From 57dcff2209ff3400d00bacbd5d875583d8cf8f36 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Wed, 15 Jan 2025 11:07:44 +0100
Subject: [PATCH] Replaced `randga()` with `rgamma()` (closes #9)

---
 NAMESPACE      |  1 +
 R/randdir.R    |  4 ++--
 R/randga.R     | 61 --------------------------------------------------
 man/randdir.Rd |  3 ---
 man/randga.Rd  | 25 ---------------------
 5 files changed, 3 insertions(+), 91 deletions(-)
 delete mode 100644 R/randga.R
 delete mode 100644 man/randga.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 3094ed5..0b79163 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -36,6 +36,7 @@ importFrom(matlab2r,times)
 importFrom(matlab2r,uiputfile)
 importFrom(matlab2r,zeros)
 importFrom(methods,is)
+importFrom(stats,rgamma)
 importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(utils,read.delim)
diff --git a/R/randdir.R b/R/randdir.R
index 7ee626d..066db2e 100644
--- a/R/randdir.R
+++ b/R/randdir.R
@@ -3,11 +3,11 @@
 #' @examples rBAPS:::randdir(matrix(c(10, 30, 60), 3), 3)
 #' @param counts shape parameter
 #' @param nc number of rows on output
-#' @seealso randga
+#' @importFrom stats rgamma
 randdir <- function(counts, nc) {
   svar <- zeros(nc, 1)
   for (i in 1:nc) {
-    svar[i, 1] <- randga(counts[i, 1], 1)
+    svar[i, 1] <- rgamma(1L, shape = counts[i, 1], rate = 1)
   }
   svar <- svar / sum(svar)
   return(svar)
diff --git a/R/randga.R b/R/randga.R
deleted file mode 100644
index 24fb960..0000000
--- a/R/randga.R
+++ /dev/null
@@ -1,61 +0,0 @@
-#' @title Generates random number from a Gamma distribution
-#' @description Generates one random number from shape parameter a and rate
-#' parameter b
-#' @param a shape
-#' @param b rate
-#' @return One realization of Gamma(a, b)
-#' @details The generated random variable has mean a / b. It will be
-#' positively-skewed for small values, but converges to a symmetric distribution
-#' for very large numbers of a and b.
-randga <- function(a, b) {
-  flag <- 0
-  if (a > 1) {
-    c1 <- a - 1
-    c2 <- (a - (1 / (6 * a))) / c1
-    c3 <- 2 / c1
-    c4 <- c3 + 2
-    c5 <- 1 / sqrt(a)
-    U1 <- 1
-    while (flag == 0) {
-      if (a <= 2.5) {
-        U1 <- rand()
-        U2 <- rand()
-      } else {
-        while (!(U1 > 0 & U1 < 1)) {
-          U1 <- rand()
-          U2 <- rand()
-          U1 <- U2 + c5 * (1 - 1.86 * U1)
-        }
-      }
-      W <- c2 * U2 / U1
-      if (c3 * U1 + W + (1 / W) <= c4) {
-        flag <- 1
-        g <- c1 * W / b
-      } else if (c3 * log(U1) - log(W) + W < 1) {
-        flag <- 1
-        g <- c1 * W / b
-      } else {
-        U1 <- -1
-      }
-    }
-  } else if (a == 1) {
-    g <- sum(-(1 / b) * log(rand(a, 1)))
-  } else {
-    while (flag == 0) {
-      U <- rand(2, 1)
-      if (U[1] > exp(1) / (a + exp(1))) {
-        g <- -log(((a + exp(1)) * (1 - U[1])) / (a * exp(1)))
-        if (U[2] <= g^(a - 1)) {
-          flag <- 1
-        }
-      } else {
-        g <- ((a + exp(1)) * U[1] / ((exp(1))^(1 / a)))
-        if (U[2] <= exp(-g)) {
-          flag <- 1
-        }
-      }
-    }
-    g <- g / b
-  }
-  return(g)
-}
diff --git a/man/randdir.Rd b/man/randdir.Rd
index 59c69b4..812a160 100644
--- a/man/randdir.Rd
+++ b/man/randdir.Rd
@@ -20,6 +20,3 @@ Generates random numbers
 \examples{
 rBAPS:::randdir(matrix(c(10, 30, 60), 3), 3)
 }
-\seealso{
-randga
-}
diff --git a/man/randga.Rd b/man/randga.Rd
deleted file mode 100644
index 7045249..0000000
--- a/man/randga.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/randga.R
-\name{randga}
-\alias{randga}
-\title{Generates random number from a Gamma distribution}
-\usage{
-randga(a, b)
-}
-\arguments{
-\item{a}{shape}
-
-\item{b}{rate}
-}
-\value{
-One realization of Gamma(a, b)
-}
-\description{
-Generates one random number from shape parameter a and rate
-parameter b
-}
-\details{
-The generated random variable has mean a / b. It will be
-positively-skewed for small values, but converges to a symmetric distribution
-for very large numbers of a and b.
-}