Example

First, load in the bayesassurance package.

library(bayesassurance)

Specify the following inputs:

1. n: sample size (either vector or scalar).
2. d: precision level in in analysis objective |x̄ − θ| ≤ d
3. mu_beta_a: analysis stage mean
4. mu_beta_d: design stage mean
5. n_a: sample size at analysis stage. Quantifies the amount of prior information we have for parameter θ.
6. n_d: sample size at design stage. Quantifies the amount of prior information we have for where the data is being generated from.
7. sig_sq: known variance σ².
8. alpha: significance level
9. mc_iter: number of MC samples evaluated under the analysis objective.

As an example, we assign the following set of arbitrary inputs to pass into bayes_adcock() and save the output as out. Notice that we assign a vector of values to sample size n and choose arbitrary values for the remaining parameters.

library(ggplot2)
n <- seq(20, 145, 5)

set.seed(20)
out <- bayesassurance::bayes_adcock(n = n, d = 0.20, mu_beta_a = 0.64, mu_beta_d = 0.9, 
                                    n_a = 20, n_d = 10, sig_sq = 0.265, alpha = 0.05, 
                                    mc_iter = 10000)

Within out contains a list of three objects:

1. assurance_table: table of sample sizes and corresponding assurance values.
2. assur_plot: plot of assurance values. Returned if length of n is greater than 1.
3. mc_iter: number of MC samples generated.

The first six entries of the resulting power table is shown by calling head(out$assurance_table).

head(out$assurance_table)

The plot of assurance points is produced using the ggplot2 package. It displays the inputted sample sizes on the x-axis and the resulting assurance values on the y-axis.

out$assurance_plot

Overlapping Behaviors Between Frequentist and Bayesian Settings

To demonstrate how the frequentist setting is a special case of the Bayesian framework constructed under precision-based conditions discussed above, we refer back to the fundamental sample size formula, and perform some simple rearranging to obtain which we denote as the frequentist condition. Comparing this to the assurance formula we had derived before, we notice that both expressions have 1 − α isolated on the right hand side. Taking n_a = 0 in our assurance formula, simplification proceeds as Notice that the resulting term on the left hand side is now equivalent to that of the frequentist condition. This suggests that if we let θ take on a weak analysis prior, i.e. n_a = 0, we revert back to the frequentist setting in the analysis stage.

We construct a simple function that returns the left hand side of the frequentist condition expressed above.

freq_cond <- function(n, d, sig_sq){
  sigma <- sqrt(sig_sq)
  lhs <- 2 * pnorm(d / (sigma / sqrt(n))) - 1 
  return(lhs)
}

Minor modifications can be implemented in the bayes_adcock() function such that only the left-hand term is returned (function edits not shown). We will denote this modified function as adcock_lhs(). Assigning n_a = 0, d = 0.15 and arbitrary values to all other inputs, we obtain left-hand side values for both frequentist and Bayesian conditions, which we denote as lhs1 and lhs2 respectively. Plots are subsequently produced using the ggplot2 package.

library(ggplot2)
n <- seq(5, 300, 5)
n_a <- 1e-8
n_d <- n_a
d <- 0.15
set.seed(1)
sig_sq <- runif(1, 0, 1)
mu_beta_d <- runif(1, 0, 1) 
mu_beta_a <- runif(1, 0, 1) 

lhs1 <- freq_cond(n, d, sig_sq)
lhs2 <- sapply(n, function(i) adcock_lhs(n = i, d, mu_beta_a, mu_beta_d, n_a, 
                                         n_d, sig_sq))

df1 <- as.data.frame(cbind(n, lhs1))
df2 <- as.data.frame(cbind(n, lhs2))

p <- ggplot(df1) + geom_line(data = df1, alpha = 0.5, aes(x = n, y = lhs1, 
     color="Adcock Cond"), lwd = 1.2)

p1 <- p + geom_point(data = df2, alpha = 0.5, aes(x = n, y = lhs2, 
      color="Bayesian Sim"),lwd=1.2) + ylab("Probability of Meeting Analysis Objective") +
      xlab("Sample Size n") + ggtitle("Comparison Between Adcock Conditiion and Bayesian
                                      Simulation Results")


p1  <- p1 + geom_label(
      label="d = 0.15", 
      x=25,
      y=0.98,
      color = "black", size = 3
      )

We repeat this using various precision values to showcase the overlapping scenario. Notice that the overall assurance values tend to decrease as the precision is lowered.

