In keaven/gsDesign2: Group Sequential Design with Non-Constant Effect

library(gsDesign)
library(tibble)
library(gt)
# load the develop version of gsDesign2
# it will finally be replaced by `libraray(gsDesign2)`
devtools::load_all()

Parameters

# Enrollment rate
enrollRates <- tibble::tibble(
   Stratum = "All", 
   duration = 18, 
   rate = 20)

# Failure rates
failRates <- tibble::tibble(
   Stratum = "All", 
   duration = c(4, 100), 
   failRate = log(2) / 12,
   hr = c(1, .6), 
   dropoutRate = .001)

# Study duration in months
studyDuration <- 36

# Experimental / Control randomization ratio
ratio <- 1 

# 1-sided Type I error
alpha <- 0.025 
# Type II error (1 - power)
beta <- 0.1 

AHR {.tabset}

under fixed power

x <- fixed_design(x = "AHR", 
             alpha = alpha, power = 1 - beta, 
             enrollRates = enrollRates, failRates = failRates, 
             studyDuration = studyDuration, ratio = ratio) 

x %>% summary()

x %>% summary() %>% as_gt()

under fixed sample size

fixed_design(x = "AHR", 
             alpha = alpha,  
             enrollRates = enrollRates, failRates = failRates, 
             studyDuration = studyDuration, ratio = ratio) %>% 
  summary() %>% 
  as_gt()

FH {.tabset}

under fixed power (default rho/gamma)

# fixed design with a given power with default rho/gamma
x <- fixed_design(x = "FH", 
             alpha = alpha, power = 1 - beta, 
             enrollRates = enrollRates, failRates = failRates, 
             studyDuration = studyDuration, ratio = ratio) 
x %>% summary() 
x %>% summary() %>% as_gt()

under fixed power (custom rho/gamma)

# fixed design with a given power with input rho/gamma
fixed_design(x = "FH", 
             alpha = alpha, power = 1 - beta, 
             enrollRates = enrollRates, failRates = failRates, 
             studyDuration = studyDuration, ratio = ratio,
             rho = 0.5, gamma = 0.5) %>% 
  summary() %>%  
  as_gt()

under fixed sample size (default rho/gamma)

# fixed design with power calculated
fixed_design(x = "FH", 
             alpha = alpha,  
             enrollRates = enrollRates, failRates = failRates, 
             studyDuration = studyDuration, ratio = ratio) %>% 
  summary() %>%  
  as_gt()

under fixed sample size (custom rho/gamma)

# fixed design with power calculated
fixed_design(x = "FH", 
             alpha = alpha,  
             enrollRates = enrollRates, failRates = failRates, 
             studyDuration = studyDuration, ratio = ratio,
             rho = 0.5, gamma = 0.5) %>% 
  summary() %>%  
  as_gt()

MB {.tabset}

under fixed power (default tau)

x <- fixed_design(x = "MB", 
             ratio = ratio, 
             alpha = alpha, power = 1 - beta,
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration) 
x %>% summary() 
x %>% summary() %>% as_gt()

under fixed power (custom tau)

fixed_design(x = "MB", 
             ratio = ratio, 
             alpha = alpha, power = 1 - beta,
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration,
             tau = 4) %>% 
  summary() %>%  
  as_gt()

under fixed sample size (default tau)

fixed_design(x = "MB",
             ratio = ratio,
             alpha = alpha,
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration) %>% 
  summary() %>%  
  as_gt()

under fixed sample size (custom tau)

fixed_design(x = "MB",
             ratio = ratio,
             alpha = alpha,
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration,
             tau = 4) %>% 
  summary() %>%  
  as_gt()

LF {.tabset}

under fixed power

fixed_design(x = "LF", alpha = alpha, power = 1 - beta, 
             ratio = ratio,
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration) %>% 
  summary() %>%  
  as_gt()

under sample size

fixed_design(x = "LF", alpha = alpha,  
             ratio = ratio, 
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration) %>% 
  summary() %>%  
  as_gt()

