Calculate sample size and bounds given targeted power and Type I error in group sequential design using average hazard ratio under non-proportional hazards
Source:R/gs_design_ahr.R
gs_design_ahr.RdCalculate sample size and bounds given targeted power and Type I error in group sequential design using average hazard ratio under non-proportional hazards
Usage
gs_design_ahr(
enroll_rate = define_enroll_rate(duration = c(2, 2, 10), rate = c(3, 6, 9)),
fail_rate = define_fail_rate(duration = c(3, 100), fail_rate = log(2)/c(9, 18), hr =
c(0.9, 0.6), dropout_rate = 0.001),
alpha = 0.025,
beta = 0.1,
info_frac = NULL,
analysis_time = 36,
ratio = 1,
binding = FALSE,
upper = gs_spending_bound,
upar = list(sf = gsDesign::sfLDOF, total_spend = alpha),
lower = gs_spending_bound,
lpar = list(sf = gsDesign::sfLDOF, total_spend = beta),
h1_spending = TRUE,
test_upper = TRUE,
test_lower = TRUE,
info_scale = c("h0_h1_info", "h0_info", "h1_info"),
r = 18,
tol = 1e-06,
interval = c(0.01, 1000)
)Arguments
- enroll_rate
Enrollment rates defined by
define_enroll_rate().- fail_rate
Failure and dropout rates defined by
define_fail_rate().- alpha
One-sided Type I error.
- beta
Type II error.
- info_frac
Targeted information fraction for analyses. See details.
- analysis_time
Targeted calendar timing of analyses. See details.
- ratio
Experimental:Control randomization ratio.
- binding
Indicator of whether futility bound is binding; default of
FALSEis recommended.- upper
Function to compute upper bound.
gs_spending_bound(): alpha-spending efficacy bounds.gs_b(): fixed efficacy bounds.
- upar
Parameters passed to
upper.If
upper = gs_b, thenuparis a numerical vector specifying the fixed efficacy bounds per analysis.If
upper = gs_spending_bound, thenuparis a list includingsffor the spending function family.total_spendfor total alpha spend.paramfor the parameter of the spending function.timingspecifies spending time if different from information-based spending; see details.
- lower
Function to compute lower bound, which can be set up similarly as
upper. See this vignette.- lpar
Parameters passed to
lower, which can be set up similarly asupar.- h1_spending
Indicator that lower bound to be set by spending under alternate hypothesis (input
fail_rate) if spending is used for lower bound. If this isFALSE, then the lower bound spending is under the null hypothesis. This is for two-sided symmetric or asymmetric testing under the null hypothesis; See this vignette.- test_upper
Indicator of which analyses should include an upper (efficacy) bound; single value of
TRUE(default) indicates all analyses; otherwise, a logical vector of the same length asinfoshould indicate which analyses will have an efficacy bound.- test_lower
Indicator of which analyses should include an lower bound; single value of
TRUE(default) indicates all analyses; single valueFALSEindicated no lower bound; otherwise, a logical vector of the same length asinfoshould indicate which analyses will have a lower bound.- info_scale
Information scale for calculation. Options are:
"h0_h1_info"(default): variance under both null and alternative hypotheses is used."h0_info": variance under null hypothesis is used."h1_info": variance under alternative hypothesis is used.
- r
Integer value controlling grid for numerical integration as in Jennison and Turnbull (2000); default is 18, range is 1 to 80. Larger values provide larger number of grid points and greater accuracy. Normally,
rwill not be changed by the user.- tol
Tolerance parameter for boundary convergence (on Z-scale); normally not changed by the user.
- interval
An interval presumed to include the times at which expected event count is equal to targeted event. Normally, this can be ignored by the user as it is set to
c(.01, 1000).
Value
A list with input parameters, enrollment rate, analysis, and bound.
The
$inputis a list includingalpha,beta,ratio, etc.The
$enroll_rateis a table showing the enrollment for arriving the targeted power (1 - beta).The
$fail_rateis a table showing the failure and dropout rates, which is the same as input.The
$boundis a table summarizing the efficacy and futility bound per analysis.The
analysisis a table summarizing the analysis time, sample size, events, average HR, treatment effect and statistical information per analysis.
Details
The parameters info_frac and analysis_time are used to determine the timing for interim and final analyses.
