---
title: "PlatformDesign"
output:
html_document: default
pdf_document: default
vignette: >
%\VignetteIndexEntry{PlatformDesign}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
```{r setup, warning = FALSE}
library(PlatformDesign)
library(ggplot2)
```
This vignette provides a guidance for designing an optimal two-period K+M-experimental arm platform trial with M delayed experimental arms added during the trial using the package `PlatformDesign`, controlling for family-wise type-I error rate (FWER) or pair-wise type-I error rate (PWER). The K+M-experimental arm trial has K experimental arms and one control arm during the first period, and later M experimental arms are added on the start of the second period. The one common control arm is shared among all experimental arms across the trial. The design method suits any K+M-experimental arm trial, with the examples here shows how to design a 2+2-experimental arm trial (see Fig 1 for the scheme). The goal of the proposed method is to find the optimal design with a minimum total sample size while making the marginal and disjunctive power no less than their counterparts in the K-experimental arm trial it is based on, controlling for FWER or PWER.
![Fig 1.Schema of a two-period 2+2-experimental arm
platform trial. Left part of the figure shows a traditional
three-arm trial, in the context of this paper, we refer it as
a 2-experimental arm trial as it has 2 experimental arms
and 1 common control. In the right part of this figure, it is
the 2+2-experimental arm trial. During the first period, the
2+2-experimental arm trial has two experimental arms, Trt
1 and Trt 2 (light blue segments), and a control arm (the
dark blue segment). The first vertical line (solid) separates
the first and second period of the 2+2-experimental arm
trial, and indicates the opening of the two new experimental
arms, Trt 3 and Trt 4. The second vertical line (dashed)
separates two parts of the second period, and indicates the
closing of Trt 1 and Trt 2. In the first part of the second
period, the control arm (the dark purple segment) is shared
among the four experimental arms (light purple segments).
During the second part of the second period, the control
(dark green), Trt 3, and Trt 4 (light green) continue to accrue
patients until reaching the planned sample sizes. The
nt and n0t (blue brackets) indicate the numbers of patients
enrolled in each of Trt 1 and Trt 2, and the control, respectively,
when Trt 3 and Trt 4 are added. The n1 and n01
(orange brackets) indicate the sample sizes for each of the
two experimental arms and the control, respectively, in the
2-experimental arm trial. The n2 and n02 (green brackets)
indicate the sample sizes for each of the four experimental
arms and their corresponding concurrent control in the
two-period 2+2-experimental arm trial. A1 denotes the allocation
ratio (control to experimental arm) during the first
period of the 2+2-experimental arm trial. A2 denotes the
allocation ratio during the the first part of the second period,
when all four experiments arms are open. A3 is equal to A1.](../vignettes/newArm.PNG)
## Example 1: the optimal two-period multiarm trial design with delayed arms, controlling for FWER
The following steps contain two parts: 1) Steps 1 to 5 derive the design parameters in the K-experimental arm trial that the K+M-experimental arm trial is based on. The K+M-experimental
arm trial is based on the K-experimental arm trial in the sense that we will keep the same FWER and marginal power for the K+M-experimental arm trial as in the K-experimental arm trial, despite M new experimental arms are added during the second period of the K+M experimental
arm trial. 2) Steps 6 to 14 illustrate how the design parameters are calculated for the K+M-experimental arm trial.
For users who are less interested in the theoretical details, you can skip other steps and focus on Steps 1, 7, 13, and 14.
### Step 1: initial setup
Four design parameters for the K-experimental arm trial should be pre-specified: the number of experimental arms ($K$), the family-wise error rate ($FWER_1$), the marginal type II error ($\beta_1$), and the allocation ratio (control-to-each experimental arm, denoted as $A_1$). In our method, we use $A_1=\sqrt{K}$, according to the K-root optimal allocation rule. In the following code, we assume $K=2$, $FWER_1=0.025$, $\beta_1=0.2$, and $A_1=\sqrt{2}$. In addition, $z_{\beta_1}$ (\texttt{z$\_$beta1} in the following code) is the corresponding critical value for the power of $1-\beta_1$.
```{r}
K <- 2
FWER_1 <- 0.025
beta1 <- 0.2
z_beta1 <- qnorm(1-beta1) #z_(1-beta1)
A1 <- sqrt(K)
```
### Step 2: Correlation Matrix 1
We use $Z_1$ and $Z_2$ to denote the two test statistics for comparing the two experimental arm to the control in the original design. Given $A_1$, the correlation between $Z_1$ and $Z_2$ (denoted as $\rho_0$) and the correlation matrix (denoted as $\Sigma_{1}$) can be calculated (see below).
