82_Design-ocRctPredProbDist (#83)

Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanes_bove@roche.com>
Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>

.gitignore

@@ -30,9 +30,3 @@ coverage.*
 .vscode/
 .rds
 node_modules
-
-tests/testthat/junit-result.xml
-
-tests/unit_testing_results.rds
-
-tests/testthat/testthat-problems.rds

.pre-commit-config.yaml

@@ -3,12 +3,13 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: v0.4.2
     hooks:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
       - id: roxygenize
         additional_dependencies:
+          - devtools
           - shiny
           - checkmate
           - openpharma/roxytypes
@@ -64,7 +65,7 @@ repos:
           design/.*
           )$
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=200"]
@@ -89,6 +90,6 @@ repos:
         files: '\.Rhistory|\.RData|\.Rds|\.rds$'
         # `exclude: <regex>` to allow committing specific files.
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.39.0
+    rev: v0.40.0
     hooks:
       - id: markdownlint

DESCRIPTION

@@ -31,6 +31,7 @@ Suggests:
     testthat (>= 3.0.0)
 Imports:
     checkmate,
+    devtools,
     lifecycle
 VignetteBuilder:
     knitr

R/ocRctPostprobDist.R

@@ -130,6 +130,7 @@ h_get_oc_rct <- function(all_sizes, Nmax, nActive, nControl, decision) {
   assert_numeric(nActive, any.missing = FALSE, len = length(all_sizes))
   assert_numeric(nControl, any.missing = FALSE, len = length(all_sizes))
   assert_true(all(nActive + nControl == all_sizes))
+  assert_true(Nmax >= max(all_sizes))
 
   tmp <- h_get_oc(
     all_sizes = all_sizes,

design/design-doc_ocRctPostprobDist.Rmd

@@ -195,7 +195,7 @@ looks_nnrE <- looks$nnrE
 looks_nnrF <- looks$nnrF
 
 h_get_decisionDist_rct(
-  nnr = input$nn,
+  nnr = input$nnE,
   nnrE = looks$nnrE,
   nnrF = looks$nnrF,
   pE = input$pE,
@@ -206,7 +206,9 @@ h_get_decisionDist_rct(
   tU = input$tU,
   deltaE = input$deltaE,
   deltaF = input$deltaF,
-  relativeDelta = TRUE
+  relativeDelta = TRUE,
+  randRatio = 1,
+  Nmax = 30
 )
 ```
 # helper also works when `relativeDelta = FALSE`
@@ -217,7 +219,7 @@ looks_nnrE <- looks$nnrE
 looks_nnrF <- looks$nnrF
 
 h_get_decisionDist_rct(
-  nnr = input$nn,
+  nnr = input$nnE,
   nnrE = looks$nnrE,
   nnrF = looks$nnrF,
   pE = input$pE,
@@ -228,7 +230,9 @@ h_get_decisionDist_rct(
   tU = input$tU,
   deltaE = input$deltaE,
   deltaF = input$deltaF,
-  relativeDelta = FALSE
+  relativeDelta = FALSE,
+  randRatio = 1,
+  Nmax = 30
 )
 ```
 # h_get_oc_rct
@@ -311,7 +315,7 @@ new_RctPostprobDist <- function(nnE,
   if (sim < 50000) {
     warning("Advise to use sim >= 50000 to achieve convergence")
   }
-  decision <- all_sizes <- vector(length = sim)
+  decision <- all_sizes <- nActive <- nControl <- vector(length = sim)
   nnE <- sort(nnE)
   nnF <- sort(nnF)
   nn <- sort(unique(c(nnF, nnE)))
@@ -353,7 +357,13 @@ new_RctPostprobDist <- function(nnE,
     nActive[k] <- tmp$nActive
     nControl[k] <- tmp$nControl
   }
-  oc <- h_get_oc_rct(all_sizes = all_sizes, nnr = nnr, Nmax = Nmax, nActive = nActive, nControl = nControl, decision = decision)
+  oc <- h_get_oc_rct(
+    all_sizes = all_sizes,
+    Nmax = Nmax,
+    nActive = nActive,
+    nControl = nControl,
+    decision = decision
+  )
   list(
     oc = oc,
     ExpectedN = mean(all_sizes),
@@ -375,7 +385,7 @@ new_RctPostprobDist <- function(nnE,
 ```{r}
 set.seed(2000)
 new_RctPostprobDist(
-  nnE = input$nn,
+  nnE = input$nnE,
   pE = input$pE,
   pS = input$pS,
   deltaE = input$deltaE,