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Optimize return object preparation from gs_power_npe() #624

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Merged
LittleBeannie merged 1 commit into from
May 5, 2026
Merged

Optimize return object preparation from gs_power_npe() #624

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14 changes: 5 additions & 9 deletions R/gs_power_npe.R
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Original file line number Diff line number Diff line change
Expand Up @@ -384,22 +384,18 @@ gs_power_npe <- function(theta = .1, theta0 = 0, theta1 = theta, # 3 theta
}
}

ans <- tibble(
ans <- data.frame(
analysis = rep(1:n_analysis, 2),
bound = c(rep("upper", n_analysis), rep("lower", n_analysis)),
z = c(b, a),
probability = c(cumsum(upper_prob), cumsum(lower_prob)),
theta = rep(theta, 2),
theta1 = rep(theta1, 2),
info_frac = rep(info / max(info), 2),
info = rep(info, 2)
) |>
mutate(
info0 = rep(info0, 2),
info1 = rep(info1, 2)
) |>
# filter(abs(Z) < Inf) |>
arrange(desc(bound), analysis)
info = rep(info, 2),
info0 = rep(info0, 2),
info1 = rep(info1, 2)
)

return(ans)
}
10 changes: 5 additions & 5 deletions tests/testthat/test-developer-gs_design_npe.R
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Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ test_that("fixed design with 3 equal info", {
dplyr::mutate(bound = tolower(bound)) |>
dplyr::select(-c(theta1, info1)) |>
dplyr::arrange(analysis, bound)
expect_equal(x1_c, x2)
expect_equal(x1_c, as.data.frame(x2))
})

test_that("fixed design with 3 unequal info", {
Expand Down Expand Up @@ -128,7 +128,7 @@ test_that("fixed design with 3 unequal info", {
dplyr::mutate(bound = tolower(bound)) |>
dplyr::select(-c(theta1, info1)) |>
dplyr::arrange(analysis, bound)
expect_equal(x1_c, x2)
expect_equal(x1_c, as.data.frame(x2))
})

test_that("futility at IA1; efficacy only at IA2 +FA", {
Expand Down Expand Up @@ -170,7 +170,7 @@ test_that("futility at IA1; efficacy only at IA2 +FA", {
dplyr::mutate(bound = tolower(bound)) |>
dplyr::select(-c(theta1, info1)) |>
dplyr::arrange(analysis, bound)
expect_equal(x1_c, x2)
expect_equal(x1_c, as.data.frame(x2))
})

test_that("spending bounds", {
Expand Down Expand Up @@ -216,7 +216,7 @@ test_that("spending bounds", {
dplyr::mutate(bound = tolower(bound)) |>
dplyr::select(analysis, bound, z, probability, theta, info, info0, info1) |>
dplyr::arrange(analysis, bound)
expect_equal(x1_c, x2)
expect_equal(x1_c, as.data.frame(x2))
})

test_that("2-sided symmetric spend", {
Expand Down Expand Up @@ -266,5 +266,5 @@ test_that("2-sided symmetric spend", {
dplyr::mutate(bound = tolower(bound)) |>
dplyr::select(analysis, bound, z, probability, theta, info, info0, info1) |>
dplyr::arrange(analysis, bound)
expect_equal(x1_c, x2)
expect_equal(x1_c, as.data.frame(x2))
})
20 changes: 10 additions & 10 deletions tests/testthat/test-developer-gs_power_npe.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ test_that("The default of `gs_power_npe` is a single analysis with type I error
dplyr::filter(Bound == "Upper") |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1, x2)
expect_equal(x1, as.data.frame(x2))
})

test_that("fixed bound", {
Expand All @@ -29,7 +29,7 @@ test_that("fixed bound", {
) |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1, x2)
expect_equal(x1, as.data.frame(x2))
})

test_that("Same fixed efficacy bounds, no futility bound (i.e., non-binding bound), null hypothesis", {
Expand All @@ -48,7 +48,7 @@ test_that("Same fixed efficacy bounds, no futility bound (i.e., non-binding boun
) |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1, x2)
expect_equal(x1, as.data.frame(x2))
})

test_that("Fixed bound with futility only at analysis 1; efficacy only at analyses 2, 3", {
Expand All @@ -71,7 +71,7 @@ test_that("Fixed bound with futility only at analysis 1; efficacy only at analys
) |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1, x2)
expect_equal(x1, as.data.frame(x2))
})

test_that("Spending function bounds - Lower spending based on non-zero effect", {
Expand All @@ -94,7 +94,7 @@ test_that("Spending function bounds - Lower spending based on non-zero effect",
) |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1, x2)
expect_equal(x1, as.data.frame(x2))
})

test_that("Same bounds, but power under different theta", {
Expand All @@ -117,7 +117,7 @@ test_that("Same bounds, but power under different theta", {
) |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1, x2)
expect_equal(x1, as.data.frame(x2))
})

test_that("Two-sided symmetric spend, O'Brien-Fleming spending", {
Expand All @@ -142,7 +142,7 @@ test_that("Two-sided symmetric spend, O'Brien-Fleming spending", {
) |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1, x2)
expect_equal(x1, as.data.frame(x2))
})

test_that("Re-use these bounds under alternate hypothesis - Always use binding = TRUE for power calculations", {
Expand Down Expand Up @@ -173,7 +173,7 @@ test_that("Re-use these bounds under alternate hypothesis - Always use binding =
) |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1, x2)
expect_equal(x1, as.data.frame(x2))
})

test_that("info != info0 != info1 - If one inputs info in upar", {
Expand Down Expand Up @@ -206,7 +206,7 @@ test_that("info != info0 != info1 - If one inputs info in upar", {
) |>
dplyr::rename(analysis = Analysis, bound = Bound, z = Z, probability = Probability) |>
dplyr::mutate(bound = tolower(bound))
expect_equal(x1_c, x2)
expect_equal(x1_c, as.data.frame(x2))
})

test_that("Developer Tests 1-sided test", {
Expand Down Expand Up @@ -238,7 +238,7 @@ test_that("Developer Tests 1-sided test", {
n.I = (1:3) * 400,
b = gsDesign::gsDesign(k = 3, test.type = 1, sfu = gsDesign::sfLDOF)$upper$bound, a = rep(-20, 3), r = r
)
expect_equal(x, y)
expect_equal(x, as.data.frame(y))
expect_equal(x$z[x$bound == "upper"], z$upper$bound)
expect_equal(x$probability[x$bound == "upper"], cumsum(z$upper$prob))
})
Expand Down
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