Group sequential design for binary outcomes
Yujie Zhao
Source:vignettes/articles/story-risk-difference.Rmd
story-risk-difference.RmdOverview
We consider group sequential design examining the risk difference between two treatment groups for a binary outcome. There are several issues to consider:
- The measure of treatment difference or natural parameter; we focus on risk difference.
- Incorporation of both null and alternate hypothesis variances.
- Superiority, non-inferiority and super-superiority designs.
- Stratified populations.
- Fixed and group sequential designs.
For single stratum designs, we focus on sample size or power using
the method of Farrington and Manning
(1990) for a trial to test the difference between two binomial
event rates. The routine can be used for a test of superiority,
non-inferiority or super-superiority. For a design that tests for
superiority, the methods are consistent with those of Fleiss, Tytun, and Ury (1980), but without the
continuity correction. Methods for sample size and power are the same as
gsDesign::nBinomial() when testing on the risk-difference
scale for a single stratum. This is also consistent with the
Hmisc R package routines bsamsize() and
bpower() for superiority designs.
For trials with multiple strata, testing for a risk difference is often done by weighting each stratum according to the inverse of the variance (Mantel and Haenszel (1959)). Since risk differences may also be assumed to be different for different strata, we will also explore weighting by strata sample sizes as in Mehrotra and Railkar (2000).
The focus here is for sample sizes that are large enough for asymptotic theory to work well without continuity corrections. The concepts are incorporated in the following functions intended for use in fixed and group sequential designs:
-
gs_info_rd()to support asymptotic variance and statistical information calculation. -
gs_power_rd()to support power calculations. -
gs_design_rd()to support sample size calculations.
Simulation is used throughout to check the examples presented.
Notation
K: total number of analyses (including the final analysis) in the group sequential design. For fixed design, K= 1.
S: total number of strata. If the population is un-stratified population, then S=1.
w_{s,k}: the underlying weight assigned for the s-th strata at the k-th analysis. WHY SWITCH ORDER OF s, k FROM w?
\widehat w_{s,k}: the estimated weight assigned for the s-th strata at the k-th analysis.
N_{C,k,s}, N_{E,k,s}: the planned sample size in the control/treatment group at the k-th analysis of the s-th strata.
\widehat N_{C,k,s}, \widehat N_{E,k,s}: the observed sample size in the control/treatment group at the k-th analysis of the s-th strata.
r: planned randomization ratio, i.e., r = N_{E,k,s} / N_{C,k,s} \;\; \forall k = 1, \ldots, K \;\; \text{and} \;\; s = 1, \ldots, S.
p_{C,s}, p_{E,s}: the planned rate of the control/treatment arm, i.e., the independent observations in the control/treatment group with a binary outcome that is observed with probability p_{C,s} at any k-th analysis of the s-th strata.
d: an indicator whether is an outcome is failure (bad outcome) or response (good outcome), i.e., d = \left\{ \begin{array}{lll} -1 & \text{if } p_{C,s} < p_{E,s} & \text{the control arm is better}\\ 1 & \text{if } p_{C,s} > p_{E,s} & \text{the treatment arm is better}\\ \end{array} \right. Here we assume if \exists s^* \in \{1, \ldots, S\}, s.t., p_{C,s^*} < p_{E,s^*}, then p_{C,s} < p_{E,s}, \forall s \in \{1, \ldots, S\}, and vice versa.
X_{C,k,s}, X_{E,k,s}: random variables indicating the number of subjects failed in control/treatment arm, i.e., X_{C,k,s} \sim \text{Binomial}(N_{C,k,s}, p_{C,k,s}), X_{E,k,s} \sim \text{Binomial}(N_{E,k,s}, p_{E,k,s}) at the k-th analysis of the s-th strata.
x_{C,k,s}, x_{E,k,s}: the observed outcome of X_{C, k, s}, X_{E, k, s} at the k-th analysis of the s-th strata, respectively.
\widehat p_{C,k,s}, \widehat p_{E,k,s}: observed rates of the control/treatment group at the k-th analysis of the s-th strata, i.e., \widehat p_{C,k,s} = x_{C,k,s} / \widehat N_{C,k,s}.\\ \widehat p_{E,k,s} = x_{E,k,s} / \widehat N_{E,k,s}.
\delta_{s}^{null}: the planned risk difference under H_0 at any k-th analysis of the s-th strata.
\delta_{s}: the planned risk difference under H_1 at any k-th analysis of the s-th strata is denoted by \delta_{s} = |p_{C,s} - p_{E,s}|.
\hat\delta_{s}: estimation of risk difference with \widehat\theta_{k,s} = |\widehat p_{C,k,s} - \widehat p_{E,k,s}| We have E(\widehat\theta_{k,s}) = \theta_{s}, \;\forall k = 1, \ldots, K.
Testing
The test statistics at the k-th analysis is Z_{k} = \frac{ \sum_{s=1}^S \widehat w_{s,k} \; |\widehat \delta_{k,s} - \delta_{s}^{null} | }{ \sqrt{\sum_{s=1}^S \widehat w_{s,k}^2 \widehat\sigma_{H_0,k,s}^2} } where \widehat\sigma^2_{k,s} = \widehat{\text{Var}}(\widehat p_C -\widehat p_E). And the value of \widehat\sigma^2_{k,s} depends on the hypothesis and design, i.e., whether it is a superiority design, or non-inferiority design, or super-superiority design. We will discuss \widehat\sigma^2_{k,s} in the following 3 subsections.
Superiority Design
A superiority design (\delta_{s}^{null} = 0) is to show that experimental group is superior to the control group above some thresholds. Its hypothesis is H_0: \delta_{s} = 0 \text{ vs. } H_1: \delta_{s} > 0, \; \forall k = 1, \ldots, K, s = 1, \ldots, S
-
Variance per strata per analysis:
Under the null hypothesis, we have \begin{array}{ll} \sigma^2_{H_0,k,s} & = \text{Var}(p_C - p_E | H_0) = p_{k,s}^{pool} \left(1 - p^{pool}_{k,s} \right) \left(\frac{1}{N_{C,k,s}} + \frac{1}{N_{E,k,s}} \right), \\ \widehat\sigma^2_{H_0,k,s} & = \widehat{\text{Var}}(\hat p_C - \hat p_E | H_0) = \widehat p_{k,s}^{pool} \left(1 - \widehat p^{pool}_{k,s} \right) \left(\frac{1}{N_{C,k,s}} + \frac{1}{N_{E,k,s}} \right), \end{array} where p_{k,s}^{pool} = (p_{C,s} N_{C,k,s} + p_{E,s} N_{E,k,s}) / (N_{C,k,s} + N_{E,k,s}) and \widehat p_{k,s}^{pool} = (x_{C,k,s} + x_{E,k,s}) / (\widehat N_{C,k,s} + \widehat N_{E,k,s}).
Under the alternative hypothesis, we have \begin{array}{ll} \sigma_{H_1,k,s}^2 & = \text{Var}(p_C - p_E | H_1) = \frac{p_{C,s} (1- p_{C,s})}{N_{C,k,s}} + \frac{p_{E,s} (1 - p_{E,s})}{N_{E,k,s}} \\ \widehat\sigma_{H_1,k,s}^2 & = \widehat{\text{Var}}(\hat p_C - \hat p_E | H_1) = \frac{\widehat p_{C,k,s} (1- \widehat p_{C,k,s})}{N_{C,k,s}} + \frac{\widehat p_{E,k,s} (1 - \widehat p_{E,k,s})}{N_{E,k,s}} \end{array} where \widehat p_{C,k,s} = x_{C,k,s} / N_{C,k,s} \text{ and } \widehat p_{E,k,s} = x_{E,k,s} / N_{E,k,s}. Testing will be one-sided at level \alpha \in (0, 1) and the null hypothesis will be rejected if Z_k cross the upper boundary. And the upper boundary can be either fixed or derived from spending functions.