If the interim analysis is determined by targeted information fraction and the study duration is known, then
info_fracis a numerical vector where each element (greater than 0 and less than or equal to 1) represents the information fraction for each analysis. Theanalysis_time, which defaults to 36, indicates the time for the final analysis.If interim analyses are determined solely by the targeted calendar analysis timing from start of study, then
analysis_timewill be a vector specifying the time for each analysis.If both the targeted analysis time and the targeted information fraction are utilized for a given analysis, then timing will be the maximum of the two with both
info_fracandanalysis_timeprovided as vectors.
Examples
library(gsDesign)
#>
#> Attaching package: ‘gsDesign’
#> The following objects are masked from ‘package:gsDesign2’:
#>
#> as_gt, as_rtf
library(gsDesign2)
library(dplyr)
# Example 1 ----
# call with defaults
gs_design_ahr()
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.025
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 1
#>
#> $input$analysis_time
#> [1] 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.025
#>
#>
#> $input$lower
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> $input$lpar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$lpar$total_spend
#> [1] 0.1
#>
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] FALSE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 13.2
#> 2 All 2 26.4
#> 3 All 10 39.7
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 1 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.9 0.025 1.96 0.795 0.0250
#>
#> $analysis
#> # A tibble: 1 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 36 476. 292. 0.683 0.381 71.7 73.0 1 1
#>
#> attr(,"class")
#> [1] "non_binding" "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# Example 2 ----
# Single analysis
gs_design_ahr(analysis_time = 40)
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.025
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 1
#>
#> $input$analysis_time
#> [1] 40
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.025
#>
#>
#> $input$lower
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> $input$lpar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$lpar$total_spend
#> [1] 0.1
#>
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] FALSE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 11.9
#> 2 All 2 23.8
#> 3 All 10 35.6
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 1 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.9 0.025 1.96 0.791 0.0250
#>
#> $analysis
#> # A tibble: 1 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 40 428. 280. 0.678 0.389 68.8 69.9 1 1
#>
#> attr(,"class")
#> [1] "non_binding" "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# Example 3 ----
# Multiple analysis_time
gs_design_ahr(analysis_time = c(12, 24, 36))
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.025
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 0.3080415 0.7407917 1.0000000
#>
#> $input$analysis_time
#> [1] 12 24 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.025
#>
#>
#> $input$lower
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> $input$lpar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$lpar$total_spend
#> [1] 0.1
#>
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] FALSE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 14.5
#> 2 All 2 29.1
#> 3 All 10 43.6
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 6 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.00248 0.0000538 3.87 0.459 0.0000538
#> 2 1 lower 0.00321 0.0443 -1.70 1.41 0.956
#> 3 2 upper 0.579 0.00921 2.36 0.736 0.00919
#> 4 2 lower 0.0556 0.830 0.953 0.884 0.170
#> 5 3 upper 0.900 0.0244 2.01 0.799 0.0222
#> 6 3 lower 0.100 0.976 2.01 0.799 0.0223
#>
#> $analysis
#> # A tibble: 3 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 12 436. 98.8 0.811 0.210 24.4 24.7 0.309 0.308
#> 2 2 24 523. 238. 0.715 0.335 58.1 59.4 0.738 0.741
#> 3 3 36 523. 321. 0.683 0.381 78.8 80.2 1 1
#>
#> attr(,"class")
#> [1] "non_binding" "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# Example 4 ----
