Clean up pbetaMix and qbetaMix #9 (#10)

* cleaning up dbetabinom

* removed rounding, not needed

* rmarkdown language and assert for dbetabinom

* changed x and m to number instead of numeric

* test

* pbetaMix function and test

* added new tests and changed documentation

* upper case for test_that comments and more tests for qbeta

* test_thats for pbetaMix and qbetaMix

* tidy syntax and last checks

* tidy syntax and last checks

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* [skip actions] Roxygen Man Pages Auto Update

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* Update examples/pbetaMix.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* p and q inputs

* q,p changes

* Update R/dbetabinom.R

Co-authored-by: Daniel Sabanes Bove <[email protected]>

* [skip actions] Roxygen Man Pages Auto Update

* documentation to reflect p and q changes

* amending qt

* intro x-> q

* amented postprob file

* amended postprob file

* fixed mistake on x

* qbetaMix was in postprobDist

* trying to find R CMD check error

* [skip actions] Roxygen Man Pages Auto Update

* manual of ocPostprobDist

* fixing roxygen type to p

* see if this fixes the CMD check

* see if fixes CMD check error

* xi removed

* example post prob works

* clean

* assert_number

* in postprobDist, I changed p-> q

* change p to q

* change q to p

* fix postprobDist (for now)

---------

Co-authored-by: Daniel Sabanes Bove <[email protected]>
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 <[email protected]>

R/dbetabinom.R

@@ -145,46 +145,67 @@ dbetaMix <- function(x, par, weights, log = FALSE) {
 dbetaMix <- Vectorize(dbetaMix, vectorize.args = "x")
 
 
-#' Beta-mixture cdf
+#' 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 distribution.
+#'
+#' @typed q : 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 : numeric
+#'  the mixture weights of the beta mixture prior which add up to 1.
+#' @typed lower.tail : flag
+#'  if `TRUE` (default), probabilities are `P[X <= x]`,
+#'  and otherwise `P[X > x]`.
+#' @return The (one minus) cdf value
 #'
+#' @note `q` can be a vector.
+#'
+#' @example examples/pbetaMix.R
 #' @export
-pbetaMix <- function(x, par, weights, lower.tail = TRUE) {
-  ret <- sum(weights * pbeta(x, par[, 1], par[, 2], lower.tail = lower.tail))
-  return(ret)
+pbetaMix <- function(q, par, weights, lower.tail = TRUE) {
+  assert_number(q, lower = 0, upper = 1, finite = TRUE)
+  assert_numeric(weights, lower = 0, upper = 1, finite = TRUE)
+  assert_matrix(par)
+  assert_flag(lower.tail)
+  sum(weights * pbeta(q, par[, 1], par[, 2], lower.tail = lower.tail))
 }
-pbetaMix <- Vectorize(pbetaMix, vectorize.args = "x")
+pbetaMix <- Vectorize(pbetaMix, vectorize.args = "q")
 
 
-#' Beta-mixture quantile function
+#' Beta-Mixture Quantile function
 #'
-#' Note that `x` can be a vector.
+#' @description `r lifecycle::badge("experimental")`
+#'
+#' Calculates the quantile of the Beta-Mixture distribution for a given probability.
 #'
-#' @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.
-#' @return the abscissa.
+#' @typed p : numeric
+#'  the required probability
+#' @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(p, par, weights, lower.tail = TRUE) {
   f <- function(pi) {
-    pbetaMix(x = pi, par = par, weights = weights) - q
+    pbetaMix(q = pi, par = par, weights = weights, lower.tail = lower.tail) - p
   }
   unirootResult <- uniroot(f, lower = 0, upper = 1)
   if (unirootResult$iter < 0) {
-    return(NA)
+    NA
   } else {
-    return(unirootResult$root)
+    assert_number(unirootResult$root)
+    unirootResult$root
   }
 }
-qbetaMix <- Vectorize(qbetaMix, vectorize.args = "q")
+qbetaMix <- Vectorize(qbetaMix, vectorize.args = "p")

