test for dbetabinom.R (#7)

* cleaning up dbetabinom * removed rounding, not needed * rmarkdown language and assert for dbetabinom * changed x and m to number instead of numeric * test2 * testing dbetabinomMix and asserting inputs * for dbetabinom and dbetabinomMix, created/edited : test functions and example files * syntax * update dbetabinom.R * 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 tests/testthat/test-dbetabinom.R Co-authored-by: Daniel Sabanes Bove <[email protected]> * Update tests/testthat/test-dbetabinom.R Co-authored-by: Daniel Sabanes Bove <[email protected]> * Update tests/testthat/test-dbetabinom.R Co-authored-by: Daniel Sabanes Bove <[email protected]> * Update R/dbetabinom.R Co-authored-by: Daniel Sabanes Bove <[email protected]> * periods * [skip actions] Roxygen Man Pages Auto Update * added period for roxygen document added log option in dbetabinom document build successful * [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]> * [skip actions] Roxygen Man Pages Auto Update * log in dbetabinomMix * assert_flag for log input * Update R/dbetabinom.R Co-authored-by: Daniel Sabanes Bove <[email protected]> * polish and fix tests --------- 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>
Genentech · Aug 25, 2023 · e649e9c · e649e9c
1 parent be3c928
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diff --git a/.gitignore b/.gitignore
@@ -28,3 +28,7 @@ vignettes/*.md
 vignettes/*.R
 coverage.*
 .vscode/
+
+tests/testthat/junit-result.xml
+
+tests/unit_testing_results.rds
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -42,6 +42,8 @@ Roxygen:
 RoxygenNote: 7.2.3
 Config/Needs/documentation:
     roxytypes
+Remotes:
+    openpharma/roxytypes
 Config/roxytypes: list(format = "({type}):\\cr {description}")
 Collate:
     'Phase1b-package.R'

diff --git a/R/dbetabinom.R b/R/dbetabinom.R
@@ -1,47 +1,73 @@
 #' Beta-binomial density function
 #'
-#' Calculates the density function of the beta-binomial distribution
+#' @description `r lifecycle::badge("experimental")`
 #'
-#' Note that \code{x} can be a vector.
+#' Calculates the density function of the beta-binomial distribution.
 #'
 #' The beta-binomial density function has the following form:
-#' \deqn{p(x) = (m! / (x!*(m-x)!)) * Beta(x+a,m-x+b) / Beta(a,b)}
-#'
-#' @param x number of successes
-#' @param m number of trials
-#' @param a first parameter of the beta distribution
-#' @param b second parameter of the beta distribution
-#' @return the density values of the beta-binomial distribution at \code{x}
+#' `p(x) = (m! / (x!*(m-x)!)) * Beta(x+a,m-x+b) / Beta(a,b)`
+#'
+#' @typed x : numeric
+#'  number of successes.
+#' @typed m : number
+#'  number of trials.
+#' @typed a : numeric
+#'  first parameter of the beta distribution.
+#' @typed b : numeric
+#'  second parameter of the beta distribution.
+#' @typed log : flag
+#'  whether to return the log density value (not default).
+#' @return The density values of the beta-binomial distribution at `x`.
+#'
+#' @note `x`, `a` and `b` can be vectors.
 #'
 #' @example examples/dbetabinom.R
 #' @export
-dbetabinom <- function(x, m, a, b) {
-  logRet <- lchoose(m, x) + lbeta(x + a, m - x + b) - lbeta(a, b)
-  exp(logRet)
+dbetabinom <- function(x, m, a, b, log = FALSE) {
+  assert_numeric(x, lower = 0, upper = m, finite = TRUE)
+  assert_number(m, lower = 0, finite = TRUE)
+  assert_numeric(a, lower = 0, finite = TRUE)
+  assert_numeric(b, lower = 0, finite = TRUE)
+  assert_flag(log)
+  log_ret <- lchoose(m, x) + lbeta(x + a, m - x + b) - lbeta(a, b)
+  if (log) {
+    log_ret
+  } else {
+    exp(log_ret)
+  }
 }
 