# Specified information fraction
# \donttest{
gs_design_ahr(info_frac = c(.25, .75, 1), analysis_time = 36)
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.025
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 0.25 0.75 1.00
#>
#> $input$analysis_time
#> [1] 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.025
#>
#>
#> $input$lower
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> $input$lpar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$lpar$total_spend
#> [1] 0.1
#>
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] FALSE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 14.6
#> 2 All 2 29.1
#> 3 All 10 43.7
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 6 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.000295 0.00000737 4.33 0.380 0.00000737
#> 2 1 lower 0.00108 0.0135 -2.21 1.64 0.987
#> 3 2 upper 0.599 0.00965 2.34 0.740 0.00965
#> 4 2 lower 0.0570 0.843 1.01 0.878 0.157
#> 5 3 upper 0.900 0.0244 2.01 0.799 0.0221
#> 6 3 lower 0.100 0.976 2.01 0.799 0.0221
#>
#> $analysis
#> # A tibble: 3 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 10.7 382. 80.4 0.823 0.195 19.8 20.1 0.251 0.250
#> 2 2 24.4 524. 241. 0.714 0.337 59.0 60.3 0.747 0.750
#> 3 3 36 524. 322. 0.683 0.381 79.0 80.4 1 1
#>
#> attr(,"class")
#> [1] "non_binding" "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# }
# Example 5 ----
# multiple analysis times & info_frac
# driven by times
gs_design_ahr(info_frac = c(.25, .75, 1), analysis_time = c(12, 25, 36))
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.025
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 0.25 0.75 1.00
#>
#> $input$analysis_time
#> [1] 12 25 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.025
#>
#>
#> $input$lower
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> $input$lpar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$lpar$total_spend
#> [1] 0.1
#>
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] FALSE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 14.6
#> 2 All 2 29.3
#> 3 All 10 43.9
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 6 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.00251 0.0000538 3.87 0.460 0.0000538
#> 2 1 lower 0.00321 0.0446 -1.70 1.41 0.955
#> 3 2 upper 0.635 0.0105 2.31 0.746 0.0104
#> 4 2 lower 0.0599 0.862 1.09 0.871 0.138
#> 5 3 upper 0.900 0.0243 2.02 0.799 0.0219
#> 6 3 lower 0.100 0.976 2.01 0.799 0.0220
#>
#> $analysis
#> # A tibble: 3 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 12 439. 99.5 0.811 0.210 24.5 24.9 0.309 0.308
#> 2 2 25 527. 248. 0.711 0.341 60.5 61.9 0.763 0.766
#> 3 3 36 527. 323. 0.683 0.381 79.3 80.7 1 1
#>
#> attr(,"class")
#> [1] "non_binding" "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# driven by info_frac
# \donttest{
gs_design_ahr(info_frac = c(1 / 3, .8, 1), analysis_time = c(12, 25, 36))
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.025
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 0.3333333 0.8000000 1.0000000
#>
#> $input$analysis_time
#> [1] 12 25 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.025
#>
#>
#> $input$lower
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> $input$lpar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$lpar$total_spend
#> [1] 0.1
#>
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] FALSE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 14.7
#> 2 All 2 29.5
#> 3 All 10 44.2
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 6 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.00510 0.000104 3.71 0.490 0.000104
#> 2 1 lower 0.00459 0.0665 -1.50 1.33 0.934
#> 3 2 upper 0.701 0.0122 2.25 0.756 0.0122
#> 4 2 lower 0.0655 0.896 1.26 0.856 0.104
#> 5 3 upper 0.900 0.0241 2.03 0.799 0.0214
#> 6 3 lower 0.100 0.976 2.02 0.799 0.0216
#>
#> $analysis
#> # A tibble: 3 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 12.5 465. 108. 0.806 0.216 26.7 27.1 0.334 0.333
#> 2 2 26.4 530. 260. 0.706 0.348 63.7 65.1 0.797 0.800
#> 3 3 36 530. 325. 0.683 0.381 79.9 81.3 1 1
#>
#> attr(,"class")
#> [1] "non_binding" "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# }