First, we have,
$$\rho_{0} = \frac{n_{0kk^{'}}}{\frac{(n_{01})^{2}}{n_{1}}+n_{01}}$$
where $n_1$ is the number of patients on each of the experimental arm, $n_{01}$ is the number of patients on the control in the K-experimental arm trial, and $n_{0kk^{\prime}}$ is number of control patients shared between 2 experimental arms $k$ and $k'$.
Since the two experimental arms share a common control arm, that is, $n_{0kk^{'}}=n_{01}$. The correlation of $Z_1$ and $Z_2$ is computed as
$$\rho_0 = \frac{1}{(n_{01}/n_{1}+1)}=\frac{1}{(A_1+1)}=0.4142$$
We can see that in our "2+2"-experimental arm example, where K=2, we have
$$\Sigma_{1} =\begin{bmatrix}
1& \rho_0\\
\rho_0& 1
\end{bmatrix}=\begin{bmatrix}
1& 0.4142\\
0.4142& 1
\end{bmatrix}$$
Based on the above description, the function `one_stage_multiarm` can be used to find $\rho_0$ and the correlation matrix $\Sigma_1$ of $Z_1$ and $Z_2$ as shown below.
```{r}
multi <- one_stage_multiarm(K = 2, fwer = 0.025, marginal.power = 0.8, delta = 0.4)
corMat1 <- multi$corMat1
corMat1
```
### Step 3: Critical Value 1
Given $K$, $\Sigma_{1}$ and $FWER_1$, we can find the associated critical value (denoted as $z_{1-\alpha_1}$) for the marginal type I error rate in the 2-experimental arm trial (denoted as $\alpha_1$) based on the following equation.
$$FWER_1=1-\int_{-\infty }^{z_{1-\alpha_1}}\int_{-\infty }^{z_{1-\alpha_1}}...\int_{-\infty }^{z_{1-\alpha_1}}\pi _{z}(Z(z_{1},z_{2},...z_{K}), 0, \Sigma_1 )dz_{1}dz_{2}...dz_{K}$$
This calculation can also be achieved using the function `one_stage_multiarm`.
```{r}
multi$z_alpha1
```
### Step 4: Sample Sizes 1
Given $\beta_1$, $A_1=\sqrt{K}$, an effective standardized effect size $\Delta$ (assumed to be 0.4 for all experimental arms in our paper), and $z_{1-\alpha_1}$ derived above, we can derive sample sizes for the experimental ($n_1$) and control arms ($n_{0_1}=A_1n_1=\sqrt{K}n_1$), respectively, as shown below.
Since we have
$$z_{1-\alpha_1}+z_{1-\beta_1}=\frac{\mu_i-\mu_0}{\sigma\sqrt{\frac{1}{n_{1}}+\frac{1}{\sqrt{K}n_{1}}}}=\frac{\Delta }{\sqrt{\frac{1}{n_{1}}+\frac{1}{\sqrt{K}n_{1}}}}$$
Therefore,
$$n_{1}= \frac{(z_{\alpha_1}+z_{\beta_1})^2}{\Delta^2}(1+\frac{\sqrt{K})}{K})$$
and $$n_{0_{1}}= \frac{(z_{\alpha_1}+z_{\beta_1})^2}{\Delta^2}(1+\sqrt{K})$$
In sum, the total sample size of the K-experimental arm trial is
$$N_1=Kn_{1}+n_{0_{1}}$$
With our "2+2" example, we again use the function `one_stage_multiarm` to derive the sample sizes for the first period.
```{r}
multi$n1
multi$n0_1
multi$N1
```
### Step 5: Disjunctive Power 1
With $\beta_1$ and $\Sigma_{1}$, we can also derive the overall (disjunctive) power $\Omega1=0.922$ based on equation below.
$$\Omega_{1}=1-\int_{-\infty }^{z_{\beta1}}\int_{-\infty }^{z_{\beta1}}...\int_{-\infty }^{z_{\beta1}}\pi _{z}(Z(z_{1},z_{2},...z_{K}), 0, \sum )dz_{1}dz_{2}...dz_{K}$$
This result is also included as part of the output from the function `one_stage_multiarm`, i.e., `$Power1`.
```{r}
multi$Power1
```
From the above outputs, we can see that the computed disjunctive power is 0.922.
Based Steps 1 to 5, we demonstrated given $K, FWER_1$, marginal power $1-\beta_1$ and the standardized effect size $\Delta$, how to derive the marginal type I error rate $\alpha_1$ and its corresponding critical value, sample size $n_1$ for each of the experimental arm and $n_{0_1}$ for the control arm, and disjunctive power $\Omega_1$ for the K-experimental arm trial.
