From fb3fa6de4b41673925f5c2f8985270eb57839e28 Mon Sep 17 00:00:00 2001
From: Jouni Helske <jouni.helske@utu.fi>
Date: Wed, 25 Sep 2024 21:32:42 +0300
Subject: [PATCH] alpha, stats::, docs

---
 R/simulate_pars.R    | 16 +++++++++-------
 man/simulate_pars.Rd | 16 ++++++++--------
 2 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/R/simulate_pars.R b/R/simulate_pars.R
index b038a5ee..46d04d60 100644
--- a/R/simulate_pars.R
+++ b/R/simulate_pars.R
@@ -20,12 +20,12 @@ simulate_initial_probs <- function(n_states, n_clusters = 1, alpha = 1) {
   n_states <- rep(n_states, length = n_clusters)
   
   if (n_clusters == 1) {
-    x <- rgamma(n_states, alpha)
+    x <- stats::rgamma(n_states, alpha)
     x / sum(x)
   } else {
     probs <- vector("list", n_clusters)
     for (i in 1:n_clusters) {
-      x <- rgamma(n_states[i], alpha)
+      x <- stats::rgamma(n_states[i], alpha)
       probs[[i]] <- x / sum(x)
     }
     probs
@@ -33,10 +33,11 @@ simulate_initial_probs <- function(n_states, n_clusters = 1, alpha = 1) {
 }
 #' @export
 #' @rdname simulate_pars
-simulate_transition_probs <- function(n_states, n_clusters = 1, left_right = FALSE, diag_c = 0, alpha = 1) {
+simulate_transition_probs <- function(n_states, n_clusters = 1, 
+                                      left_right = FALSE, diag_c = 0, alpha = 1) {
   n_states <- rep(n_states, length = n_clusters)
   if (n_clusters == 1) {
-    x <- matrix(rgamma(n_states^2, alpha), n_states, n_states, TRUE) + 
+    x <- matrix(stats::rgamma(n_states^2, alpha), n_states, n_states, TRUE) + 
       diag(diag_c, n_states)
     if (left_right) x[lower.tri(x)] <- 0
     probs <- x / rowSums(x)
@@ -44,7 +45,7 @@ simulate_transition_probs <- function(n_states, n_clusters = 1, left_right = FAL
     probs <- vector("list", n_clusters)
     for (i in seq_len(n_clusters)) {
       x <- matrix(
-        rgamma(n_states[i]^2, alpha), n_states[i], n_states[i], TRUE
+        stats::rgamma(n_states[i]^2, alpha), n_states[i], n_states[i], TRUE
       ) + diag(diag_c, n_states[i])
       if (left_right) x[lower.tri(x)] <- 0
       probs[[i]] <- x / rowSums(x)
@@ -64,7 +65,7 @@ simulate_emission_probs <- function(n_states, n_symbols, n_clusters = 1,
       emiss[[i]] <- vector("list", n_channels)
       for (j in seq_len(n_channels)) {
         emiss[[i]][[j]] <- matrix(
-          rgamma(n_states[i] * n_symbols[j], alpha), n_states[i], n_symbols[j],
+          stats::rgamma(n_states[i] * n_symbols[j], alpha), n_states[i], n_symbols[j],
           TRUE)
         emiss[[i]][[j]] <- emiss[[i]][[j]] / rowSums(emiss[[i]][[j]])
       }
@@ -72,7 +73,8 @@ simulate_emission_probs <- function(n_states, n_symbols, n_clusters = 1,
   } else {
     for (i in seq_len(n_clusters)) {
       emiss[[i]] <- matrix(
-        rgamma(n_states[i] * n_symbols), n_states[i], n_symbols, TRUE
+        stats::rgamma(n_states[i] * n_symbols, alpha), n_states[i], n_symbols, 
+        TRUE
       )
       emiss[[i]] <- emiss[[i]] / rowSums(emiss[[i]])
     }
diff --git a/man/simulate_pars.Rd b/man/simulate_pars.Rd
index 2ed3f068..e752c8bc 100644
--- a/man/simulate_pars.Rd
+++ b/man/simulate_pars.Rd
@@ -6,22 +6,27 @@
 \alias{simulate_emission_probs}
 \title{Simulate Parameters of Hidden Markov Models}
 \usage{
-simulate_initial_probs(n_states, n_clusters = 1)
+simulate_initial_probs(n_states, n_clusters = 1, alpha = 1)
 
 simulate_transition_probs(
   n_states,
   n_clusters = 1,
   left_right = FALSE,
-  diag_c = 0
+  diag_c = 0,
+  alpha = 1
 )
 
-simulate_emission_probs(n_states, n_symbols, n_clusters = 1)
+simulate_emission_probs(n_states, n_symbols, n_clusters = 1, alpha = 1)
 }
 \arguments{
 \item{n_states}{Number of states in each cluster.}
 
 \item{n_clusters}{Number of clusters.}
 
+\item{alpha}{A scalar, or a vector of length S (number of states) or M
+(number of symbols) defining the parameters of the Dirichlet distribution
+used to simulate the probabilities.}
+
 \item{left_right}{Constrain the transition probabilities to upper triangular.
 Default is \code{FALSE}.}
 
@@ -34,8 +39,3 @@ These are helper functions for quick construction of initial values for various
 model building functions.
 Mostly useful for global optimization algorithms which do not depend on initial values.
 }
-\seealso{
-\code{\link[=build_hmm]{build_hmm()}}, \code{\link[=build_mhmm]{build_mhmm()}},
-\code{\link[=build_mm]{build_mm()}}, \code{\link[=build_mmm]{build_mmm()}}, and  \code{\link[=build_lcm]{build_lcm()}}
-for constructing different types of models.
-}