131 make oc preds faster (#140)

Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

Author: audreyyeoCH

DESCRIPTION

@@ -53,7 +53,7 @@ Language: en-US
 LazyData: true
 Roxygen:
     list(markdown = TRUE, packages = "roxytypes")
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Config/Needs/documentation:
     roxytypes
 Remotes:

R/dbetabinom.R

@@ -92,7 +92,8 @@ h_getBetamixPost <- function(x, n, par, weights) {
   postPar[, 2] <- postPar[, 2] + n - x
   # We compute updated mixture probabilities.
   tmp <- exp(
-    lbeta(a = postPar[, 1], b = postPar[, 2]) - lbeta(a = par[, 1], b = par[, 2])
+    lbeta(a = postPar[, 1], b = postPar[, 2]) -
+      lbeta(a = par[, 1], b = par[, 2])
   )
   # We compute the updated weights of the posterior
   postWeights <- weights * tmp / sum(weights * tmp)
@@ -121,7 +122,13 @@ h_getBetamixPost <- function(x, n, par, weights) {
 #' @example examples/dbetaMix.R
 #' @export
 dbetaMix <- function(x, par, weights, log = FALSE) {
-  assert_numeric(weights, lower = 0, upper = 1, finite = TRUE, any.missing = FALSE)
+  assert_numeric(
+    weights,
+    lower = 0,
+    upper = 1,
+    finite = TRUE,
+    any.missing = FALSE
+  )
   assert_true(all.equal(sum(weights), 1))
   assert_true(identical(length(weights), nrow(par)))
   degree <- length(weights)
@@ -221,7 +228,10 @@ qbetaMix <- function(p, par, weights, lower.tail = TRUE) {
 
     diff <- f_grid - p
     pos <- diff > 0
-    grid_interval <- c(grid[!pos][which.max(diff[!pos])], grid[pos][which.min(diff[pos])])
+    grid_interval <- c(
+      grid[!pos][which.max(diff[!pos])],
+      grid[pos][which.min(diff[pos])]
+    )
 
     uniroot(
       f = function(q) .pbetaMix(q, par, weights, lower.tail = lower.tail) - p,

examples/ocPredprobDist.R

@@ -8,7 +8,6 @@
 # - Interim look for Efficacy: Pr( success at final ) > 80%
 # - Interim look for Futility: Pr( failure at final ) < 20%
 # We assume a prior of treatment arm parE = Beta(1,1), unless otherwise indicated.
-
 set.seed(20)
 result <- ocPredprobDist(
   nnE = c(10, 20, 30),
@@ -43,7 +42,8 @@ result$oc
 # - Interim look for Futility: Pr( failure at final ) < 20%
 # We assume a prior of treatment arm parE = Beta(1,1), unless otherwise indicated.
 #
-set.seed(20)
+\donttest{
+  set.seed(20)
 result <- ocPredprobDist(
   nnE = c(10, 20, 30),
   truep = 0.40,
@@ -64,6 +64,7 @@ result <- ocPredprobDist(
 )
 result$oc
 
+
 # Here we illustrate an example for Decision 2 with the following assumptions :
 # Efficacy Looks and Futility looks are identical at sample size of 10, 20 and 30
 # where sample looks are allowed to wiggle.
@@ -130,3 +131,4 @@ result <- ocPredprobDist(
   decision1 = FALSE
 )
 result$oc
+}