-
Standardized treatment effect per analysis:
Under the null hypothesis, we have \theta_{H_0,k} = 0 \\ \widehat \theta_{H_0,k} = 0
Under the alternative hypothesis, we have \begin{array}{ll} \theta_{H_1,k} & = \frac{\sum_{s=1}^S w_{k,s} (p_{C,s} - p_{E,s})}{\sqrt{\sum_{s=1}^S w_{k,s}^2 \sigma_{H_1, k,s}^2}}\\ \widehat\theta_{H_1,k} & = \frac{ \sum_{s=1}^S \widehat w_{k,s} (\widehat p_C - \widehat p_E) }{ \sqrt{\sum_{s=1}^S \widehat w_{k,s}^2 \widehat\sigma_{H_1, k,s}^2} }. \end{array}
-
Standardized information per analysis:
Lachin (2009) or Lachin (1981) provide fixed sample size calculations based on the values \psi_0 under the null hypothesis and \psi_1 under the alternate hypothesis. Here we propose using the same variance calculations to compute statistical information for a group sequential design and apply the formulation for power and sample size calculation in the vignette Computing Bounds Under Non-Constant Treatment Effect.
Under the null hypothesis, we have \begin{array}{ll} \mathcal I_{H0,k} & = \left[ \sum_{s=1}^S w_{k,s}^2 \frac{p_{k,s}^{pool} (1 - p_{k,s}^{pool})}{N_{C, k, s}} + w_{k,s}^2 \frac{p_{k,s}^{pool} (1 - p_{k,s}^{pool})}{N_{E, k, s}} \right]^{-1} \\ \widehat{\mathcal I}_{H0,k} & = \left[ \sum_{s=1}^S \widehat w_{k,s}^2 \frac{\widehat p_{k,s}^{pool} (1 - \widehat p_{k,s}^{pool})}{\widehat N_{C,k,s}} + \widehat w_{k,s}^2 \frac{\widehat p_{k,s}^{pool} (1 - \widehat p_{k,s}^{pool})}{\widehat N_{C,k,s}} \right]^{-1} \end{array}
Under the alternative hypothesis, we have \begin{array}{ll} \mathcal I_{H1,k} = \left[ \sum_{s=1}^S w_{k,s}^2 \frac{p_{C,k,s} (1 - p_{C,k,s})}{N_{C,k,s}} + \sum_{s=1}^S w_{k,s}^2 \frac{p_{E,k,s} (1 - p_{E,k,s})}{N_{E,k,s}} \right]^{-1}\\ \widehat{\mathcal I}_{H1,k} = \left[ \sum_{s=1}^S \widehat w_{k,s}^2 \frac{\widehat p_{C,k,s} (1 - \widehat p_{C,k,s})}{\widehat N_{C,k,s}} + \sum_{s=1}^S \widehat w_{k,s}^2 \frac{\widehat p_{E,k,s} (1 - \widehat p_{E,k,s})}{\widehat N_{E,k,s}} \right]^{-1} \end{array}
Super-Superiority Design
The hypothesis of the super-superiority design is
H_0: \delta_{k,s} = \delta_{k,s}^{null} \;\; vs. \;\; H_1: \delta > \delta_{k,s}^{null} \text{ with } \delta_{k,s}^{null} > 0. Here \theta_{k,s_1}^{null} = \theta_{k,s_2}^{null} or \theta_{k,s_1}^{null} \neq \theta_{k,s_2}^{null} for s_1 \neq s_2.
Under the null hypothesis \theta_{0,k,s} \neq 0, the estimation of rates \widehat p_{C0,k,s}, \widehat p_{E0,k,s} satisfy \left\{ \begin{array}{l} \widehat p_{C0,k,s} = \widehat p_{E0,k,s} + d_{k,s} \times \delta_{k,s}^{null} \\ \widehat p_{C0,k,s} + r\widehat p_{E0,k,s} = \widehat p_{C,k,s} + r\widehat p_{E,k,s} . \end{array} \right. Solving these 2 equations with 2 unknowns yields \left\{ \begin{array}{l} \widehat p_{E0,k,s} & = (\widehat p_{C,k,s} + r \widehat p_{E,k,s} - d_{k,s} \delta_{k,s}^{null}) / (r + 1)\\ \widehat p_{C0,k,s} & = \widehat p_{E0,k,s} + d_{k,s} \delta_{k,s}^{null}. \end{array} \right.
-
Variance per strata per analysis:
- Under H_0, we have
\hat\sigma^2_{H_0,k,s} = \frac{\widehat p_{C0,k,s}(1- \widehat p_{C0,k,s})}{N_{C,k,s}} + \frac{ \widehat p_{E0,k,s} (1 - \widehat p_{E0,k,s})}{N_{E,k,s}}.
- Under H_1, we have
\widehat\sigma_{H_1,k,s}^2 = \frac{\widehat p_{C,k,s} (1- \widehat p_{C,k,s})}{N_{C,k,s}} + \frac{\widehat p_{E,k,s} (1 - \widehat p_{E,k,s})}{N_{E,k,s}}.
-
Standardized treatment effect per analysis:
- Under the null hypothesis, we have
\widehat \theta_{H_0,k} = \frac{ \sum_{s=1}^S w_{k,s} \delta_{s,k}^{null} }{ \sqrt{\sum_{s=1}^S w_{k,s}^2 \widehat \sigma_{H_0,k,s}}^2 }.
- Under the alternative hypothesis, we have
\widehat \theta_{H_1} = \frac{ \sum_{s=1}^S w_{k,s} d_{k,s} \times (\widehat p_{C,k,s} - \widehat p_{E,k,s}) }{ \sqrt{\sum_{s=1}^S w_{k,s}^2 \widehat \sigma_{H_1,k,s}^2} }.
-
Standardized information per analysis:
- Under the null hypothesis, we have
\widehat{\mathcal I}_{H0,k} = \left[ \sum_{s=1}^S w_{k,s}^2 \frac{\bar p_{C0,s} (1 - \bar p_{C0,s})}{N_{C,s}} + w_{k,s}^2\frac{\bar p_{E0,s} (1 - \bar p_{E0,s})}{N_{E,s}} \right]^{-1}.
- Under the alternative hypothesis, we have
\widehat{\mathcal I}_{H1,k} = \left[ \sum_{s=1}^S \left( w_{k,s}^2 \frac{\bar p_{C,k,s} (1 - \bar p_{C,k,s})}{N_{C,k,s}} + w_{k,s}^2 \frac{\bar p_{E,k,s} (1 - \bar p_{E,k,s})}{N_{E,k,s}} \right) \right]^{-1}.
Non-inferiority Design
The non-inferiority Design means that, while the treatment group is definitely not better than the control group, it is not unacceptably worse. Its hypothesis is H_0: \delta_{k,s} = \delta_{k,s}^{null} \;\; vs. \;\; H_1: \delta_{k,s} > \delta_{k,s}^{null} with \delta_{k,s}^{null} <0. Its variance, standardized treatment effect and statistical information is the same as that from super-superiority design by setting \delta_{k,s}^{null} as negative numbers.
Weighting Options
As previously noted, we will consider weighting based on either inverse-variance weights (Mantel and Haenszel (1959)) or strata sample size weights (Mehrotra and Railkar (2000)).