Frequentist Setting

Let p_i, i = 1, 2 denote two independent proportions. In the frequentist setting, suppose we want to test H₀ : p₁ − p₂ = 0 vs. H_a : p₁ − p₂ ≠ 0. The goal is to detect whether there is a significant difference between the two proportions. One way to check this condition is to see if 0 is contained within the confidence bands of the true difference in proportions, i.e.  $$ 0 \in \displaystyle (\hat{p_1} - \hat{p_2}) \pm z_{1-\alpha/2}(SE(\hat{p_1})^2 + SE(\hat{p_2})^2)^{1/2},$$ where z_{1 − α/2} denotes the critical region, and $SE(\hat{p_i})$ denotes the standard error of p_i. An interval without 0 contained within the confidence bands suggests there exists a significant difference between the two proportions.

Bayesian Setting

The Bayesian setting uses posterior credible intervals as an analog to the frequentist confidence interval approach. In this setting, two distinct priors are assigned to p₁ and p₂ such that p_i ∼ Beta(α_i, β_i) for i = 1, 2.

Let X be a random variable taking on values x = 0, 1, ..., n denoting the number of favorable outcomes out of n trials. The proportion of favorable outcomes is p = x/n. Suppose a Beta prior is assigned to p such that p ∼ Beta(α, β). The prior mean and variance are respectively $\mu_{prior} = \frac{\alpha}{\alpha + \beta}$ and $\sigma^2_{prior} = \frac{\alpha\beta}{(\alpha + \beta)^2(\alpha + \beta + 1)}$. Conveniently, given that p is assigned a Beta prior, the posterior of p also takes on a Beta distribution with mean and variance

Analysis Stage

Within the analysis stage, we assign two beta priors for p₁ and p₂ such that p_i ∼ Beta(α_i, β_i), i = 1, 2. Letting p_d = p₁ − p₂ and p_post and var(p)_post respectively denote the posterior mean and variance of p_d, it is straightforward to deduce that $p_{\text{post}} = \frac{\alpha_1 + x_1}{\alpha_1 + \beta_1 + n_1} - \frac{\alpha_2 + x_2}{\alpha_2 + \beta_2 + n_2}$ and $\text{var}(p)_{\text{post}} = \frac{(\alpha_1 + x_1)(\beta_1 + n_1 - x_1)}{(\alpha_1 + \beta_1 + n_1)^2(\alpha_1 + \beta_1 + n_1 + 1)} + \frac{(\alpha_2 + x_2)(\beta_2 + n_2 - x_2)}{(\alpha_2 + \beta_2 + n_2)^2(\alpha_2 + \beta_2 + n_2 + 1)}.$ The resulting 100(1 − α)% credible interval therefore equates to $p_{\text{post}} \pm z_{1-\alpha/2} \sqrt{\text{var}(p)_{\text{post}}}$, which, similar to the frequentist setting, would be used to check whether 0 is contained within the credible interval bands as part of our inference procedure. This translates to become our analysis objective, where we are interested in assessing if each iterated sample outputs a credible interval that does not contain 0. We can denote this region of interest as R(p) such that It follows that the corresponding assurance for assessing a significant difference in proportions can be computed as $$ \delta = P \left\{p_d: 0 \not\in \left(p_{\text{post}} - z_{1-\alpha/2} \sqrt{\text{var}(p)_{\text{post}}}, \quad p_{\text{post}} + z_{1-\alpha/2} \sqrt{\text{var}(p)_{\text{post}}}\right) \geq 1-\alpha \right\}. $$

Design Stage

In the design stage, frequency counts, x₁ and x₂, are observed from samples of size n₁ and n₂ based on given probabilities, p₁ and p₂, that are passed in the analysis stage. Once p₁ and p₂ are assigned, x₁ and x₂ are randomly generated from their corresponding binomial distributions such that x_i ∼ Bin(n_i, p_i), i = 1, 2. The posterior credible intervals are subsequently computed to undergo assessment in the analysis stage. These steps are repeated iteratively starting from the generation of x₁ and x₂ values. The proportion of iterations with results that fall in region R(p) equates to the assurance.