# Example 6 ----
# 2-sided symmetric design with O'Brien-Fleming spending
# \donttest{
gs_design_ahr(
analysis_time = c(12, 24, 36),
binding = TRUE,
upper = gs_spending_bound,
upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
lower = gs_spending_bound,
lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
h1_spending = FALSE
)
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.025
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 0.3080415 0.7407917 1.0000000
#>
#> $input$analysis_time
#> [1] 12 24 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.025
#>
#> $input$upar$param
#> NULL
#>
#> $input$upar$timing
#> NULL
#>
#>
#> $input$lower
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> $input$lpar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$lpar$total_spend
#> [1] 0.025
#>
#> $input$lpar$param
#> NULL
#>
#> $input$lpar$timing
#> NULL
#>
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] FALSE
#>
#> $input$binding
#> [1] TRUE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 13.7
#> 2 All 2 27.5
#> 3 All 10 41.2
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 6 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.00226 0.0000538 3.87 0.449 0.0000538
#> 2 1 lower 0.000000613 0.0000538 -3.87 2.23 1.00
#> 3 2 upper 0.550 0.00921 2.36 0.730 0.00919
#> 4 2 lower 0.00000125 0.00921 -2.36 1.37 0.991
#> 5 3 upper 0.900 0.0250 2.01 0.794 0.0222
#> 6 3 lower 0.00000128 0.0250 -2.01 1.26 0.978
#>
#> $analysis
#> # A tibble: 3 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 12 412. 93.4 0.811 0.210 23.0 23.3 0.309 0.308
#> 2 2 24 494. 224. 0.715 0.335 54.9 56.1 0.738 0.741
#> 3 3 36 494. 303. 0.683 0.381 74.4 75.8 1 1
#>
#> attr(,"class")
#> [1] "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# }
# 2-sided asymmetric design with O'Brien-Fleming upper spending
# Pocock lower spending under H1 (NPH)
# \donttest{
gs_design_ahr(
analysis_time = c(12, 24, 36),
binding = TRUE,
upper = gs_spending_bound,
upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025, param = NULL, timing = NULL),
lower = gs_spending_bound,
lpar = list(sf = gsDesign::sfLDPocock, total_spend = 0.1, param = NULL, timing = NULL),
h1_spending = TRUE
)
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.025
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 0.3080415 0.7407917 1.0000000
#>
#> $input$analysis_time
#> [1] 12 24 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.025
#>
#> $input$upar$param
#> NULL
#>
#> $input$upar$timing
#> NULL
#>
#>
#> $input$lower
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> $input$lpar$sf
#> function (alpha, t, param)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> t[t > 1] <- 1
#> x <- list(name = "Lan-DeMets Pocock approximation", param = NULL,
#> parname = "none", sf = sfLDPocock, spend = alpha * log(1 +
#> (exp(1) - 1) * t), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa9a366780>
#> <environment: namespace:gsDesign>
#>
#> $input$lpar$total_spend
#> [1] 0.1
#>
#> $input$lpar$param
#> NULL
#>
#> $input$lpar$timing
#> NULL
#>
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] TRUE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 16.5
#> 2 All 2 32.9
#> 3 All 10 49.4
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 6 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.00305 0.0000538 3.87 0.481 0.0000538
#> 2 1 lower 0.0430 0.268 -0.619 1.12 0.732
#> 3 2 upper 0.638 0.00921 2.36 0.750 0.00920
#> 4 2 lower 0.0823 0.874 1.13 0.871 0.129
#> 5 3 upper 0.900 0.0250 1.98 0.813 0.0240
#> 6 3 lower 0.100 0.975 1.97 0.813 0.0243
#>
#> $analysis
#> # A tibble: 3 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 12 494. 112. 0.811 0.210 27.6 28.0 0.309 0.308
#> 2 2 24 593. 269. 0.715 0.335 65.9 67.3 0.738 0.741
#> 3 3 36 593. 364. 0.683 0.381 89.3 90.9 1 1
#>
#> attr(,"class")
#> [1] "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# }
# Example 7 ----
# \donttest{
gs_design_ahr(
alpha = 0.0125,
analysis_time = c(12, 24, 36),
upper = gs_spending_bound,
upar = list(sf = gsDesign::sfLDOF, total_spend = 0.0125, param = NULL, timing = NULL),