Inverse-variance weights (INVAR): w_{s,k} = \frac{1/\sigma^2_{s,k}}{\sum_{s=1}^S 1/\sigma^2_{s,k}}. \\ \widehat w_{s,k} = \frac{1/\widehat\sigma^2_{s,k}}{\sum_{s=1}^S 1/\widehat\sigma^2_{s,k}}. where \widehat\sigma_{s,k}^2 \in \{\widehat\sigma_{H_0, k,s}^2, \widehat\sigma_{H_1, k,s}^2 \} depending on the information scale
info_scale = ...ings_info_rd(),gs_power_rd()andgs_design_rd().Sample-Size Weights (SS): w_{s,k} = \frac{ (N_{C, s, k} \; N_{E, s, k}) / (N_{C, s, k} + N_{E, s, k}) }{ \sum_{s=1}^S (N_{C, s, k} \; N_{E, s, k}) / (N_{C, s, k} + N_{E, s, k}) },\\ \widehat w_{s,k} = \frac{ (\widehat N_{C, s, k} \; \widehat N_{E, s, k}) / (\widehat N_{C, s, k} + \widehat N_{E, s, k}) }{ \sum_{s=1}^S (\widehat N_{C, s, k} \; \widehat N_{E, s, k}) / (\widehat N_{C, s, k} + \widehat N_{E, s, k}) }, where N_{C,s,k}, N_{E,s,k} are the planned sample size of the s-th strata and k-th analysis of the control group and experimental group, respectively. And \widehat N_{C,s,k}, \widehat N_{E,s,k} are the observed sample size of the s-th strata and k-th analysis of the control group and experimental group, respectively.
Simulations
We do a quick 20,000 simulations and compare the density histogram of outcomes to the standard normal density. Assume r=1, d = 1, p_C=p_E=0.125, N=200. We then compute \sigma as 0.047. Even for this not huge sample size the normal density fits quite well other than some flatness in the middle.
# Hypothesized failure rate
p <- .125
# Other parameters
set.seed(123)
r <- 1
n <- 200
n_c <- n / (r + 1)
n_e <- r * n / (r + 1)
library(ggplot2)
# Generate random counts of events for each treatment
x_c <- rbinom(n = 20000, size = n_c, prob = p)
x_e <- rbinom(n = 20000, size = n_e, prob = p)
# Treatment difference estimate
thetahat <- x_c / n_c - x_e / n_e
# Standard error under H0
pbar <- (x_c + x_e) / n
se0 <- sqrt(pbar * (1 - pbar) * (1 / n_c + 1 / n_e))
# Z to test H0
z <- thetahat / se0
x <- seq(-4, 4, .1)
se0a <- sqrt(p * (1 - p) * (1 / n_c + 1 / n_e))
y <- data.frame(z = x, Density = dnorm(x = x, mean = 0, sd = 1))
ggplot() +
geom_histogram(data = data.frame(z), aes(x = z, y = ..density..), color = 1, fill = "white") +
geom_line(data = y, aes(x = z, y = Density), linetype = 1) +
ylab("Density") +
ggtitle("Binomial outcomes by simulation vs. asymptotic normal density",
subtitle = "Histogram of 20,000 simulations"
)
#> Warning: The dot-dot notation (`..density..`) was deprecated in ggplot2 3.4.0.
#> ℹ Please use `after_stat(density)` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
Examples
Unstratified Fixed Design
The example discussed in this section is an unstratified fixed design with equal sized groups to detect a 30% reduction in mortality associated with congestive heart failure, where the 1-year mortality in the control group is assumed to be no greater than 0.4. So p_C=0.4, p_E = .28. Under the null hypothesis, we assume p_C=p_E =0.34. We desire 90% power for a two-sided test for two proportions at \alpha = 0.05. And we would like to calculate the sample size to achieve the 90% power.
gsDesign2
First, we set the parameters.
p_c <- .28
p_e <- .4
p_pool <- (p_c + p_e) / 2
n <- 1
ratio <- 1
n_c <- n / (1 + ratio)
n_e <- n_c * ratioThen we calculate the variance under H_0 and H_1. Their mathematical formulation are shown as follows. \begin{array}{ll} \sigma^2_{H_0} = p^{pool} \left(1 - p^{pool} \right) \left(\frac{1}{N_C} + \frac{1}{N_{E}} \right) = p^{pool} \left(1 - p^{pool} \right) \left(\frac{1}{N \xi_C} + \frac{1}{N \xi_E} \right) \overset{r=1}{=} p^{pool} \left(1 - p^{pool} \right) \frac{4}{N} \\ \sigma^2_{H_1} = \frac{p_C \left(1 - p_C \right)}{N_C} + \frac{p_E \left(1 - p_E \right)}{N_E} = \frac{p_C \left(1 - p_C \right)}{N \xi_C} + \frac{p_E \left(1 - p_E \right)}{N \xi_E} \overset{r=1}{=} \left[ p_C \left(1 - p_C \right) + p_E \left(1 - p_E \right) \right] \frac{2}{N} \end{array} And their calculation results are
sigma_h0 <- sqrt(p_pool * (1 - p_pool) * 4 / n)
sigma_h1 <- sqrt((p_c * (1 - p_c) + p_e * (1 - p_e)) * 2 / n)
info_h0 <- 1 / (sigma_h0^2)
info_h1 <- 1 / (sigma_h1^2)Next, we calculate the standardized treatment effect under H_0 and H_1, whose mathematical formulation are \begin{array}{ll} \theta_{H_0} = 0; \\ \theta_{H_1} = \frac{|p_c - p_e|}{\sigma_{H_1}} \end{array}.
And their calculation results are
theta_h0 <- 0
theta_h1 <- abs(p_c - p_e) / sigma_h1
tibble::tribble(
~n_c, ~n_e, ~p_c, ~p_e, ~theta_h1, ~theta_h0, ~info_h1, ~info_h0,
n_c, n_e, p_c, p_e, theta_h1, theta_h0, info_h1, info_h0,
) %>% gt::gt()| n_c | n_e | p_c | p_e | theta_h1 | theta_h0 | info_h1 | info_h0 |
|---|---|---|---|---|---|---|---|
| 0.5 | 0.5 | 0.28 | 0.4 | 0.1276885 | 0 | 1.132246 | 1.114082 |
The above logic is implemented in the function
gs_info_rd().
x <- gs_info_rd(
p_c = tibble::tibble(stratum = "All", rate = .28),
p_e = tibble::tibble(stratum = "All", rate = .4),
n = tibble::tibble(stratum = "All", n = 1, analysis = 1),
rd0 = 0,
ratio = 1,
weight = "unstratified"
)
x %>%
gt::gt() %>%
gt::fmt_number(columns = 5:8, decimals = 6)| analysis | n | rd | rd0 | theta1 | theta0 | info1 | info0 |
|---|---|---|---|---|---|---|---|
| 1 | 1 | 0.12 | 0 | 0.120000 | 0.000000 | 1.132246 | 1.114082 |
By plugging the theta and info above into
gs_design_npe(), one can calculate the sample size to
achieve the 90% power.