Example

First, load in the bayesassurance package.

library(bayesassurance)

Specify the following inputs:

1. n1: sample size of first group (scalar)
2. n2: sample size of second group (scalar)
3. p1: proportion of successes in first group. Takes on a NULL assignment if unknown.
4. p2: proportion of successes in second group. Takes on a NULL assignment if unknown.
5. alpha_1, beta_1: shape parameters for the distribution of p1 if p1 is not known or given, i.e. p1 ∼ Beta(α₁, β₁)
6. alpha_2, beta_2: shape parameters for the distribution of p2 if p2 is not known or given, i.e. p2 ∼ Beta(α₂, β₂)
7. sig_level: significance level
8. alt: a character string specifying the alternative hypothesis when comparing p1 and p2. The options are “two.sided” (default), “greater” or “less”.

As an example, we assign the following set of arbitrary inputs to pass into bayes_sim_betabin() and save the result as out. We let n1 = n2 for the sake of simplicity and choose arbitrary values for the remaining parameters.

n <- seq(600, 1000, 10)

set.seed(30)
out <- bayesassurance::bayes_sim_betabin(n1 = n, n2 = n, p1 = 0.25, p2 = 0.2, 
                                         alpha_1 = 0.5, beta_1 = 0.5, alpha_2 = 0.5, 
                                         beta_2 = 0.5, sig_level = 0.05, alt = "two.sided")

Within out contains a list of assurance values. We can create a simple table to show the corresponding sample sizes.

head(out$assurance_table)

Overlapping Behaviors Between Frequentist and Bayesian Settings

We will demonstrate cases where the Bayesian and frequentist settings align and perform similarly in behavior.

Case 1: Known Probabilities

If p₁ and p₂ are known, there is no need rely on the Beta distribution to randomly generate values. We still, however, need to assign shape parameters in the Bayesian setting as they are needed to compute the posterior credible intervals. We will use Haldane’s priors (flat priors) for the Beta distribution, in which α and β are set to 0.5.

Recall the sample size formula for assessing differences in proportions in the frequentist setting, $$ n = \frac{(z_{1-\alpha/2} + z_{\beta})^2(p_1(1-p_1) + p_2(1-p_2))}{(p_1 - p_2)^2}, $$ where n = n₁ = n₂. Simple rearragements and noting that −(z_{1 − α/2} + z_β) = z_1 − β − z_{1 − α/2} lead us to obtain

We create a simple function corresponding to this power formula:

propdiffCI_classic <- function(n, p1, p2, sig_level){
  p <- p1 - p2
  power <- pnorm(sqrt(n / ((p1*(1-p1)+p2*(1-p2)) / (p)^2)) - qnorm(1-sig_level/2))
  return(power)
}

We define a vector of sample sizes n that are assigned to both n₁ and n₂ in the Bayesian setting. Arbitrary values are assigned to p₁ and p₂ along with vague shape parameters, i.e.  α₁ = α₂ = β₁ = β₂ = 0.5. We plot the power curve and assurance points on the same plot.

#########################################################
# alpha1 = 0.5, beta1 = 0.5, alpha2 = 0.5, beta2 = 0.5 ##
#########################################################
n <- seq(40, 1000, 10)

power_vals <- sapply(n, function(i) propdiffCI_classic(n=i, 0.25, 0.2, 0.05))
df1 <- as.data.frame(cbind(n, power_vals))

assurance_out <- bayes_sim_betabin(n1 = n, n2 = n, p1 = 0.25, 
              p2 = 0.2, alpha_1 = 0.5, beta_1 = 0.5, alpha_2 = 0.5, beta_2 = 0.5, 
              sig_level = 0.05, alt = "two.sided")
df2 <- assurance_out$assurance_table
colnames(df2) <- c("n1", "n2", "Assurance")

p1 <- ggplot(df1, alpha = 0.5, aes(x = n, y = power_vals, color="Frequentist Power"))
p1 <- p1 + geom_line(alpha = 0.5, aes(x = n, y = power_vals, 
           color="Frequentist Power"), lwd = 1.2)

p2 <- p1 + geom_point(data = df2, alpha = 0.5, aes(x = .data$n1, y = .data$Assurance, 
      color = "Bayesian Assurance"), lwd = 1.2) + ylab("Power/Assurance") + 
      xlab(~ paste("Sample Size n = ", "n"[1], " = ", "n"[2])) + 
      ggtitle("Power/Assurance Curves of Difference in Proportions")

p2 <- p2 + geom_label(aes(525, 0.6, 
                      #label="~alpha[1] == ~beta[1] == 0.5~and~alpha[2] == ~beta[2] == 0.5"), 
                      label = "~p[1]-p[2] == 0.05"), parse = TRUE,
                      color = "black", size = 3)

