Clean up pbetaMix and qbetaMix #9

R/dbetabinom.R

@@ -147,44 +147,67 @@ dbetaMix <- Vectorize(dbetaMix, vectorize.args = "x")
 
 #' Beta-mixture cdf
 #'
-#' Note that `x` can be a vector.
+#' @description `r lifecycle::badge("experimental")`
 #'
-#' @param x the abscissa.
-#' @param par the beta parameters matrix, with K rows and 2 columns,
-#' corresponding to the beta parameters of the K components.
-#' @param weights the mixture weights of the beta mixture prior.
-#' @param lower.tail logical; if TRUE (default), probabilities are `P[X <= x]`,
-#' and otherwise `P[X > x]`.
-#' @return the (one minus) cdf value.
+#' Calculates the cdf of the beta-mixture
+#'
+#' @typed x : number
+#'  the abscissa.
+#' @typed par : matrix
+#'  the beta parameters matrix, with K rows and 2 columns,
+#'  corresponding to the beta parameters of the K components.
+#' @typed weights : matrix
+#'  the mixture weights of the beta mixture prior.
+#' @typed lower.tail : logical # TODO Why not flag
+#'  if TRUE (default), probabilities are `P[X <= x]`,
+#'  and otherwise `P[X > x]`.
+#' @return the (one minus) cdf value # TODO DO WE NEED THIS return and where is the "1-".
 #'
+#' @note `x` can be a vector.
+#'
+#' @example examples/pbetaMix.R
 #' @export
 pbetaMix <- function(x, par, weights, lower.tail = TRUE) {
+  assert_numeric(x, lower = 0, finite = TRUE)
+  assert_numeric(weights, lower = 0, upper = 1, finite = TRUE)
+  assert_matrix(par)
+  assert_flag(lower.tail)
   ret <- sum(weights * pbeta(x, par[, 1], par[, 2], lower.tail = lower.tail))
-  return(ret)
+  ret
 }
 pbetaMix <- Vectorize(pbetaMix, vectorize.args = "x")
 
 
 #' Beta-mixture quantile function
 #'
-#' Note that `x` can be a vector.
+#'  @description `r lifecycle::badge("experimental")`
+#'
+#' Calculates the quantile where x support is at the intersection of cdf and quantile function
 #'
-#' @param q  the required quantile.
-#' @param par  the beta parameters matrix, with K rows and 2 columns,
-#' corresponding to the beta parameters of the K components.
-#' @param weights  the mixture weights of the beta mixture prior.
+#' @typed q : numeric
+#'  the required quantile.
+#' @typed par : number
+#'  the beta parameters matrix, with K rows and 2 columns,
+#'  corresponding to the beta parameters of the K components.
+#' @typed weights : matrix
+#'  the mixture weights of the beta mixture prior.
+#' @typed lower.tail : flag
+#'  whether cdf at x taken at lower or upper tail
 #' @return the abscissa.
 #'
+#' @example examples/qbetaMix.R
 #' @export
-qbetaMix <- function(q, par, weights) {
+qbetaMix <- function(q, par, weights, lower.tail) {
   f <- function(pi) {
+    assert_numeric(pi, lower = 0, finite = TRUE)
     pbetaMix(x = pi, par = par, weights = weights) - q
   }
   unirootResult <- uniroot(f, lower = 0, upper = 1)
+  assert_number(unirootResult$f.root)
   if (unirootResult$iter < 0) {
-    return(NA)
+    NA
   } else {
-    return(unirootResult$root)
+    unirootResult$root
   }
 }
 qbetaMix <- Vectorize(qbetaMix, vectorize.args = "q")

examples/pbetaMix.R

@@ -1,31 +1,15 @@
-## Calculating the CDF of a mixture
-## of beta densities at x, x = 0.3; a = 0.2; b = 0.4
-##
-##
-## Only 1 mixture component, i.e., weights = 1
-## Compare to pbeta(0.3,0.2,0.4) = 0.5947341
-##
 pbetaMix(x = 0.3, par = rbind(c(0.2, 0.4)), weights = 1)
 
 ## Can get the one minus CDF values
-## Need to specify lower.tail = FALSE, 1 - 0.5947341 = 0.4052659
-##
-##
 pbetaMix(x = 0.3, par = rbind(c(0.2, 0.4)), weights = 1, lower.tail = FALSE)
 