# under info_scale = "h0_info"
y_0 <- gs_design_npe(
theta = .4 - .28,
info = x$info0,
info0 = x$info0,
info_scale = "h0_info",
alpha = .025,
beta = .1,
upper = gs_b,
lower = gs_b,
upar = list(par = -qnorm(.025)),
lpar = list(par = -Inf)
)
# under info_scale = "h1_info"
y_1 <- gs_design_npe(
theta = .4 - .28,
info = x$info1,
info0 = x$info0,
info_scale = "h1_info",
alpha = .025,
beta = .1,
upper = gs_b,
lower = gs_b,
upar = list(par = -qnorm(.025)),
lpar = list(par = -Inf)
)
# under info_scale = "h0_h1_info"
y_2 <- gs_design_npe(
theta = .4 - .28,
info = x$info1,
info0 = x$info0,
info_scale = "h0_h1_info",
alpha = .025,
beta = .1,
upper = gs_b,
lower = gs_b,
upar = list(par = -qnorm(.025)),
lpar = list(par = -Inf)
)
tibble(
`info_scale = "h0_info"` = y_0$info0[1] / x$info0[1],
`info_scale = "h1_info"` = y_1$info1[1] / x$info1[1],
`info_scale = "h0_h1_info"` = y_2$info[1] / x$info1[1]
) %>%
gt::gt() %>%
gt::tab_header(title = "The sample size calculated by gsDesign2 under 3 info_scale")| The sample size calculated by gsDesign2 under 3 info_scale | ||
| info_scale = "h0_info" | info_scale = "h1_info" | info_scale = "h0_h1_info" |
|---|---|---|
| 654.9627 | 644.4553 | 650.7984 |
The above logic is implement in gs_design_rd() to
calculate the sample size given fixed power in one-step.
z_info_scale_0 <- gs_design_rd(
p_c = tibble::tibble(stratum = "All", rate = .28),
p_e = tibble::tibble(stratum = "All", rate = .4),
rd0 = 0,
alpha = 0.025,
beta = 0.1,
ratio = 1,
weight = "unstratified",
upper = gs_b,
lower = gs_b,
upar = -qnorm(.025),
lpar = -Inf,
info_scale = "h0_info"
)
z_info_scale_1 <- gs_design_rd(
p_c = tibble::tibble(stratum = "All", rate = .28),
p_e = tibble::tibble(stratum = "All", rate = .4),
rd0 = 0,
alpha = 0.025,
beta = 0.1,
ratio = 1,
weight = "unstratified",
upper = gs_b,
lower = gs_b,
upar = -qnorm(.025),
lpar = -Inf,
info_scale = "h1_info"
)
z_info_scale_2 <- gs_design_rd(
p_c = tibble::tibble(stratum = "All", rate = .28),
p_e = tibble::tibble(stratum = "All", rate = .4),
rd0 = 0,
alpha = 0.025,
beta = 0.1,
ratio = 1,
weight = "unstratified",
upper = gs_b,
lower = gs_b,
upar = -qnorm(.025),
lpar = -Inf,
info_scale = "h0_h1_info"
)
Summary
tibble::tibble(
gsDesign2_info_scale_0 = z_info_scale_0$analysis$n,
gsDesign2_info_scale_1 = z_info_scale_1$analysis$n,
gsDesign2_info_scale_2 = z_info_scale_2$analysis$n,
gsDesign = x_gsdesign$n,
EAST_unpool = 645,
EAST_pool = 651
) %>%
gt::gt() %>%
gt::tab_spanner(
label = "gsDesign2",
columns = c(gsDesign2_info_scale_0, gsDesign2_info_scale_1, gsDesign2_info_scale_2)
) %>%
gt::tab_spanner(
label = "EAST",
columns = c(EAST_unpool, EAST_pool)
) %>%
cols_label(
gsDesign2_info_scale_0 = "info_scale = \"h0_info\"",
gsDesign2_info_scale_1 = "info_scale = \"h1_info\"",
gsDesign2_info_scale_2 = "info_scale = \"h0_h1_info\"",
EAST_unpool = "un-pooled",
EAST_pool = "pooled"
)|
gsDesign2
|
gsDesign |
EAST
|
|||
|---|---|---|---|---|---|
| info_scale = "h0_info" | info_scale = "h1_info" | info_scale = "h0_h1_info" | un-pooled | pooled | |
| 654.9627 | 644.4553 | 650.7984 | 650.7984 | 645 | 651 |
Unstratified Group Sequential Design
The example discussed in this section is an unstratified group
sequential design with equal sized groups to detect p_C = 0.15, p_E = .1.
Under the null hypothesis, we assume p_C = p_E
= 0.125. We desire 90% power for a two-sided test for two
proportions at \alpha = 0.05. And we
would like to calculate the sample size to achieve the 90% power.
gsDesign2
To calculate the sample size, one can use
gs_design_rd(). The logic of gs_design_rd() is
to calculate the sample size of fixed design first.
x_gs <- gs_info_rd(
p_c = tibble::tibble(stratum = "All", rate = .15),
p_e = tibble::tibble(stratum = "All", rate = .1),
n = tibble::tibble(stratum = "All", n = 1:3 / 3, analysis = 1:3),
rd0 = 0,
ratio = 1,
weight = "unstratified"
)
x_gs %>%
gt::gt() %>%
gt::tab_header(title = "The statistical information of the group sequential design")| The statistical information of the group sequential design | |||||||
| analysis | n | rd | rd0 | theta1 | theta0 | info1 | info0 |
|---|---|---|---|---|---|---|---|
| 1 | 0.3333333 | 0.05 | 0 | 0.05 | 0 | 0.7662835 | 0.7619048 |
| 2 | 0.6666667 | 0.05 | 0 | 0.05 | 0 | 1.5325670 | 1.5238095 |
| 3 | 1.0000000 | 0.05 | 0 | 0.05 | 0 | 2.2988506 | 2.2857143 |
y_gs0 <- gs_design_npe(
theta = .05,
info = x_gs$info0,
info0 = x_gs$info0,
info_scale = "h0_info",
alpha = .025, beta = .1, binding = FALSE,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE
)
y_gs1 <- gs_design_npe(
theta = .05,
info = x_gs$info1,
info0 = x_gs$info1,
info_scale = "h0_h1_info",
alpha = .025, beta = .1, binding = FALSE,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE
)
y_gs2 <- gs_design_npe(
theta = .05,
info = x_gs$info1,
info0 = x_gs$info0,
info_scale = "h0_h1_info",
alpha = .025, beta = .1, binding = FALSE,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE
)
tibble(
`info_scale = "h0_info"` = y_gs0$info0 / x_gs$info0[3],
`info_scale = "h1_info"` = y_gs1$info1 / x_gs$info1[3],
`info_scale = "h0_h1_info"` = y_gs2$info / x_gs$info1[3]
) %>%
gt::gt() %>%
gt::tab_header(
title = "The sample size calculated by `gsDesign2` under 3 info_scale",
subtitle = "under group sequential design"
)| The sample size calculated by `gsDesign2` under 3 info_scale | ||
| under group sequential design | ||
| info_scale = "h0_info" | info_scale = "h1_info" | info_scale = "h0_h1_info" |
|---|---|---|
| 620.1976 | 616.6536 | 618.3786 |
| 620.1976 | 616.6536 | 618.3786 |
| 1240.3952 | 1233.3072 | 1236.7572 |
| 1240.3952 | 1233.3072 | 1236.7572 |
| 1860.5927 | 1849.9608 | 1855.1358 |
| 1860.5927 | 1849.9608 | 1855.1358 |
The above logic is implemented in gs_design_rd().
x_gsdesign2_info_scale_0 <- gs_design_rd(
p_c = tibble::tibble(stratum = "All", rate = .15),
p_e = tibble::tibble(stratum = "All", rate = .1),
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .1,
ratio = 1,
weight = "unstratified",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
info_scale = "h0_info"
)
x_gsdesign2_info_scale_1 <- gs_design_rd(
p_c = tibble::tibble(stratum = "All", rate = .15),
p_e = tibble::tibble(stratum = "All", rate = .1),
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .1,
ratio = 1,
weight = "unstratified",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
info_scale = "h1_info"
)
x_gsdesign2_info_scale_2 <- gs_design_rd(
p_c = tibble::tibble(stratum = "All", rate = .15),
p_e = tibble::tibble(stratum = "All", rate = .1),
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .1,
ratio = 1,
weight = "unstratified",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
info_scale = "h0_h1_info"
)
gsDesign
n_fix <- nBinomial(
# Control event rate
p1 = .15,
# Experimental event rate
p2 = .1,
# Null hypothesis event rate difference (control - experimental)
delta0 = 0,
# 1-sided Type I error
alpha = .025,
# Type II error (1 - Power)
beta = .1,
# Experimental/Control randomization ratio
ratio = 1
)
cat("The sample size of fixed-design calculated by `gsDesign` is ", n_fix, ".\n")
#> The sample size of fixed-design calculated by `gsDesign` is 1834.641 .
