clean

R/postprobDist.R

@@ -7,8 +7,8 @@ NULL
 #' The helper function to generate Integrand function when `relative Delta = TRUE`.
 #'
 #' @typed delta : number
-#'  the margin of which treatment group `E` is superior than the success rate of
-#'  the standard of care `S`. See also note about the calculation of `delta` when `relative Delta = TRUE`.
+#'  margin by which the response rate in the treatment group should
+#'  be better than in the SOC group. Must be >= `0`. See note.
 #' @typed p_s : number
 #'  probability of success or response rate of standard of care or `SOC` group.
 #' @typed activeBetamixPost : list
@@ -86,11 +86,10 @@ h_get_bounds <- function(controlBetamixPost) {
 #' @description `r lifecycle::badge("experimental")`
 #'
 #' Using the approach by Thall and Simon (Biometrics, 1994), this evaluates the
-#' posterior probability of achieving superior response rate in the treatment group compared to standard of care (SOC):
-#'
-#' `Pr(P_E > P_S | data) = \int 1-F(p_s + delta | alpha_E + x, beta_E + n- x) f(p_s; alpha_S, beta_S`.
+#' posterior probability of achieving superior response rate in the treatment group compared to standard of care (SOC).
 #' See note below for two formulations of the difference in response rates.
 #'
+#' @inheritParams h_integrand_relDelta
 #' @typed x : numeric
 #'  number of success counts in the treatment group.
 #' @typed n : number
@@ -99,9 +98,6 @@ h_get_bounds <- function(controlBetamixPost) {
 #'  number of success counts in the SOC group.
 #' @typed nS : number
 #'  number of patients in the SOC group.
-#' @typed delta : number
-#'  margin by which the response rate in the treatment group should
-#'  be better than in the SOC group. Must be >= `0`. See note.
 #' @typed relativeDelta : flag
 #'  If `TRUE`, then a `relativeDelta` is used. Represents that a minimum
 #'  response rate in magnitude of `delta` of the SOC non-responding patients. See note.

examples/postprobDist.R

@@ -46,7 +46,7 @@ postprobDist(
   delta = 0.1
 )
 
-# Experimental arm only (strictly single arm trial), uniform prior in Experimental arm. Default used.
+# Experimental arm only (strictly single arm trial), uniform prior in Experimental arm.
 # Non-uniform Prior used for SOC arm as no precedent data.
 postprobDist(
   x = 16,
@@ -56,7 +56,7 @@ postprobDist(
   delta = 0,
   relativeDelta = FALSE,
   parS = c(2, 3),
-  weightsS = c(1)
+  weightsS = 1
 )
 # Experimental arm and SOC, uniform prior in both E and S arms, default setting used.
 postprobDist(

tests/testthat/test-postprobDist.R

@@ -11,7 +11,7 @@ test_that("postprobDist gives incrementally higher values with larger x", {
   expect_true(is_lower < is_higher)
 })
 
-test_that("postprobDist gives incrementally higher values with larger x", {
+test_that("postprobDist gives higher values with larger x and returns identical result when x is a vector", {
   expected_lower <- postprobDist(x = 16, n = 23, delta = 0.1, parE = c(0.6, 0.4), parS = c(0.6, 0.4))
   expected_higher <- postprobDist(x = 20, n = 23, delta = 0.1, parE = c(0.6, 0.4), parS = c(0.6, 0.4))
   result <- postprobDist(x = c(16, 20), n = 23, delta = 0.1, parE = c(0.6, 0.4), parS = c(0.6, 0.4))
@@ -35,7 +35,7 @@ test_that("postprobDist gives the correct result for a beta-mixture example", {
   expect_equal(result, 0.3143941, tolerance = 1e-5)
 })
 
-test_that("postprobDist gives incrementally higher values with increased x", {
+test_that("postprobDist gives incrementally higher values with larger x for a beta-mixture example", {
   is_lower <- postprobDist(
     x = 10,
     n = 23,
@@ -65,7 +65,7 @@ test_that("postprobDist gives incrementally higher values with increased x", {
   expect_true(is_lower < is_higher)
 })
 
-test_that("postprobDist gives the correct result with a weighted beta-mixture", {
+test_that("postprobDist gives the correct result for a weighted beta-mixture", {
   result <- postprobDist(
     x = 10,
     n = 23,
@@ -109,7 +109,7 @@ test_that("postprobDist gives an error when xS and nS are not numbers", {
       parS = c(0.6, 0.4),
       weights = c(0.5),
       weightsS = c(0.3),
-    ), "number of items to replace is not a multiple of replacement length"
+    ), "Must have length 1"
   )
 })