 ## With 2 mixture components
-## Weight 0.6 for component 1; a = 0.2, b = 0.4
-## Weight 0.4 for component 2; a = 1.0, b = 1.0
-## Compare to 0.6*pbeta(0.3,0.2,0.4) + 0.4*pbeta(0.3,1,1) = 0.4768404
-##
 pbetaMix(
   x = 0.3, par = rbind(c(0.2, 0.4), c(1, 1)),
   weights = c(0.6, 0.4)
 )
 
-## Can also specify x as a vector, x = seq(0,1,.01)
-##
-##
+## Can also specify x as a vector.
 pbetaMix(
   x = seq(0, 1, .01), par = rbind(c(0.2, 0.4), c(1, 1)),
   weights = c(0.6, 0.4)

examples/qbetaMix.R

@@ -1,25 +1,19 @@
-## Calculating the quantile (inverse CDF) of a mixture
-## of beta densities at x where q = 0.6; a = 0.2; b = 0.4
-##
-##
 ## Only 1 mixture component, i.e., weights = 1
-## Compare to qbeta(0.6,0.2,0.4) = 0.3112065
-##
-qbetaMix(q = 0.60, par = rbind(c(0.2, 0.4)), weights = 1)
+qbetaMix(
+  q = 0.60,
+  par = rbind(c(0.2, 0.4)),
+  weights = 1
+)
 
 ## With 2 mixture components
-## Weight 0.6 for component 1; a = 0.2, b = 0.4
-## Weight 0.4 for component 2; a = 1.0, b = 1.0
-##
 qbetaMix(
   q = 0.6, par = rbind(c(0.2, 0.4), c(1, 1)),
   weights = c(0.6, 0.4)
 )
 
-## Can also specify q as a vector : q = seq(0,1,.01)
-##
-##
+## Can also specify q as a vector
 qbetaMix(
-  q = seq(0, 1, .01), par = rbind(c(0.2, 0.4), c(1, 1)),
+  q = seq(0, 1, .01),
+  par = rbind(c(0.2, 0.4), c(1, 1)),
   weights = c(0.6, 0.4)
 )

inst/WORDLIST

@@ -3239,6 +3239,7 @@ resizable
 ResourceRef
 responder
 responders
+ret
 rf
 rG
 RG

tests/testthat/test-dbetabinom.R

@@ -58,3 +58,73 @@ test_that("Beta mixture density has the correct numeric result", {
   )
   expect_equal(result, 0.03905469, tolerance = 1e-6)
 })
+
+## pbetaMix ----
+
+test_that("The pbetaMix has incrementally higher cdf with increase x support", {
+  is_lower <- pbetaMix(
+    x = 0.3,
+    par = rbind(c(0.2, 0.4)),
+    weights = 1
+  )
+  is_higher <- pbetaMix(
+    x = 0.5,
+    par = rbind(c(0.2, 0.4)),
+    weights = 1
+  )
+  expect_true(is_lower < is_higher)
+})
+
+test_that("The pbetaMix has the correct number result", {
+  result <- pbetaMix(
+    x = 0.3,
+    par = rbind(c(0.2, 0.4), c(1, 1)),
+    weights = c(0.6, 0.4)
+  )
+  expect_equal(result, 0.4768404, tolerance = 1e-5)
+})
+
+test_that("The complement of pbetaMix can be derived with a different lower.tail flag", {
+  result <- pbetaMix(
+    x = 0.3,
+    par = rbind(c(0.2, 0.4)),
+    weights = 1,
+    lower.tail = FALSE
+  )
+  result_inversed <- pbetaMix(
+    x = 0.3,
+    par = rbind(c(0.2, 0.4)),
+    weights = 1,
+    lower.tail = TRUE
+  )
+  expect_equal(result, 1 - result_inversed, tolerance = 1e-5)
+})
+
+## qbetaMix ----
+
+test_that("The qbetaMix has the correct number result", {
+  result <- qbetaMix(
+    q = 0.6,
+    par = rbind(c(0.2, 0.4)),
+    weights = 1
+  )
+  expect_equal(result, 0.3112068, tolerance = 1e-6)
+})
+
+test_that("The qbetaMix has the correct number result", {
+  result <- qbetaMix(
+    q = 0.6,
+    par = rbind(c(0.2, 0.4), c(1, 1)),
+    weights = c(0.6, 0.4)
+  )
+  expect_equal(result, 0.488759, tolerance = 1e-6)
+})
+
+test_that("The qbetaMix has a number result", {
+  result <- qbetaMix(
+    q = seq(0, 1, .01),
+    par = rbind(c(0.2, 0.4), c(1, 1)),
+    weights = c(0.6, 0.4)
+  )
+  expect_numeric(result)
+})