The package `ThreeArmedTrials`

provides a collection of functions for statistical inference in three-arm trials with the *gold standard* design. For a study assessing non-inferiority or superiority of an experimental treatment compared to an active control, tools to

- determine the optimal sample size allocation
- plan the sample size
- analyze the final data set

are provided for a variety of models (Poisson, negative binomial, normal, censored exponential, binary, non-parametric). This document provides an overview of the implemented statistical models and demonstrates the package’s usage in worked-out examples for Poisson, binary, and the non-parametric model.

Superiority is tested with a margin of \(\Delta\in [1,\infty)\) and non-inferiority with a margin of \(\Delta \in (0,1)\). In the case of non-inferiority, this hypothesis is referred to as the retention of effect (RET) hypothesis. If the null hypothesis \(H_{0}\) is rejected, non-inferiority or superiority of the experimental treatment compared to the reference is shown.

The outcomes under experimental treatment (E), reference (R), and placebo (P) are modeled as the random variables

\[X_{k,i}\quad i=1,\ldots, n_k, \quad k=E,R,P.\]

The random variables are distributed according to a parametric family with densities \[\{f(\theta,\cdot):\theta\in \Theta\}, \Theta \subseteq \mathbb{R}^d.\] We denote the parameter vectors of the experimental, reference, and placebo group as \(\theta_{E}, \theta_{R}, \theta_{P} \in \Theta\), respectively.

Let \(h:\Theta^d\to \mathbb{R}\) be a monotonic function and \(\lambda_k:=h(\theta_k), k=E,R,P,\) be the parameters of interest. The next table provides an overview of the implemented models, the respective literature, and common choices of \(h\).

Model | Literature | Distribution of \(X_{k,i}\) | Parameter vector \(\theta_k\) | h |
---|---|---|---|---|

Normal - homoscedastic | Pigeot et al. (2003) | \(\mathcal{N}(\mu_k, \sigma^2)\) | \((\mu_k,\sigma^2)\) | \((\mu_k,\sigma^2) \mapsto \mu_k\) |

Binary | Kieser and Friede (2007) | \(\mathcal{B}(1, p_k)\) | \(p_k\) | \(id, logit\) |

Normal - heteroscedastic | Hasler et al. (2008) | \(\mathcal{N}(\mu_k, \sigma^{2}_{k})\) | \((\mu_k,\sigma_{k}^2)\) | \((\mu_k,\sigma_{k}^2) \mapsto \mu_k\) |

Poisson | Mielke and Munk (2009) | \(\operatorname{Pois}(\mu_k)\) | \(\mu_k\) | \(id\) |

Censored exponential | Mielke et al. (2009) | \(\min\left(\operatorname{Exp}(\mu_k), U_{k,i}\right)\) | \((\mu_k, p_k)\) | \((\mu_k, p_k)\mapsto \log(\mu_k)\) |

Negative binomial | Mütze et al. (2016a) | \(\operatorname{NB}(\mu_k, \phi)\) | \((\mu_k, \phi)\) | \((\mu_k,\phi) \mapsto \mu_k\) |

Non-parametric | Mütze et al. (2016b) | - | \((\mu_k,\sigma_{k}^2)\) | \((\mu_k,\sigma_{k}^2) \mapsto \mu_k\) |

For the censored exponential model, \(U_{k,i}\) are the censoring times for which no particular distribution is assumed and \(p_k\) are the probabilities of an observation being uncensored. The non-parameteric model does not assume any particular distribution for the data and \(\mu_k\) and \(\sigma^2_k\) are the expected value and the variance, respectively.

The hypothesis \(H_0\) is rejected at significance level \(\alpha\) if the Wald-type test statistic \begin{align*} T=\sqrt{n}\frac{\hat{\lambda}_{E}-\Delta \hat{\lambda}_{R} + (\Delta-1)\hat{\lambda}_{P} }{\hat{\sigma}} . \end{align*}is smaller than the \(\alpha\)-quantile of a normal distribution (binary, censored exponential, negative binomial, and Poisson model), t-distribution (normal models), or a permutation distribution (non-parametric model). For the normal and the non-parametric models the variance estimator \(\hat{\sigma}^{2}\) is based on group specific sample variances. For the censored exponential model the variance is estimated by an unrestricted maximum-likelihood estimator. For the binarey, Poisson, and negative binomial model, the user can choose between an unrestricted maximum-likelihood variance estimator and a maximum-likelihood variance estimator restricted to the parameter space of the null hypothesis. The estimators \(\hat{\lambda}_{k}\) are maximum-likelihood estimators for the parameteric models and group specific means for the non-parametric model.