R/postprob.R

@@ -73,7 +73,8 @@ postprob <- function(x, n, p, parE = c(1, 1), weights, betamixPost, log.p = FALS
 
     ## now compute updated parameters
     betamixPost <- getBetamixPost(
-      x = x, n = n,
+      x = x,
+      n = n,
       par = parE,
       weights = weights
     )
@@ -82,7 +83,7 @@ postprob <- function(x, n, p, parE = c(1, 1), weights, betamixPost, log.p = FALS
   ## now compute the survival function at p, i.e. 1 - cdf at p:
   ret <- with(
     betamixPost,
-    pbetaMix(x = p, par = par, weights = weights, lower.tail = FALSE)
+    pbetaMix(q = p, par = par, weights = weights, lower.tail = FALSE)
   )
 
   if (log.p) {

R/postprobDist.R

@@ -126,14 +126,18 @@ postprobDist <- function(x, n,
   bounds <- with(
     controlBetamixPost,
     qbetaMix(
-      q = c(epsilon, 1 - epsilon),
+      p = c(epsilon, 1 - epsilon),
       par = par,
       weights = weights
     )
   )
   intRes <- integrate(
     f = integrand,
-    lower = bounds[1],
+    lower =
+      max(
+        bounds[1],
+        ifelse(relativeDelta, 0, 0 - delta)
+      ),
     upper =
       min(
         ifelse(relativeDelta, 1, 1 - delta),

examples/ocPostprobDist.R

@@ -11,8 +11,15 @@
 
 
 res1 <- ocPostprobDist(
-  nn = c(10, 20, 30), p = 0.4, deltaE = 0.1, deltaF = -0.1, tL = 0.6, tU = 0.6,
-  parE = c(1, 1), parS = c(5, 25), ns = 100
+  nn = c(10, 20, 30),
+  p = 0.4,
+  deltaE = 0.1,
+  deltaF = -0.1,
+  tL = 0.6,
+  tU = 0.6,
+  parE = c(1, 1),
+  parS = c(5, 25),
+  ns = 100
 )
 
 res1$oc
@@ -22,16 +29,32 @@ res1$oc
 # this call will generate d (distance for random looks around the look locations)
 # based on "floor(min(nn - c(0,nn[-length(nn)]))/2)" as d is missing:
 res2 <- ocPostprobDist(
-  nn = c(10, 20, 30), p = 0.4, deltaE = 0.1, deltaF = -0.1, tL = 0.6, tU = 0.6,
-  parE = c(1, 1), parS = c(5, 25), ns = 100, nr = TRUE
+  nn = c(10, 20, 30),
+  p = 0.4,
+  deltaE = 0.1,
+  deltaF = -0.1,
+  tL = 0.6,
+  tU = 0.6,
+  parE = c(1, 1),
+  parS = c(5, 25),
+  ns = 100, nr = TRUE
 )
 
 res2$oc
 
 # specify the distance for random looks around the look locations in nn (d=5 for illustration)
 res3 <- ocPostprobDist(
-  nn = c(10, 20, 30), p = 0.4, deltaE = 0.1, deltaF = -0.1, tL = 0.6, tU = 0.6,
-  parE = c(1, 1), parS = c(5, 25), ns = 100, nr = TRUE, d = 5
+  nn = c(10, 20, 30),
+  p = 0.4,
+  deltaE = 0.1,
+  deltaF = -0.1,
+  tL = 0.6,
+  tU = 0.6,
+  parE = c(1, 1),
+  parS = c(5, 25),
+  ns = 100,
+  nr = TRUE,
+  d = 5
 )
 
 res3$oc

examples/pbetaMix.R

@@ -1,32 +1,16 @@
-## 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)
+pbetaMix(q = 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)
+# Can get the one minus CDF values.
+pbetaMix(q = 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)),
+  q = 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)),
+  q = 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(
+  p = 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)),
+  p = 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)),
+  p = 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