MaxCombo {.tabset}

under fixed power (default rho/gamma/tau)

x <- fixed_design(x = "MaxCombo", alpha = alpha, power = 1 - beta,
             ratio = ratio, 
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration) 
x %>% summary() 
x %>% summary() %>% as_gt()

under fixed power (custom rho/gamma/tau)

fixed_design(x = "MaxCombo", alpha = alpha, power = 1 - beta,
             ratio = ratio, 
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration,
             rho = c(0, 0.5, 0.5),
             gamma = c(0, 0, 0.5),
             tau = c(-1, 4, 6)) %>% 
  summary() %>% 
  as_gt()

under sample size (default rho/gamma/tau)

fixed_design(x = "MaxCombo", alpha = alpha, 
             ratio = ratio, 
             enrollRates = enrollRates,
             failRates = failRates,
             studyDuration = studyDuration) %>% 
  summary() %>% 
  as_gt()

under sample size (custom rho/gamma/tau)

fixed_design(x = "MaxCombo", alpha = alpha, 
             ratio = ratio, 
             enrollRates = enrollRates,
             failRates = failRates, 
             studyDuration = studyDuration,
             rho = c(0, 0.5, 0.5),
             gamma = c(0, 0, 0.5),
             tau = c(-1, 4, 6)) %>% 
  summary() %>% 
  as_gt()

RMST {.tabset}

under fixed power

x <- fixed_design(x = "RMST", 
                  alpha = alpha, power = 1 - beta, 
                  enrollRates = enrollRates, failRates = failRates, 
                  studyDuration = studyDuration, ratio = ratio,
                  tau = 18) 

x %>% summary()

x %>% summary() %>% as_gt()

under fixed sample size

fixed_design(x = "RMST", 
             alpha = alpha,  
             enrollRates = enrollRates, failRates = failRates, 
             studyDuration = studyDuration, ratio = ratio,
             tau = 18) %>% 
  summary() %>% 
  as_gt()

Milestone {.tabset}

under fixed power

x <- fixed_design(x = "Milestone", 
                  alpha = alpha, power = 1 - beta, 
                  enrollRates = enrollRates, failRates = failRates, 
                  studyDuration = studyDuration, ratio = ratio,
                  tau = 18) 

x %>% summary()

x %>% summary() %>% as_gt()

under fixed sample size

fixed_design(x = "Milestone", 
             alpha = alpha,  
             enrollRates = enrollRates, failRates = failRates, 
             studyDuration = studyDuration, ratio = ratio,
             tau = 18) %>% 
  summary() %>% 
  as_gt()

RD {.tabset}

under fixed power

x <- fixed_design(x = "RD", 
                  alpha = alpha, power = 1 - beta, 
                  p_c = .15, p_e = .1, rd0 = 0,
                  ratio = ratio) 

x %>% summary()
x %>% summary() %>% as_gt()

under fixed sample size

fixed_design(x = "RD", 
             alpha = alpha, power = NULL, 
             p_c = .15, p_e = .1, rd0 = 0,
             N = 2000, ratio = ratio) %>% 
  summary() %>% 
  as_gt()

Multiple Designs

x_AHR <- fixed_design(x = "AHR", alpha = alpha, ratio = ratio,
                      enrollRates = enrollRates, failRates = failRates, 
                      studyDuration = studyDuration)

x_FH <- fixed_design(x = "FH", alpha = alpha, ratio = ratio, 
                     enrollRates = enrollRates, failRates = failRates, studyDuration = studyDuration,
                     rho = 0.5, gamma = 0.5) 

x_MB <- fixed_design(x = "MB", alpha = alpha, ratio = ratio, 
                     enrollRates = enrollRates,failRates = failRates, studyDuration = studyDuration, 
                     tau = 4)

x_LF <- fixed_design(x = "LF", alpha = alpha, ratio = ratio, 
                     enrollRates = enrollRates, failRates = failRates, studyDuration = studyDuration)

x_MaxCombo <- fixed_design(x = "MaxCombo", alpha = alpha, ratio = ratio, 
                           enrollRates = enrollRates, failRates = failRates, studyDuration = studyDuration,
                           rho = c(0, 0.5, 0.5), gamma = c(0, 0, 0.5), tau = c(-1, 4, 6))

x_RMST <- fixed_design(x = "RMST", alpha = alpha, ratio = ratio, 
                       enrollRates = enrollRates, failRates = failRates, studyDuration = studyDuration,
                       tau = 30)

x_Milestone <- fixed_design(x = "Milestone", alpha = alpha, ratio = ratio, 
                       enrollRates = enrollRates, failRates = failRates, studyDuration = studyDuration,
                       tau = 30)

rbind(summary(x_AHR), summary(x_FH), summary(x_MB), summary(x_LF), summary(x_MaxCombo), summary(x_RMST), summary(x_Milestone)) %>% gt()

keaven/gsDesign2 documentation built on Oct. 13, 2022, 8:42 p.m.