This package is implemented such that the function names for each of the three tasks (optimal sample size allocation calculation, sample size calculation, data analysis) do not depend on the statistical model. The model is then specfied when calling the functions. The next table lists the task and the corresponding R-function for performing this task.

Task | R-function |
---|---|

Optimal sample size allocation calculation | `opt_alloc_RET()` |

Sample size and power related calculation | `power_RET()` |

Testing the retention of effect hypothesis | `test_RET()` |

The functions `opt_alloc_RET()`

and `power_RET()`

require the user to specify a parameter vector. For each of the models, this parameter vector corresponds to the vector \(\theta_k\) defined above.

In the following, we will focus on planning and analyzing a three-arm trial with the hypothesis \(H_{0, logit}\).

The trial will be designed in two steps. Firstly, we calculate an optimal sample size allocation for a given alternative. Then, we calculate the sample sample of the trial.

The following information is required for calculating the optimal sample size of a trial with the function `opt_alloc_RET()`

:

- The vector of probabilities \((p_{E}, p_{R}, p_{P})\) in the alternative. Here: \((p_{E}, p_{R}, p_{P}) = (0.5, 0.3, 0.2)\).
- A non-inferiority margin \(\Delta\). Here: \(\Delta = 0.8\).
- The function \(h\) which is used to define the hypothesis. Here, the function \(h\) is defined as
`h = function(x){-log(x/(1-x))}`

.

The optimal sample size allocation is calculated and given by

```
w <- ThreeArmedTrials::opt_alloc_RET(experiment = 0.5,
reference = 0.3,
placebo = 0.2,
Delta = 0.8,
distribution = "binary",
h = function(x){-log(x/(1-x))})
```

The function `opt_alloc_RET()`

returns a vector \((w_E^{*}, w_R^{*}, w_P^{*})\) with the optimal sample size allocation.

`print(w)`

`## [1] 0.4710601 0.4111749 0.1177650`

For calculating the sample size of a trial with the function `power_RET()`

, we require the following information:

- The vector of probabilities \((p_{E}, p_{R}, p_{P})\) in the alternative. Here: \((p_{E}, p_{R}, p_{P}) = (0.5, 0.3, 0.2)\).
- A non-inferiority margin \(\Delta\). Here: \(\Delta = 0.8\).
- A significance level and a power. Here: \(\alpha=0.025\) and \(\operatorname{power}=0.8\).
- A sample size allocation. Here: the optimal allocation
`w`

- Whether the variance in the Wald-type test will be estimated restricted to the null hypothesis (default and recommended) or unrestricted. Here we choose restricted (
`"RML"`

; unrestricted would be obtained with`"ML`

). - The function \(h\) which is used to define the alternative as well as its inverse function \(h^{-1}\). The function \(h\) is defined as
`h = function(x){-log(x/(1-x))}`

and its inverse function is defined as`h_inv = function(x){exp(-x)/(1+exp(-x))}`

.

Then, the function `power_RET()`

returns the sample size as part of an object of class *power.htest*.

```
ThreeArmedTrials::power_RET(experiment = 0.5, reference = 0.3, placebo = 0.2,
Delta = 0.8,
sig_level = 0.025,
power = 0.8,
allocation = w,
distribution = "binary",
h = function(x){-log(x/(1-x))},
h_inv = function(x){exp(-x)/(1+exp(-x))},
var_estimation = "RML")
```

```
##
## Power calculation for Wald-type test (with restriced variance estimation) in three-arm trial with binary endpoints
##
## Rate - Experimental = 0.5
## Rate - Reference = 0.3
## Rate - Placebo = 0.2
## n = 151
## sig.level = 0.025
## power = 0.8041344
## Delta = 0.8
## allocation = 0.4701987, 0.4105960, 0.1192053
## nExp = 71
## nRef = 62
## nPla = 18
```

The object of class *power.htest* then contains the input information, the calculated sample size `n`

, and the group specific sample sizes `nExp`

, `nRef`

, and `nPla`

.

Analyzing a three-arm trial with binary data will be demonstrated with data from a clinical trial in patients with depression which is included as the `remission`

data set. The data set contains the three columns `experimental`

, `reference`

, and `placebo`

with data from 86, 84, and 88 patients, respectively. In the experimental treatment group 43 patients (\(50\%\)) went into remission, in the reference group 31 patients (\(36.9\%\)) went into remission, and 26 patients (\(29.54\%\)) in the placebo group went into remission.