 
 #' Beta-mixture-binomial density function
 #'
-#' Calculates the density function for a mixture of beta-binomial distributions.
+#' @description `r lifecycle::badge("experimental")`
 #'
-#' Note that \code{x} can be a vector.
-#'
-#' @param x number of successes
-#' @param m number of trials
-#' @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 log return the log value? (not default)
-#' @return The (log) density values of the mixture of beta-binomial distributions at \code{x}.
+#' Calculates the density function for a mixture of beta-binomial distributions.
 #'
+#' @typed x : numeric
+#'  number of successes.
+#' @typed m : number
+#'  number of trials.
+#' @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.
+#' @typed log : flag
+#'  whether to return the log density value (not default).
+#' @return The (log) density values of the mixture of beta-binomial distributions at `x`.
+#' @note `x` can be a vector.
+#'
+#' @example examples/dbetabinomMix.R
 #' @export
 dbetabinomMix <- function(x, m, par, weights, log = FALSE) {
+  assert_matrix(par, min.rows = 1, min.cols = 2)
+  assert_flag(log)
   ret <- sum(weights * dbetabinom(x, m, par[, 1], par[, 2]))
   if (log) {
-    return(log(ret))
+    log(ret)
   } else {
-    return(ret)
+    ret
   }
 }
 dbetabinomMix <- Vectorize(dbetabinomMix, vectorize.args = "x")
@@ -98,7 +124,7 @@ getBetamixPost <- function(x, n, par, weights) {
 
 #' Beta-mixture density function
 #'
-#' Note that \code{x} can be a vector.
+#' Note that `x` can be a vector.
 #'
 #' @param x the abscissa
 #' @param par the beta parameters matrix, with K rows and 2 columns,
@@ -121,15 +147,15 @@ dbetaMix <- Vectorize(dbetaMix, vectorize.args = "x")
 
 #' Beta-mixture cdf
 #'
-#' Note that \code{x} can be a vector.
+#' Note that `x` can be a vector.
 #'
-#' @param x the abscissa
+#' @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
+#' 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
+#' and otherwise `P[X > x]`.
+#' @return the (one minus) cdf value.
 #'
 #' @export
 pbetaMix <- function(x, par, weights, lower.tail = TRUE) {
@@ -141,13 +167,13 @@ pbetaMix <- Vectorize(pbetaMix, vectorize.args = "x")
 
 #' Beta-mixture quantile function
 #'
-#' Note that \code{q} can be a vector.
+#' Note that `x` can be a vector.
 #'
-#' @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
+#' @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.
 #'
 #' @export
 qbetaMix <- function(q, par, weights) {

diff --git a/examples/dbetabinom.R b/examples/dbetabinom.R
@@ -1,10 +1,5 @@
-## Calculating the beta binomial density, x = 2; m = 29; a = 0.2; b = 0.4
-##
-## when p(x) = choose(29,2)*beta(2.2,27.4)/beta(0.2,0.4) = 0.04286893
-##
-dbetabinom(2, 29, 0.2, 0.4)
+dbetabinom(x = 2, m = 29, a = 0.2, b = 0.4, log = FALSE)
 
-## Can also specify x as a vector, x = 1:28
-##
-##
-dbetabinom(1:28, 29, 0.2, 0.4)
+# Can also specify x as a vector.
+
+dbetabinom(x = 1:28, m = 29, a = 0.2, b = 0.4, log = FALSE)
diff --git a/examples/dbetabinomMix.R b/examples/dbetabinomMix.R
@@ -1,26 +1,10 @@
-## Calculating the density of a mixture
-## of beta binomial densities at x, x = 2; m = 29; a = 0.2; b = 0.4
-##
-##
-## Only 1 mixture component, i.e., weights = 1, p(x) = choose(29,2)*beta(2.2,27.4)/beta(0.2,0.4) = 0.04286893
-##
-##
 dbetabinomMix(x = 2, m = 29, 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
-## when p(x) = 0.6*choose(29,2)*beta(2.2,27.4)/beta(0.2,0.4) + 0.4*choose(29,2)*beta(3,28)/beta(1,1) = 0.03905469
-##
-##
 dbetabinomMix(
   x = 2, m = 29, par = rbind(c(0.2, 0.4), c(1, 1)),
   weights = c(0.6, 0.4)
 )
-
-## Can also specify x as a vector, x = 1:28
-##
-##
+# x could be a vector
 dbetabinomMix(
   x = 1:28, m = 29, par = rbind(c(0.2, 0.4), c(1, 1)),
   weights = c(0.6, 0.4)

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1630,6 +1630,7 @@ datepicker
 datetime
 db<U+034A>
 dBe
+dbetabinom
 DCBCBC
 dcc
 DCC

diff --git a/man/dbetabinom.Rd b/man/dbetabinom.Rd
diff --git a/man/dbetabinomMix.Rd b/man/dbetabinomMix.Rd
diff --git a/man/pbetaMix.Rd b/man/pbetaMix.Rd
diff --git a/man/qbetaMix.Rd b/man/qbetaMix.Rd
-Original file line number
+Diff line change
@@ Expand Up / @@ -1630,6 +1630,7 @@ datepicker @@
     datetime
     db<U+034A>
     dBe
+    dbetabinom
     DCBCBC
     dcc
     DCC
@@ Expand Down @@