alpha, stats::, docs

R/simulate_pars.R

@@ -20,31 +20,32 @@ 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
   }
 }
 #' @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)
   } else {
     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)
@@ -64,15 +65,16 @@ 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]])
       }
     }
   } 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]])
     }