x_gsdesign <- gsDesign(
k = 3,
test.type = 1,
# 1-sided Type I error
alpha = .025,
# Type II error (1 - Power)
beta = .1,
# If test.type = 5 or 6, this sets maximum spending for futility
# under the null hypothesis. Otherwise, this is ignored.
astar = 0,
timing = 1:3 / 3,
sfu = sfLDOF,
sfupar = NULL,
sfl = sfLDOF,
sflpar = NULL,
# Difference in event rates under alternate hypothesis
delta = 0,
# Difference in rates under H1
delta1 = .05,
# Difference in rates under H0
delta0 = 0,
endpoint = "Binomial",
# Fixed design sample size from nBinomial above
n.fix = n_fix
)
cat("The sample size calcuated by `gsDesign` is ", x_gsdesign$n.I, ".\n")
#> The sample size calcuated by `gsDesign` is 618.7954 1237.591 1856.386 .
gsBoundSummary(x_gsdesign, digits = 4, ddigits = 2, tdigits = 1)
#> Analysis Value Efficacy
#> IA 1: 33% Z 3.7103
#> N: 619 p (1-sided) 0.0001
#> ~delta at bound 0.0985
#> P(Cross) if delta=0 0.0001
#> P(Cross) if delta=0.05 0.0338
#> IA 2: 67% Z 2.5114
#> N: 1238 p (1-sided) 0.0060
#> ~delta at bound 0.0472
#> P(Cross) if delta=0 0.0060
#> P(Cross) if delta=0.05 0.5603
#> Final Z 1.9930
#> N: 1857 p (1-sided) 0.0231
#> ~delta at bound 0.0306
#> P(Cross) if delta=0 0.0250
#> P(Cross) if delta=0.05 0.9000
Summary
tibble::tibble(
gsDesign2_info_scale_0 = x_gsdesign2_info_scale_0$analysis$n,
gsDesign2_info_scale_1 = x_gsdesign2_info_scale_1$analysis$n,
gsDesign2_info_scale_2 = x_gsdesign2_info_scale_2$analysis$n,
gsDesign = x_gsdesign$n.I,
EAST_unpool = c(617, 1233, 1850),
EAST_pool = c(619, 1238, 1857)
) %>%
gt::gt() %>%
gt::tab_spanner(
label = "gsDesign2",
columns = c(gsDesign2_info_scale_0, gsDesign2_info_scale_1, gsDesign2_info_scale_2)
) %>%
gt::tab_spanner(
label = "EAST",
columns = c(EAST_unpool, EAST_pool)
) %>%
cols_label(
gsDesign2_info_scale_0 = "info_scale = \"h0_info\"",
gsDesign2_info_scale_1 = "info_scale = \"h1_info\"",
gsDesign2_info_scale_2 = "info_scale = \"h0_h1_info\"",
EAST_unpool = "un-pooled",
EAST_pool = "pooled"
)|
gsDesign2
|
gsDesign |
EAST
|
|||
|---|---|---|---|---|---|
| info_scale = "h0_info" | info_scale = "h1_info" | info_scale = "h0_h1_info" | un-pooled | pooled | |
| 620.1976 | 616.6536 | 618.3786 | 618.7954 | 617 | 619 |
| 1240.3952 | 1233.3072 | 1236.7572 | 1237.5909 | 1233 | 1238 |
| 1860.5927 | 1849.9608 | 1855.1358 | 1856.3863 | 1850 | 1857 |
Stratified Group Sequential Design
In this example, we consider 3 strata in a group sequential design with 3 analyses.
ratio <- 1
prevalence_ratio <- c(4, 5, 6)
p_c_by_stratum <- c(.3, .37, .6)
p_e_by_stratum <- c(.25, .3, .5)
p_c <- tibble::tibble(stratum = c("S1", "S2", "S3"), rate = p_c_by_stratum)
p_e <- tibble::tibble(stratum = c("S1", "S2", "S3"), rate = p_e_by_stratum)
ratio_strata_c <- tibble::tibble(stratum = c("S1", "S2", "S3"), ratio = prevalence_ratio)
ratio_strata_e <- ratio_strata_c
n <- 1
info_frac <- 1:3 / 3
n_c <- n / (1 + ratio)
n_e <- ratio * n_c
x <- p_c %>%
rename(p_c = rate) %>%
left_join(p_e) %>%
rename(p_e = rate) %>%
mutate(p_pool = (p_c + p_e) / 2) %>%
mutate(
xi_c = (
ratio_strata_c %>% mutate(prop = ratio / sum(ratio))
)$prop
) %>%
mutate(
xi_e = (
ratio_strata_e %>% mutate(prop = ratio / sum(ratio))
)$prop
) %>%
mutate(n_c = n_c * xi_c, n_e = n_e * xi_e)
x %>%
gt::gt() %>%
gt::fmt_number(columns = 4:8, decimals = 4) %>%
gt::tab_footnote(
footnote = "p_pool = (p_c * n_c + p_e * n_e) / (n_c * n_e).",
locations = gt::cells_column_labels(columns = p_pool)
) %>%
gt::tab_footnote(
footnote = "xi_c = sample size of a strata / sample size of the control arm.",
locations = gt::cells_column_labels(columns = xi_c)
) %>%
gt::tab_footnote(
footnote = "xi_e = sample size of a strata / sample size of the experimental arm.",
locations = gt::cells_column_labels(columns = xi_e)
) %>%
gt::tab_footnote(
footnote = "n_c = total sample size of the control arm.",
locations = gt::cells_column_labels(columns = n_c)
) %>%
gt::tab_footnote(
footnote = "n_e = total size of the experimental arm.",
locations = gt::cells_column_labels(columns = n_e)
) %>%
gt::tab_header(title = "Stratified Example")| Stratified Example | |||||||
| stratum | p_c | p_e | p_pool1 | xi_c2 | xi_e3 | n_c4 | n_e5 |
|---|---|---|---|---|---|---|---|
| S1 | 0.30 | 0.25 | 0.2750 | 0.2667 | 0.2667 | 0.1333 | 0.1333 |
| S2 | 0.37 | 0.30 | 0.3350 | 0.3333 | 0.3333 | 0.1667 | 0.1667 |
| S3 | 0.60 | 0.50 | 0.5500 | 0.4000 | 0.4000 | 0.2000 | 0.2000 |
| 1 p_pool = (p_c * n_c + p_e * n_e) / (n_c * n_e). | |||||||
| 2 xi_c = sample size of a strata / sample size of the control arm. | |||||||
| 3 xi_e = sample size of a strata / sample size of the experimental arm. | |||||||
| 4 n_c = total sample size of the control arm. | |||||||
| 5 n_e = total size of the experimental arm. | |||||||
First, we calculate the variance \left\{ \begin{array}{ll} \sigma^2_{H_0,k,s} & = p_{k,s}^{pool} \left(1 - p^{pool}_{k,s} \right) \left(\frac{1}{N_{C,k,s}} + \frac{1}{N_{E,k,s}} \right) = p_{k,s}^{pool} \left(1 - p^{pool}_{k,s} \right) \left(\frac{1}{ \frac{\xi_s}{1+r} N_{k}} + \frac{1}{ \frac{r \xi_s}{1+r} N_{k}} \right) \\ \sigma_{H_1,k,s}^2 & = \frac{p_{C,s} (1- p_{C,s})}{N_{C,k,s}} + \frac{p_{E,s} (1 - p_{E,s})}{N_{E,k,s}} = \frac{p_{C,s} (1- p_{C,s})}{\frac{\xi_s}{1+r} N_{k}} + \frac{p_{E,s} (1 - p_{E,s})}{\frac{r \xi_s}{1+r} N_{k}} \end{array} \right.