In sum, the function `one_stage_multiarm` in R package `PlatformDesign` can complete step 1 to 5 all at once. Below are the complete outputs generated by applying this function.
```{r}
multi
```
Based on these knowledge, we can introduce our proposed methods when adding new arms in the following from steps 6 to 14.
### Step 6: Timing of Adding New Arms
Timing is the first component to consider if planning to add new experimental arms during a study. In practice, we can use a fraction to denote the timing. In this paper, we use the number of patients already being enrolled in the experimental arm (denoted as $n_t$) when new arms added to define the timing of adding. By this definition, at the time of adding new arms, number of patients enrolled in the control arm is $n_{0t}=[A_1n_t]$.
For example, the following codes describe a scenario if new arms are added when there have 30 patients enrolled for each of the experimental arms.
```{r}
nt <- 30
nt
n_0t <- ceiling(nt*A1)
n_0t
```
### Step 7: Initial Setup 2
Then we need to decide the family-wise error rate when adding new arms, denoted as $FWER_2$. In this example, we control the $FWER_2$ at the same level to the $FWER_1$. With $FWER_2$, we can find the marginal type I error rate (denoted as $\alpha_1$). With $\alpha_1$, we can find the updated marginal power (denoted as $\omega_2=1-\beta_2$), and then the disjunctive power (denoted as $\Omega_2$). We will describe these updates with details in the following steps.
The goal of a two-period K+M experimental arm platform design is to minimize the sample size (denoted as $N_2$) while keeping the marginal power ($\omega_2$) and disjunctive power ($\Omega_2$) no less than their counterparts in the first period ($\omega_1$ and $\Omega_1$). That is, we set the lower limit of $\omega_2$ (denoted as $\omega_{2min}$) to be 0.8, the lower limit of $\Omega_2$ (denoted as $\Omega_{2min}$) to be 0.922 (which is obtained by using function `one_stage_multiarm` in the previous steps) as for our "2+2" example.
These two limits will be used to select the recommended optimal design(s) (details shown in Step 13).
```{r}
FWER_2 <- FWER_1
FWER_2
omega2_min <- 1-beta1
omega2_min
Omega2_min <- multi$Power1
Omega2_min
```
### Step 8: Admissible Set
Because we need to keep $FWER_2$ equal to $FWER_1$ when adding new arms, we then have to update $n_1$ to $n_2$ and $n_{01}$ to $n_{02}$ for each experimental arm (See Fig 1). Here $n_{2}$ and $n_{02}$ are the sample sizes for each of the experimental arms and for the concurrent control in the 2+2-experimental arm trial.
We define an admissible set for pairs of $(n_{2}, n_{02})$ based on the following three constraints. The first two constraints for $(n_{2}, n_{02})$ is related to the allocation ratio after adding the new arms, denoted as $A_2$. In the first period with two experimental arms (before adding the new arms), the control allocation ratio is $A_1$. Once the two new experimental arms are added, we need to use an allocation ratio $A_2$ to achieve desired design properties (e.g., control the FWER and achieve the marginal power). After the initially opened two experimental arms are completed, the trial will again have only two experimental arms left. Therefore, the allocation ratio will go back from $A_2$ to $A_1$.
Here we have,
$$A_2=(n_{0_2}-n_{0t})/(n_2-n_t) > 0$$
where $n_t$ and $n_{0t}$ are number of enrolled patients for each of the experimental arms and the control at the time of adding new arms. That is, the value of $A_2$ needs to be a non-infinite positive number. For example, the first two constraints in our "2+2" example are
$$n_{0_2} > n_{0t}=43$$
and $$n_2>n_t=30$$
We also need to set an upper limit for the total sample size $N_2$. A reasonable upper limit is that $N_2$ should not exceed the required sample sizes (denoted as $S$) of separately conducting two multiarm trials, i.e., a K-experimental arm trial and a M-experimental arm trial. To recap, $K$ and $M$ refer to the numbers of initially and newly added experimental arms.
Therefore, S can be calculated as
$$
S= \frac{(z_{1-\alpha_1}+z_{1-\beta_1})^2}{\Delta^2}(1+2\sqrt{K}+K) +
\frac{(z_{1-\alpha_1^*}+z_{1-\beta_1})^2}{\Delta^2}(1+2\sqrt{M}+M).
$$
, where $z_{1-\alpha_1}$ and $z_{1-\alpha_1^*}$ are the critical values for the K- and M-experimental arm trial, separately. In our "2+2" example, $z_{1-\alpha_1}=z_{1-\alpha_1^*}$ as $K=M=2$ and $S=2N_1=690$.
Therefore, the third constraint for $(n_{2}, n_{0_{2}})$ is
$$
N_2=(K+M)n_2+n_{0_2}+n_{0t}