We test the hypothesis specified with \(h\) as the logit function. The analysis will be performed with the function `test_RET()`

. The distribution is specified by the argument `distribution = "binary"`

. Moreover, we select the non-inferiority margin \(\Delta=0.8\) and the variance for the Wald-type test will be estimated restricted to the null hypothesis, i.e. `var_estimation = "RML"`

.

```
library(ThreeArmedTrials)
noninf_test <- ThreeArmedTrials::test_RET(xExp = remission$experimental,
xRef = remission$reference,
xPla = remission$placebo,
Delta = 0.8,
var_estimation = "RML",
distribution = "binary",
h = function(x){-log(x/(1-x))},
h_inv = function(x){exp(-x)/(1+exp(-x))})
```

The output of `test_RET()`

is an object of class *h.test*.

`print(noninf_test)`

```
##
## Wald-type test for the retention of effect hypothesis (with
## restriced variance estimation) for the 'binary model'
##
## data: remission$experimental, remission$reference, and remission$placebo
## T = -2.1183, p-value = 0.01707
## sample estimates:
## Mean Exp Mean Ref Mean Pla
## 0.5000000 0.3690476 0.2954545
```

The output lists the test statistic, the p-value, and the group specific remission rates.

To demonstrate the functionality of the package *ThreeArmedTrials* for the Poisson model, we consider trials in epilepsy as an example. In trials in epilepsy a common endpoint is the number of seizures per person which is in general modelled as Poisson distributed.

The following information is required to successfully calculate the sample size

- The vector of rates \((\mu_{E}, \mu_{R}, \mu_{P})\) in the alternative. Here: \((\mu_{E}, \mu_{R}, \mu_{P}) = (15, 17, 20)\).
- A non-inferiority margin \(\Delta\). Here: \(\Delta = 0.8\).
- A significance level and a power. Here: \(\alpha=0.025\) and \(\operatorname{Power}=0.8\).
- A sample size allocation. Here: \(n_E:n_R:n_P=1:1:1\), i.e. a balanced design.
- Whether the variance in the Wald-type test will be estimated restricted to the null hypothesis (default and recommended) or unrestricted. Here we choose restricted (
`"RML"`

; unrestricted would be obtained with`"ML`

).

To calculate the sample size, we use the `power_RET()`

function with the parameter `distribution = "poisson"`

to specify that our data is modeled as Poisson distributed. The output of the function `power_RET()`

is an object of class *power.htest*:

```
library(ThreeArmedTrials)
power_RET(experiment = 15, reference = 17, placebo = 20,
Delta = 0.8, sig_level = 0.025, power = 0.8,
allocation = c(1, 1, 1) / 3,
var_estimation = "RML",
distribution = "poisson")
```

```
##
## Power calculation for Wald-type test (with restriced variance estimation) in three-arm trial with Poisson endpoints
##
## Rate - Experiment = 15
## Rate - Reference = 17
## Rate - Placebo = 20
## n = 96
## sig.level = 0.025
## power = 0.8047648
## Delta = 0.8
## allocation = 0.3333333, 0.3333333, 0.3333333
## nExp = 32
## nRef = 32
## nPla = 32
```

First the setup is described with a note. Then, the output lists of the numeric input parameters as well as the caculated total sample size `n`

and the group sample sizes `nExp`

, `nRef`

, and `nPla`

.

Here, we planned the sample size for a balanced design, i.e. \(n_E:n_R:n_P=1:1:1\). Alternatively, the sample size allocation could be calculated for a given alternative such that the power is maximized. The resulting sample size allocation is referred to as the optimal sample size allocation. The optimal sample size allocation can be calculated with the function `opt_alloc_RET()`

. Thereto, the vector of rates \((\mu_{E}, \mu_{R}, \mu_{P})\), the non-inferiority margin \(\Delta\), and the distribution must be specified. For the example from above, the optimal sample size allocation can be calculated by:

```
opt_alloc_RET(experiment = 15,
reference = 17,
placebo = 20,
Delta = 0.8,
distribution = "poisson")
```

`## [1] 0.4801678 0.4089422 0.1108900`

The function `opt_alloc_RET()`

returns the vector with the optimal sample size allocation. The first element referes to the experimental treatment, the second to the reference, and the third to the placebo.