lower = gs_b,
lpar = rep(-Inf, 3)
)
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.0125
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 0.3080415 0.7407917 1.0000000
#>
#> $input$analysis_time
#> [1] 12 24 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (k = 1, par = list(sf = gsDesign::sfLDOF, total_spend = 0.025,
#> param = NULL, timing = NULL, max_info = NULL), hgm1 = NULL,
#> theta = 0.1, info = 1:3, efficacy = TRUE, test_bound = TRUE,
#> r = 18, tol = 1e-06)
#> {
#> if (length(test_bound) == 1 && k > 1) {
#> test_bound <- rep(test_bound, k)
#> }
#> if (!is.null(par$timing)) {
#> timing <- par$timing
#> }
#> else {
#> if (is.null(par$max_info)) {
#> timing <- info/max(info)
#> }
#> else {
#> timing <- info/par$max_info
#> }
#> }
#> if (!is.function(sf <- par$sf))
#> sf <- tryCatch(match.fun(sf), error = function(e) {
#> getExportedValue("gsDesign", sf)
#> })
#> spend <- sf(alpha = par$total_spend, t = timing, param = par$param)$spend
#> old_spend <- 0
#> for (i in 1:k) {
#> if (test_bound[i]) {
#> xx <- spend[i] - old_spend
#> old_spend <- spend[i]
#> spend[i] <- xx
#> }
#> else {
#> spend[i] <- 0
#> }
#> }
#> spend <- spend[k]
#> if (!efficacy) {
#> if (spend <= 0) {
#> return(-Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> a <- qnorm(spend) + sqrt(info[k]) * theta[k]
#> if (k == 1) {
#> return(a)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> adelta <- 1
#> j <- 0
#> while (abs(adelta) > tol) {
#> hg <- hupdate(theta = theta[k], info = info[k], a = -Inf,
#> b = a, thetam1 = theta[k - 1], im1 = info[k -
#> 1], gm1 = hgm1, r = r)
#> i <- length(hg$h)
#> pik <- sum(hg$h)
#> adelta <- spend - pik
#> dplo <- hg$h[i]/hg$w[i]
#> if (adelta > dplo) {
#> adelta <- 1
#> }
#> else if (adelta < -dplo) {
#> adelta <- -1
#> }
#> else {
#> adelta <- adelta/dplo
#> }
#> a <- a + adelta
#> if (a > extreme_high) {
#> a <- extreme_high
#> }
#> else if (a < extreme_low) {
#> a <- extreme_low
#> }
#> if (abs(adelta) < tol) {
#> return(a)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> else {
#> if (spend <= 0) {
#> return(Inf)
#> }
#> if (length(theta) == 1)
#> theta <- rep(theta, length(info))
#> b <- qnorm(spend, lower.tail = FALSE)
#> if (k == 1) {
#> return(b)
#> }
#> mu <- theta[k] * sqrt(info[k])
#> extreme_low <- mu - 3 - 4 * log(r)
#> extreme_high <- mu + 3 + 4 * log(r)
#> bdelta <- 1
#> j <- 1
#> while (abs(bdelta) > tol) {
#> hg <- hupdate(theta = 0, info = info[k], a = b, b = Inf,
#> thetam1 = 0, im1 = info[k - 1], gm1 = hgm1, r = r)
#> pik <- sum(hg$h)
#> bdelta <- spend - pik
#> dpikdb <- hg$h[1]/hg$w[1]
#> if (bdelta > dpikdb) {
#> bdelta <- 1
#> }
#> else if (bdelta < -dpikdb) {
#> bdelta <- -1
#> }
#> else {
#> bdelta <- bdelta/dpikdb
#> }
#> b <- b - bdelta
#> if (b > extreme_high) {
#> b <- extreme_high
#> }
#> else if (b < extreme_low) {
#> b <- extreme_low
#> }
#> if (abs(bdelta) < tol) {
#> return(b)
#> }
#> j <- j + 1
#> if (j > 20) {
#> stop(paste("gs_spending_bound(): bound_update did not converge for lower bound calculation, analysis",
#> k, " !"))
#> }
#> }
#> }
#> }
#> <bytecode: 0x55fa9e8d5da8>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> $input$upar$sf
#> function (alpha, t, param = NULL)
#> {
#> checkScalar(alpha, "numeric", c(0, Inf), c(FALSE, FALSE))
#> checkVector(t, "numeric", c(0, Inf), c(TRUE, FALSE))
#> if (is.null(param) || param < 0.005 || param > 20)
#> param <- 1
#> checkScalar(param, "numeric", c(0.005, 20), c(TRUE, TRUE))
#> t[t > 1] <- 1
#> if (param == 1) {
#> rho <- 1
#> txt <- "Lan-DeMets O'Brien-Fleming approximation"
#> parname <- "none"
#> }
#> else {
#> rho <- param
#> txt <- "Generalized Lan-DeMets O'Brien-Fleming"
#> parname <- "rho"
#> }
#> z <- -qnorm(alpha/2)
#> x <- list(name = txt, param = param, parname = parname, sf = sfLDOF,
#> spend = 2 * (1 - pnorm(z/t^(rho/2))), bound = NULL, prob = NULL)
#> class(x) <- "spendfn"
#> x
#> }
#> <bytecode: 0x55fa98af3b98>
#> <environment: namespace:gsDesign>
#>
#> $input$upar$total_spend
#> [1] 0.0125
#>
#> $input$upar$param
#> NULL
#>
#> $input$upar$timing
#> NULL
#>
#>
#> $input$lower
#> function (par = NULL, k = NULL, ...)
