683 replace/remove is.probability/is.range/is.prob range with applicable additional checkmate assertions

R/Rules-methods.R

@@ -3017,7 +3017,7 @@ setMethod("stopTrial",
       prob_target <- stopping@prob_target
 
       ## checks
-      stopifnot(is.probability(prob_target))
+      assert_probability(prob_target)
       stopifnot(is(Effmodel, "ModelEff"))
       stopifnot(is(Effsamples, "Samples"))
       stopifnot(is.function(TDderive))
@@ -3135,7 +3135,7 @@ setMethod("stopTrial",
       prob_target <- stopping@prob_target
 
       ## checks
-      stopifnot(is.probability(prob_target))
+      assert_probability(prob_target)
       stopifnot(is(Effmodel, "ModelEff"))
 
 

R/fromQuantiles.R

@@ -76,8 +76,10 @@ Quantiles2LogisticNormal <- function(dosegrid,
                                        )) {
   ## extracts and checks
   nDoses <- length(dosegrid)
+
   assert_flag(logNormal)
   assert_flag(verbose)
+  assert_probability(level, bounds_closed = FALSE)
   stopifnot(
     !is.unsorted(dosegrid, strictly = TRUE),
     ## the medians must be monotonically increasing:
@@ -87,7 +89,6 @@ Quantiles2LogisticNormal <- function(dosegrid,
     identical(length(upper), nDoses),
     all(lower < median),
     all(upper > median),
-    is.probability(level, bounds = FALSE),
     identical(length(parlower), 5L),
     identical(length(parupper), 5L),
     all(parlower < parstart),
@@ -234,10 +235,8 @@ Quantiles2LogisticNormal <- function(dosegrid,
 ##' @export
 ##' @keywords programming
 getMinInfBeta <- function(p, q) {
-  stopifnot(
-    is.probability(p, bounds = FALSE),
-    is.probability(q, bounds = FALSE)
-  )
+  assert_probability(p, bounds_closed = FALSE)
+  assert_probability(q, bounds_closed = FALSE)
 
   ret <-
     if (q > p) {
@@ -309,12 +308,13 @@ MinimalInformative <- function(dosegrid,
                                ...) {
   ## extracts and checks
   nDoses <- length(dosegrid)
+
+  assert_probability(threshmin, bounds_closed = FALSE)
+  assert_probability(threshmax, bounds_closed = FALSE)
+  assert_probability(probmin, bounds_closed = FALSE)
+  assert_probability(probmax, bounds_closed = FALSE)
   stopifnot(
-    !is.unsorted(dosegrid, strictly = TRUE),
-    is.probability(threshmin, bounds = FALSE),
-    is.probability(threshmax, bounds = FALSE),
-    is.probability(probmin, bounds = FALSE),
-    is.probability(probmax, bounds = FALSE)
+    !is.unsorted(dosegrid, strictly = TRUE)
   )
   xmin <- dosegrid[1]
   xmax <- dosegrid[nDoses]

R/helpers.R

@@ -127,47 +127,6 @@ safeInteger <- function(x) {
   as.integer(x)
 }
 
-##' Predicate checking for a probability
-##'
-##' @param x the object being checked
-##' @param bounds whether to include the bounds 0 and 1 (default)
-##' @return Returns \code{TRUE} if \code{x} is a probability
-##'
-##' @keywords internal
-is.probability <- function(x,
-                           bounds = TRUE) {
-  if (bounds) {
-    return(test_numeric(x, lower = 0, upper = 1, any.missing = FALSE))
-  } else {
-    return(test_numeric(x, lower = 0, upper = 1, any.missing = FALSE) && x != 0 && x != 1)
-  }
-}
-
-##' Predicate checking for a numeric range
-##'
-##' @param x the object being checked
-##' @return Returns \code{TRUE} if \code{x} is a numeric range
-##'
-##' @keywords internal
-is.range <- function(x) {
-  return(identical(length(x), 2L) &&
-    x[1] < x[2])
-}
-
-##' Predicate checking for a probability range
-##'
-##' @param x the object being checked
-##' @param bounds whether to include the bounds 0 and 1 (default)
-##' @return Returns \code{TRUE} if \code{x} is a probability range
-##'
-##' @keywords internal
-is.probRange <- function(x,
-                         bounds = TRUE) {
-  return(is.range(x) &&
-    all(sapply(x, is.probability, bounds = bounds)))
-}
-
-
 ##' Shorthand for logit function
 ##'
 ##' @param x the function argument