FALSE
)
```
# OptimalGoldstandardDesigns <a href='https://github.com/jan-imbi/OptimalGoldstandardDesigns'><img src='man/figures/sticker.png' align="right" height="550" /></a>
<!-- badges: start -->
[](https://doi.org/10.1002/sim.9630)
[](https://app.codecov.io/gh/jan-imbi/OptimalGoldstandardDesigns?branch=master)
[](https://github.com/jan-imbi/OptimalGoldstandardDesigns/actions/workflows/R-CMD-check.yaml)
[](https://github.com/jan-imbi/OptimalGoldstandardDesigns/blob/master/LICENSE.md)
<!-- badges: end -->
This package contains the code used in the calculations for
our [paper](https://doi.org/10.1002/sim.9630)
on the optimization of the two-stage group sequential three-arm gold-standard
design for non-inferiority trials.
It allows for the simultaneous optimization of the
allocation ratios for both stages (in two-stage designs),
the efficacy boundaries, and the
futility boundaries. The optimization is performed
under type I and II error constraints and the objective function is
customizable by the user.
Methods to optimize two- and one-stage designs are available.
# Installation
You can install the CRAN version of this package by typing the following
command into your R console:
```{r, eval=FALSE}
install.packages("OptimalGoldstandardDesigns")
```
You can install the GitHub Version by typing:
```{r, eval=FALSE}
remotes::install_github("jan-imbi/OptimalGoldstandardDesigns")
```
You can also [clone this repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
directly from github. This will
give you access to the /data/ subdirectory, which contains code to reproduce
the examples from the paper.
# Documentation
You can check out an online version of the documentation
[using this link.](https://jan-imbi.github.io/OptimalGoldstandardDesigns/).
In particular, you might be interested in reading the [*Usage guidance* article](https://jan-imbi.github.io/OptimalGoldstandardDesigns/articles/Introduction.html).
# Example
## A one-stage desgin
```{r}
library(OptimalGoldstandardDesigns)
optimize_design_onestage(
alpha = .025,
beta = .2,
alternative_TP = .4,
alternative_TC = 0,
Delta = .2,
print_progress = FALSE
)
```
## A two-stage design
```{r}
optimize_design_twostage(
beta = 0.2,
alternative_TP = 0.4,
alternative_TC = 0,
Delta = 0.2,
print_progress = FALSE,
binding_futility = TRUE
)
```
# References
Meis, J, Pilz, M, Herrmann, C, Bokelmann, B, Rauch, G, Kieser, M. Optimization of the two-stage group
sequential three-arm gold-standard design for non-inferiority trials. *Statistics in Medicine.* 2023; 42(
4): 536– 558. [doi:10.1002/sim.9630](https://doi.org/10.1002/sim.9630).