#> {
#> if (is.null(k)) {
#> return(par)
#> }
#> else {
#> return(par[k])
#> }
#> }
#> <bytecode: 0x55fa9e8aab90>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> [1] -Inf -Inf -Inf
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] FALSE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 16.1
#> 2 All 2 32.2
#> 3 All 10 48.3
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 3 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.000619 0.00000679 4.35 0.435 0.00000679
#> 2 2 upper 0.505 0.00371 2.68 0.719 0.00371
#> 3 3 upper 0.900 0.0125 2.28 0.785 0.0114
#>
#> $analysis
#> # A tibble: 3 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 12 483. 109. 0.811 0.210 27.0 27.4 0.309 0.308
#> 2 2 24 579. 263. 0.715 0.335 64.3 65.8 0.738 0.741
#> 3 3 36 579. 355. 0.683 0.381 87.2 88.8 1 1
#>
#> attr(,"class")
#> [1] "non_binding" "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
gs_design_ahr(
alpha = 0.0125,
analysis_time = c(12, 24, 36),
upper = gs_b,
upar = gsDesign::gsDesign(
k = 3, test.type = 1, n.I = c(.25, .75, 1),
sfu = sfLDOF, sfupar = NULL, alpha = 0.0125
)$upper$bound,
lower = gs_b,
lpar = rep(-Inf, 3)
)
#> $input
#> $input$enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 3
#> 2 All 2 6
#> 3 All 10 9
#>
#> $input$fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $input$alpha
#> [1] 0.0125
#>
#> $input$beta
#> [1] 0.1
#>
#> $input$ratio
#> [1] 1
#>
#> $input$info_frac
#> [1] 0.3080415 0.7407917 1.0000000
#>
#> $input$analysis_time
#> [1] 12 24 36
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$upper
#> function (par = NULL, k = NULL, ...)
#> {
#> if (is.null(k)) {
#> return(par)
#> }
#> else {
#> return(par[k])
#> }
#> }
#> <bytecode: 0x55fa9e8aab90>
#> <environment: namespace:gsDesign2>
#>
#> $input$upar
#> [1] 4.859940 2.658446 2.280095
#>
#> $input$lower
#> function (par = NULL, k = NULL, ...)
#> {
#> if (is.null(k)) {
#> return(par)
#> }
#> else {
#> return(par[k])
#> }
#> }
#> <bytecode: 0x55fa9e8aab90>
#> <environment: namespace:gsDesign2>
#>
#> $input$lpar
#> [1] -Inf -Inf -Inf
#>
#> $input$test_upper
#> [1] TRUE
#>
#> $input$test_lower
#> [1] TRUE
#>
#> $input$h1_spending
#> [1] TRUE
#>
#> $input$binding
#> [1] FALSE
#>
#> $input$info_scale
#> [1] "h0_h1_info"
#>
#> $input$r
#> [1] 18
#>
#> $input$tol
#> [1] 1e-06
#>
#>
#> $enroll_rate
#> # A tibble: 3 × 3
#> stratum duration rate
#> <chr> <dbl> <dbl>
#> 1 All 2 16.1
#> 2 All 2 32.2
#> 3 All 10 48.3
#>
#> $fail_rate
#> # A tibble: 2 × 5
#> stratum duration fail_rate dropout_rate hr
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 All 3 0.0770 0.001 0.9
#> 2 All 100 0.0385 0.001 0.6
#>
#> $bound
#> # A tibble: 3 × 7
#> analysis bound probability probability0 z `~hr at bound` `nominal p`
#> <int> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 upper 0.0000938 0.000000587 4.86 0.395 0.000000587
#> 2 2 upper 0.513 0.00393 2.66 0.721 0.00393
#> 3 3 upper 0.900 0.0125 2.28 0.785 0.0113
#>
#> $analysis
#> # A tibble: 3 × 10
#> analysis time n event ahr theta info info0 info_frac info_frac0
#> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 12 483. 110. 0.811 0.210 27.0 27.4 0.309 0.308
#> 2 2 24 580. 263. 0.715 0.335 64.4 65.9 0.738 0.741
#> 3 3 36 580. 356. 0.683 0.381 87.3 88.9 1 1
#>
#> attr(,"class")
#> [1] "non_binding" "ahr" "gs_design" "list"
#> attr(,"uninteger_is_from")
#> [1] "gs_design_ahr"
# }