x <- x %>%
union_all(x) %>%
union_all(x) %>%
mutate(Analysis = rep(1:3, each = 3)) %>%
left_join(tibble(Analysis = 1:3, IF = info_frac)) %>%
mutate(n_c = n_c * IF, n_e = n_e * IF) %>%
select(Analysis, stratum, p_c, p_pool, p_e, n_c, n_e, xi_c, xi_e) %>%
mutate(
sigma_h0 = sqrt(p_pool * (1 - p_pool) * (1 / n_c + 1 / n_e)),
sigma_h1 = sqrt(p_c * (1 - p_c) / n_c + p_e * (1 - p_e) / n_e)
)
x %>%
gt() %>%
gt::fmt_number(6:11, decimals = 4) %>%
gt::tab_footnote(
footnote = "sigma_h0 = the H0 sd per stratum per analysis.",
locations = gt::cells_column_labels(columns = sigma_h0)
) %>%
gt::tab_footnote(
footnote = "sigma_h1 = the H0 sd per stratum per analysis.",
locations = gt::cells_column_labels(columns = sigma_h1)
)| Analysis | stratum | p_c | p_pool | p_e | n_c | n_e | xi_c | xi_e | sigma_h01 | sigma_h12 |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | S1 | 0.30 | 0.275 | 0.25 | 0.0444 | 0.0444 | 0.2667 | 0.2667 | 2.9953 | 2.9906 |
| 1 | S2 | 0.37 | 0.335 | 0.30 | 0.0556 | 0.0556 | 0.3333 | 0.3333 | 2.8319 | 2.8241 |
| 1 | S3 | 0.60 | 0.550 | 0.50 | 0.0667 | 0.0667 | 0.4000 | 0.4000 | 2.7249 | 2.7111 |
| 2 | S1 | 0.30 | 0.275 | 0.25 | 0.0889 | 0.0889 | 0.2667 | 0.2667 | 2.1180 | 2.1147 |
| 2 | S2 | 0.37 | 0.335 | 0.30 | 0.1111 | 0.1111 | 0.3333 | 0.3333 | 2.0025 | 1.9970 |
| 2 | S3 | 0.60 | 0.550 | 0.50 | 0.1333 | 0.1333 | 0.4000 | 0.4000 | 1.9268 | 1.9170 |
| 3 | S1 | 0.30 | 0.275 | 0.25 | 0.1333 | 0.1333 | 0.2667 | 0.2667 | 1.7293 | 1.7266 |
| 3 | S2 | 0.37 | 0.335 | 0.30 | 0.1667 | 0.1667 | 0.3333 | 0.3333 | 1.6350 | 1.6305 |
| 3 | S3 | 0.60 | 0.550 | 0.50 | 0.2000 | 0.2000 | 0.4000 | 0.4000 | 1.5732 | 1.5652 |
| 1 sigma_h0 = the H0 sd per stratum per analysis. | ||||||||||
| 2 sigma_h1 = the H0 sd per stratum per analysis. | ||||||||||
Second, we calculate the weight by using inverse variance
w_{s,k} = \frac{1/\sigma^2_{s,k}}{\sum_{s=1}^S 1/\sigma^2_{s,k}}.
temp <- x %>%
group_by(Analysis) %>%
summarise(
sum_invar_H0 = sum(1 / sigma_h0^2),
sum_invar_H1 = sum(1 / sigma_h1^2),
sum_ss = sum((n_c * n_e) / (n_c + n_e))
)
x <- x %>%
left_join(temp) %>%
mutate(
weight_invar_H0 = 1 / sigma_h0^2 / sum_invar_H0,
weight_invar_H1 = 1 / sigma_h1^2 / sum_invar_H1,
weight_ss = (n_c * n_e) / (n_c + n_e) / sum_ss
) %>%
select(-c(sum_invar_H0, sum_invar_H1, sum_ss))
x %>%
gt() %>%
fmt_number(6:14, decimals = 4) %>%
gt::tab_footnote(
footnote = "weight_invar_H0 = the weight per stratum per analysis calculated by INVAR by using variance under H0.",
locations = gt::cells_column_labels(columns = weight_invar_H0)
) %>%
gt::tab_footnote(
footnote = "weight_invar_H1 = the weight per stratum per analysis calculated by INVAR by using variance under H1.",
locations = gt::cells_column_labels(columns = weight_invar_H1)
) %>%
gt::tab_footnote(
footnote = "weight_ss = the weight per stratum per analysis calculated by SS.",
locations = gt::cells_column_labels(columns = weight_ss)
)| Analysis | stratum | p_c | p_pool | p_e | n_c | n_e | xi_c | xi_e | sigma_h0 | sigma_h1 | weight_invar_H01 | weight_invar_H12 | weight_ss3 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | S1 | 0.30 | 0.275 | 0.25 | 0.0444 | 0.0444 | 0.2667 | 0.2667 | 2.9953 | 2.9906 | 0.3006 | 0.2996 | 0.2667 |
| 1 | S2 | 0.37 | 0.335 | 0.30 | 0.0556 | 0.0556 | 0.3333 | 0.3333 | 2.8319 | 2.8241 | 0.3362 | 0.3359 | 0.3333 |
| 1 | S3 | 0.60 | 0.550 | 0.50 | 0.0667 | 0.0667 | 0.4000 | 0.4000 | 2.7249 | 2.7111 | 0.3632 | 0.3645 | 0.4000 |
| 2 | S1 | 0.30 | 0.275 | 0.25 | 0.0889 | 0.0889 | 0.2667 | 0.2667 | 2.1180 | 2.1147 | 0.3006 | 0.2996 | 0.2667 |
| 2 | S2 | 0.37 | 0.335 | 0.30 | 0.1111 | 0.1111 | 0.3333 | 0.3333 | 2.0025 | 1.9970 | 0.3362 | 0.3359 | 0.3333 |
| 2 | S3 | 0.60 | 0.550 | 0.50 | 0.1333 | 0.1333 | 0.4000 | 0.4000 | 1.9268 | 1.9170 | 0.3632 | 0.3645 | 0.4000 |
| 3 | S1 | 0.30 | 0.275 | 0.25 | 0.1333 | 0.1333 | 0.2667 | 0.2667 | 1.7293 | 1.7266 | 0.3006 | 0.2996 | 0.2667 |
| 3 | S2 | 0.37 | 0.335 | 0.30 | 0.1667 | 0.1667 | 0.3333 | 0.3333 | 1.6350 | 1.6305 | 0.3362 | 0.3359 | 0.3333 |
| 3 | S3 | 0.60 | 0.550 | 0.50 | 0.2000 | 0.2000 | 0.4000 | 0.4000 | 1.5732 | 1.5652 | 0.3632 | 0.3645 | 0.4000 |
| 1 weight_invar_H0 = the weight per stratum per analysis calculated by INVAR by using variance under H0. | |||||||||||||
| 2 weight_invar_H1 = the weight per stratum per analysis calculated by INVAR by using variance under H1. | |||||||||||||
| 3 weight_ss = the weight per stratum per analysis calculated by SS. | |||||||||||||
Third, we calculate the weighted risk difference and weighted statistical information. \left\{ \begin{array}{ll} \delta_{H_0,k} & = 0\\ \delta_{H_1,k} & = \sum_{s=1}^S w_{k,s} |p_{C,s} - p_{E,s}| \end{array} \right. \\ \left\{ \begin{array}{ll} \mathcal I_{H_0,k} & = \left[ \sum_{s=1}^S w_{k,s}^2 \frac{p_{k,s}^{pool} (1 - p_{k,s}^{pool})}{N_{C, k, s}} + w_{k,s}^2 \frac{p_{k,s}^{pool} (1 - p_{k,s}^{pool})}{N_{E, k, s}} \right]^{-1}\\ \mathcal I_{H_1,k} & = \left[ \sum_{s=1}^S w_{k,s}^2 \frac{p_{C,k,s} (1 - p_{C,k,s})}{N_{C,k,s}} + \sum_{s=1}^S w_{k,s}^2 \frac{p_{E,k,s} (1 - p_{E,k,s})}{N_{E,k,s}} \right]^{-1} \end{array} \right. \\
x <- x %>%
group_by(Analysis) %>%
summarise(
rd_invar_H0 = sum(weight_invar_H0 * abs(p_c - p_e)),
rd_invar_H1 = sum(weight_invar_H1 * abs(p_c - p_e)),
rd_ss = sum(weight_ss * abs(p_c - p_e)),
rd0 = 0,
info_invar_H0 = 1 /
sum(
weight_invar_H0^2 * p_c * (1 - p_c) /
n_c + weight_invar_H0^2 * p_e * (1 - p_e) / n_e