Notice that the power and simulated assurance points overlap. This relies on the fact that the normal distribution can be used to approximate binomial distributions for large sample sizes given that the Beta distribution is approximately normal when its parameters α and β are set to be equal.

We repeat these steps for different p₁ and p₂ values while maintaining the same shape parameters.

Case 2: Unknown Probabilities

The following code segments are plots demonstrate overlapping behaviors of the frequentist and Bayesian settings when p₁ and p₂ are not known. We try this for various shape parameters, recalling the fact that the normal distribution can be used to approximate binomial distributions for large sample sizes given that the Beta distribution is approximately normal when its parameters α and β are set to be equal.

We will modify the frequentist power function to include shape parameters as inputs.

propdiffCI_classic <- function(n, p1, p2, alpha_1, beta_1, alpha_2, beta_2, sig_level){
  set.seed(1)
  if(is.null(p1) == TRUE & is.null(p2) == TRUE){
    p1 <- rbeta(n=1, alpha_1, beta_1)
    p2 <- rbeta(n=1, alpha_2, beta_2)
  }else if(is.null(p1) == TRUE & is.null(p2) == FALSE){
    p1 <- rbeta(n=1, alpha_1, beta_1)
  }else if(is.null(p1) == FALSE & is.null(p2) == TRUE){
    p2 <- rbeta(n=1, alpha_2, beta_2)
  }
  p <- p1 - p2

  power <- pnorm(sqrt(n / ((p1*(1-p1)+p2*(1-p2)) / (p)^2)) - qnorm(1-sig_level/2))
  return(power)
}

The following code chunk assigns NULL values to p₁ and p₂ in both functions and assigns equal sets of shape parameters for the Beta distributions.

################################################
# alpha1 = 2, beta1 = 2, alpha2 = 6, beta2 = 6 #
################################################
library(ggplot2)

power_vals <- propdiffCI_classic(n=n, p1 = NULL, p2 = NULL, 2, 2, 6, 6, 0.05)
df1 <- as.data.frame(cbind(n, power_vals))

assurance_vals <- bayes_sim_betabin(n1 = n, n2 = n, 
              p1 = NULL, p2 = NULL, alpha_1 = 2, beta_1 = 2, alpha_2 = 6, 
              beta_2 = 6, sig_level = 0.05, alt = "two.sided")
df2 <- assurance_vals$assurance_table



p1 <- ggplot(df1, aes(x = n, y = power_vals))
p1 <- p1 + geom_line(alpha = 0.5, aes(x = n, y = power_vals, 
                                      color="Frequentist Power"), lwd = 1.2)

p2 <- p1 + geom_point(data = df2, alpha = 0.5, aes(x = n1, y = Assurance, 
      color = "Bayesian Assurance"), lwd = 1.2) +
  ylab("Power/Assurance") + xlab(~ paste("Sample Size n = ", "n"[1], " = ", "n"[2])) + 
    ggtitle("Power/Assurance Curves for Difference in Proportions", 
      subtitle = expression(paste(p[1], "~ Beta(", alpha[1], ", ", beta[1], "); ", 
                                      p[2], "~ Beta(", alpha[2], ", ", beta[2], ")")))

p2 <- p2 + geom_label(aes(75, 1.03, label="~alpha[1] == ~beta[1] == 0.5~and~alpha[2] == ~beta[2] == 0.5"), parse=TRUE,
  color = "black", size = 2.5) + ylim(0.45, 1.03) + xlim(40, 350)

We repeat these steps for various shape parameters. Notice that the assurance points do not align perfectly to the corresponding power curves as we rely on an approximate relationship rather than identifying prior assignments that allow direct ties to the frequentist case. The approximations are still very similar.