As an example for a trial with Poisson data we considered the dataset `seizures`

which is included in the *ThreeArmedTrials* package. The `seizures`

dataset contains the number of seizures per patient for three different add-on treatments, i.e. placebo, reference, and experimental treatment, evaluating an anti-epileptic drug. The dataset includes 32 patiens.

pla | ref | exp | |
---|---|---|---|

1 | 21 | 13 | 14 |

2 | 12 | 14 | 13 |

3 | 21 | 5 | 11 |

4 | 26 | 19 | 18 |

5 | 20 | 17 | 14 |

6 | 17 | 21 | 18 |

For the `seizures`

data set non-inferiority of the experimental treatment compared to the reference will be tested with a non-inferiority margion of \(\Delta=0.8\). The standard deviation for the Wald-type test will be estimated using a maximum-likelihood estimator restricted to the parameter space of the null hypothesis. Thus, we set the parameter `var_estimation = "RML"`

. For the unrestricted estimator, `var_estimation = "ML"`

can be used. The hypothesis test is performed with the function `test_RET()`

:

```
noninf_test <- ThreeArmedTrials::test_RET(xExp = seizures$exp,
xRef = seizures$ref,
xPla = seizures$pla,
Delta = 0.8,
var_estimation = "RML",
distribution = "poisson")
```

The output of the function `test_RET()`

is an object of class *h.test*.

`print(noninf_test)`

```
##
## Wald-type test for the retention of effect hypothesis (with
## restriced variance estimation) for the 'poisson model'
##
## data: seizures$exp, seizures$ref, and seizures$pla
## T = -2.1824, p-value = 0.01454
## sample estimates:
## Mean Exp Mean Ref Mean Pla
## 15.15625 16.31250 20.56250
```

The output starts with a note describing the setup. Then, the names of the data variables are listed followed by the test statistic `T`

and the p-value. The output is concluded with the group specific means.

In this section the focus is on analyzing a three-arm study in the *gold standard* design using the non-parametric method, i.e. a studentized permutation test. We focus on the exemplary data set `GElesions`

.

experimental | reference | placebo | |
---|---|---|---|

1 | 0 | 0 | 3 |

2 | 10 | 6 | 0 |

3 | 0 | 3 | 15 |

4 | 2 | 0 | 20 |

5 | 0 | 8 | 0 |

6 | 0 | 0 | 0 |

We test non-inferiority of the experimental treatment compared to the reference with a margin of \(\Delta=0.8\). Additionally, we must specify the number of permutations considered when calculating the rejection area. Here, we choose `n_perm = 50000`

. As before, hypothesis is test with the function `test_RET()`

:

```
set.seed(12345)
noninf_test <- ThreeArmedTrials::test_RET(xExp = GElesions$experimental,
xRef = GElesions$reference,
xPla = GElesions$placebo,
Delta = 0.8,
n_perm = 50000,
distribution = "nonparametric")
```

The output of the function `test_RET()`

is an object of class *h.test*.

`print(noninf_test)`

```
##
## Studentized permutation test for the retention of effect
## hypothesis
##
## data: GElesions$experimental, GElesions$reference, and GElesions$placebo
## T = -0.45875, p-value = 0.3482
## sample estimates:
## Mean Exp Mean Ref Mean Pla
## 2.82 2.78 5.56
```

Here, we see that due to the p-value of about 34%, non-inferiority could not be shown with a commonly considered significance level.

- I. Pigeot, J. Schäfer, J. Röhmel, D. Hauschke.
*Assessing non-inferiority of a new treatment in a three-arm clinical trial including a placebo.*Statistics in Medicine, 22:883-899 (2003). - M. Kieser, T. Friede.
*Planning and analysis of three‐arm non‐inferiority trials with binary endpoints.*Statistics in Medicine, 26:253-273 (2007). - M. Hasler, R. Vonk, L.A. Hothorn.
*Assessing non-inferiority of a new treatment in a three-arm trial in the presence of heteroscedasticity.*Statistics in Medicine, 27:490-503 (2008). - M. Mielke, A. Munk, and A. Schacht.
*The assessment of non‐inferiority in a gold standard design with censored, exponentially distributed endpoints.*Statistics in Medicine 27:5093-5110 (2008). - M. Mielke and A. Munk.
*The assessment and planning of non-inferiority trials for retention of effect hypotheses-towards a general approach.*arXiv preprint arXiv:0912.4169 (2009). - M. Mielke.
*Maximum Likelihood Theory for Retention of Effect Non-inferiority Trials* - T. Mütze, A. Munk, T. Friede.
*Design and analysis of three‐arm trials with negative binomially distributed endpoints*. Statistics in Medicine. 35:505-521 (2016a). - T. Mütze, F. Konietschke, T. Friede.
*A studentized permutation test for three-arm trials in the `gold standard’ design*. Submitted. (2016b).