),
info_invar_H1 = 1 /
sum(
weight_invar_H1^2 * p_c * (1 - p_c) /
n_c + weight_invar_H1^2 * p_e * (1 - p_e) / n_e
),
info_ss = 1 /
sum(
weight_ss^2 * p_c * (1 - p_c) / n_c + weight_ss^2 * p_e * (1 - p_e) / n_e
),
info0_invar_H0 = 1 /
sum(
weight_invar_H0^2 * p_pool * (1 - p_pool) / n_c +
weight_invar_H0^2 * p_pool * (1 - p_pool) / n_e
),
info0_invar_H1 = 1 /
sum(
weight_invar_H1^2 * p_pool * (1 - p_pool) /
n_c + weight_invar_H1^2 * p_pool * (1 - p_pool) / n_e
),
info0_ss = 1 /
sum(
weight_ss^2 * p_pool * (1 - p_pool) / n_c +
weight_ss^2 * p_pool * (1 - p_pool) / n_e
)
)
x %>%
gt::gt() %>%
fmt_number(c(2:4, 6:11), decimals = 6) %>%
gt::tab_footnote(
footnote = "info_invar_H0 = the statistical information under H1
per stratum per analysis calculated by INVAR by using variance under H0.",
locations = gt::cells_column_labels(columns = info_invar_H0)
) %>%
gt::tab_footnote(
footnote = "info_invar_H1 = the statistical information under H1
per stratum per analysis calculated by INVAR by using variance under H0.",
locations = gt::cells_column_labels(columns = info_invar_H1)
) %>%
gt::tab_footnote(
footnote = "info_ss = the statistical information under H1
per stratum per analysis calculated by SS.",
locations = gt::cells_column_labels(columns = info_ss)
) %>%
gt::tab_footnote(
footnote = "info0_invar_H0 = the statistical information under H0
per stratum per analysis calculated by INVAR by using variance under H0.",
locations = gt::cells_column_labels(columns = info0_invar_H0)
) %>%
gt::tab_footnote(
footnote = "info0_invar_H1 = the statistical information under H0
per stratum per analysis calculated by INVAR by using variance under H0.",
locations = gt::cells_column_labels(columns = info0_invar_H1)
) %>%
gt::tab_footnote(
footnote = "info0_ss = the statistical information under H0
per stratum per analysis calculated by SS.",
locations = gt::cells_column_labels(columns = info0_ss)
)| Analysis | rd_invar_H0 | rd_invar_H1 | rd_ss | rd0 | info_invar_H01 | info_invar_H12 | info_ss3 | info0_invar_H04 | info0_invar_H15 | info0_ss6 |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 0.074884 | 0.074944 | 0.076667 | 0 | 0.373240 | 0.373244 | 0.370617 | 0.370829 | 0.370826 | 0.368039 |
| 2 | 0.074884 | 0.074944 | 0.076667 | 0 | 0.746481 | 0.746487 | 0.741235 | 0.741659 | 0.741652 | 0.736079 |
| 3 | 0.074884 | 0.074944 | 0.076667 | 0 | 1.119721 | 1.119731 | 1.111852 | 1.112488 | 1.112479 | 1.104118 |
| 1 info_invar_H0 = the statistical information under H1 per stratum per analysis calculated by INVAR by using variance under H0. | ||||||||||
| 2 info_invar_H1 = the statistical information under H1 per stratum per analysis calculated by INVAR by using variance under H0. | ||||||||||
| 3 info_ss = the statistical information under H1 per stratum per analysis calculated by SS. | ||||||||||
| 4 info0_invar_H0 = the statistical information under H0 per stratum per analysis calculated by INVAR by using variance under H0. | ||||||||||
| 5 info0_invar_H1 = the statistical information under H0 per stratum per analysis calculated by INVAR by using variance under H0. | ||||||||||
| 6 info0_ss = the statistical information under H0 per stratum per analysis calculated by SS. | ||||||||||
# Sample size under H0 ----
y_invar_h0 <- gs_design_npe(
theta = x$rd_invar_H0,
info = x$info0_invar_H0,
info0 = x$info0_invar_H0,
info_scale = "h0_h1_info",
alpha = 0.025,
beta = 0.2,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
)
y_invar_h1 <- gs_design_npe(
theta = x$rd_invar_H1,
info = x$info0_invar_H1,
info0 = x$info0_invar_H1,
info_scale = "h0_h1_info",
alpha = 0.025,
beta = 0.2,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
)
y_ss <- gs_design_npe(
theta = x$rd_ss,
info = x$info0_ss,
info0 = x$info0_ss,
info_scale = "h0_h1_info",
alpha = 0.025,
beta = 0.2,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
)
# Sample size under H1 ----
yy_invar_h0 <- gs_design_npe(
theta = x$rd_invar_H0,
info = x$info_invar_H0,
info0 = x$info0_invar_H0,
info_scale = "h0_h1_info",
alpha = 0.025,
beta = 0.2,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
)
yy_invar_h1 <- gs_design_npe(
theta = x$rd_invar_H1,
info = x$info_invar_H1,
info0 = x$info0_invar_H1,
info_scale = "h0_h1_info",
alpha = 0.025,
beta = 0.2,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
)
yy_ss <- gs_design_npe(
theta = x$rd_ss,
info = x$info_ss,
info0 = x$info0_ss,
info_scale = "h0_h1_info",
alpha = 0.025,
beta = 0.2,
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = rep(-Inf, 3),
test_lower = FALSE,
)
ans_math <- tibble::tibble(
`Weighting method` = rep(c("INVAR-H0", "INVAR-H1", "Sample Size"), 2),
`Calculated under` = c(rep("H0", 3), rep("H1", 3)),
`Sample size` = c(
y_invar_h0$info[3] / x$info0_invar_H0[3],
y_invar_h1$info[3] / x$info0_invar_H1[3],
y_ss$info[3] / x$info0_ss[3],
yy_invar_h0$info[3] / x$info_invar_H0[3],
yy_invar_h1$info[3] / x$info_invar_H1[3],
yy_ss$info[3] / x$info_ss[3]
)
)
ans_math %>%
gt::gt() %>%
gt::tab_header(title = "Sample size calculated by INVAR and SS")| Sample size calculated by INVAR and SS | ||
| Weighting method | Calculated under | Sample size |
|---|---|---|
| INVAR-H0 | H0 | 849.4965 |
| INVAR-H1 | H0 | 848.1421 |
| Sample Size | H0 | 816.5992 |
| INVAR-H0 | H1 | 845.1771 |
| INVAR-H1 | H1 | 843.8182 |
| Sample Size | H1 | 812.1270 |
The above logic is implemented in gs_design_rd().
## sample size weighting + information scale = "h0_info"
x_ss0 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 4:6),
weight = "ss",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h0_info",
binding = FALSE
)
## sample size weighting + information scale = "h1_info"
x_ss1 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 4:6),
weight = "ss",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h1_info",
binding = FALSE
)
## sample size weighting + information scale = "h0_h1_info"
x_ss2 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 4:6),
weight = "ss",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h0_h1_info",
binding = FALSE
)
## inverse variance weighting + information scale = "h0_info"
x_invar0 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 1:3),
weight = "invar",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h0_info",
binding = FALSE
)
## inverse variance weighting + information scale = "h1_info"
x_invar1 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 1:3),
weight = "invar",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h1_info",
binding = FALSE
)
## inverse variance weighting + information scale = "h0_h1_info"
x_invar2 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 1:3),
weight = "invar",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h0_h1_info",
binding = FALSE
)
## inverse variance weighting + information scale = "h0_info"
x_invar_h1_0 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 1:3),
weight = "invar",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h0_info",
binding = FALSE
)
## inverse variance weighting + information scale = "h1_info"
x_invar_h1_1 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 1:3),
weight = "invar",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h1_info",
binding = FALSE
)
## inverse variance weighting + information scale = "h0_h1_info"
x_invar_h1_2 <- gs_design_rd(
p_c = p_c,
p_e = p_e,
info_frac = 1:3 / 3,
rd0 = 0,
alpha = .025,
beta = .2,
ratio = 1,
stratum_prev = tibble::tibble(stratum = c("S1", "S2", "S3"), prevalence = 1:3),
weight = "invar",
upper = gs_b,
lower = gs_b,
upar = gsDesign(k = 3, test.type = 1, sfu = sfLDOF, sfupar = NULL)$upper$bound,
lpar = c(qnorm(.1), rep(-Inf, 2)),
info_scale = "h0_h1_info",
binding = FALSE
)
ans <- tibble::tibble(
INVAR0 = x_invar0$analysis$n[1:3],
INVAR1 = x_invar1$analysis$n[1:3],
INVAR2 = x_invar2$analysis$n[1:3],
SS0 = x_ss0$analysis$n[1:3],
SS1 = x_ss1$analysis$n[1:3],
SS2 = x_ss2$analysis$n[1:3]
)
ans %>%
gt::gt() %>%
gt::tab_header(title = "Sample size calculated by INVAR and SS") %>%
gt::tab_spanner(
label = "Inverse variance weighting ",
columns = c(
"INVAR0",
"INVAR1",
"INVAR2"
)
) %>%
gt::tab_spanner(
label = "Sample size weighting",
columns = c(SS0, SS1, SS2)
) %>%
cols_label(
INVAR0 = "info_scale = \"h0_info\"",
INVAR1 = "info_scale = \"h1_info\"",
INVAR2 = "info_scale = \"h0_h1_info\"",
SS0 = "info_scale = \"h0_info\"",
SS1 = "info_scale = \"h1_info\"",
SS2 = "info_scale = \"h0_h1_info\""
)| Sample size calculated by INVAR and SS | |||||
|
Inverse variance weighting
|
Sample size weighting
|
||||
|---|---|---|---|---|---|
| info_scale = "h0_info" | info_scale = "h1_info" | info_scale = "h0_h1_info" | info_scale = "h0_info" | info_scale = "h1_info" | info_scale = "h0_h1_info" |
| 379.3680 | 376.6377 | 377.2186 | 408.5056 | 405.6640 | 406.2689 |
| 758.7361 | 753.2753 | 754.4373 | 817.0112 | 811.3281 | 812.5379 |
| 1138.1041 | 1129.9130 | 1131.6559 | 1225.5168 | 1216.9921 | 1218.8068 |
Summary
| Parameters | Notes |
|---|---|
| risk difference: | |
| \widehat\delta _{H_0,k} = \sum_{s=1}^S w _{k,s} \delta_{k,s}^{null} |
\delta_{k,s}^{null} is the risk difference under H_0. It is 0, positive, and negative for superiority, super-superiority and non-inferiority design, respectively. |
| \widehat \delta_{H_1,k} =\sum_{s=1}^S w_{k,s} (p_{C,k,s} -\widehat p_{E,k,s}) | \widehat p_{C,k,s} = \frac{ x _{C,k,s}}{N_{C,k,s}}, \; \widehat p_{ E,k,s} = \frac{x_{E,k,s} }{N_{E,k,s}} |
| standardized treatment effect: | |
| \widehat\theta_{H_0,k} = \frac{\sum_{s=1}^S w_{k,s}\delta_{s,k}^{null}} {\sqrt { \sum_{s=1}^S w_{k,s}^2 \widehat \sigma _{H_0,k,s}^2}} |
For superiority design, \widehat \sigma^2_{H_0,k,s}
= \widehat p
_{k,s}^{pool} \left(1 - \widehat p
^{pool}_{k,s} \right) \left(
\frac{1}{N_{C,k,s}} +
\frac{1}{N_{E,k,s}} \right) For super-superiority design and non-inferiority design, \hat \sigma^2 _{H_0,k,s} = \frac {\widehat p _{C0,k,s}(1- \widehat p_{C0,k,s})}{N_ {C,k,s}} + \frac{ \widehat p_{E0,k,s} (1 - \widehat p_{E0,k,s})}{N_{E,k,s}} |
| \widehat\theta_{H_1 ,k} = \frac{\sum_{s=1}^S w_{k ,s} (\widehat p_{C,k,s} - \widehat p_{E,k,s})}{\sqrt {\sum_{s=1}^S w_{k,s}^2 \widehat \sigma_{H_1,k,s}^2}} | \widehat \sigma_{H_1,k,s} = \sqrt{\frac{\widehat p_{C,k,s} (1- \widehat p_{C,k,s})}{ N_{C,k,s}} + \frac{\widehat p_{E,k,s} (1 - \widehat p_{E,k,s})}{N_{E,k,s}}} |
| statistical information: | |
| \widehat{\mathcal I} _{H_0,k} = \left\{ \begin {array}{ll} \left[ \sum_{ s=1}^S w_{k,s}^2 \frac{p_ { k,s}^{pool} (1 - p_{k,s}^{ pool})}{N_{k,s}}\right]^{-1} & \text{for superiority design } \\ \left[ \sum_{s=1 }^S w _{k,s}^2 \frac{\bar p_{C0,s} (1 - \bar p_{C0,s})} {N _{C,s}} + w_{k,s}^2 \frac{ \bar p_{E0,s} (1 - \bar p _{E0,s})}{N_{E,s}} \right] ^{-1} & \text{for super-superiority and non-inferiority design} \end{array} \right. | N_{k,s} = N_{C,k,s} + N_{E,k,s} and \widehat p_{k,s } = (x_{C,k,s} + x_{E,k,s}) / N_{k,s} |
| \widehat{ \mathcal I}_{H_1,k} = \left[ \sum_{s=1}^S w_{k,s}^2 \frac {\widehat p_{C,k,s} (1 - \widehat p_{C,k,s})}{N_{C,k, s}} + \sum_{s=1} ^S w _{k,s}^2 \frac{\widehat p _{E,k,s} (1 - \widehat p _{E,k,s})}{N_{E,k,s}} \right]^{-1} |