time index as numeric, symbol names as character

R/ame_obs.R

@@ -102,7 +102,7 @@ ame_obs.nhmm <- function(
   X2 <- update(model, newdata)[c("X_pi", "X_A", "X_B")]
   C <- model$n_channels
   if (C == 1L) {
-    times <- colnames(model$observations)
+    times <- as.numeric(colnames(model$observations))
     symbol_names <- list(model$symbol_names)
     obs <- create_obsArray(model)[1L, , ]
     out <- ame_obs_nhmm_singlechannel( 
@@ -121,14 +121,14 @@ ame_obs.nhmm <- function(
     )
     d <- data.frame(
       observation = model$symbol_names,
-      time = rep(colnames(model$observations), each = model$n_symbols),
+      time = rep(as.numeric(colnames(model$observations)), each = model$n_symbols),
       estimate = c(out$point_estimate)
     )
     for(i in seq_along(probs)) {
       d[paste0("q", 100 * probs[i])] <- c(out$quantiles[, , i])
     }
   } else {
-    times <- colnames(model$observations[[1]])
+    times <- as.numeric(colnames(model$observations[[1]]))
     symbol_names <- model$symbol_names
     obs <- create_obsArray(model)
     out <- ame_obs_nhmm_multichannel( 
@@ -147,7 +147,7 @@ ame_obs.nhmm <- function(
     )
     d <- data.frame(
       observation = model$symbol_names,
-      time = rep(colnames(model$observations), each = model$n_symbols),
+      time = rep(as.numeric(colnames(model$observations)), each = model$n_symbols),
       estimate = c(out$point_estimate)
     )
     for(i in seq_along(probs)) {

R/ame_param.R

@@ -86,10 +86,10 @@ ame_param.nhmm <- function(
   model2 <- update(model, newdata)
   C <- model$n_channels
   if (C == 1L) {
-    times <- colnames(model$observations)
+    times <- as.numeric(colnames(model$observations))
     symbol_names <- list(model$symbol_names)
   } else {
-    times <- colnames(model$observations[[1]])
+    times <- as.numeric(colnames(model$observations[[1]]))
     symbol_names <- model$symbol_names
   }
   if (attr(model$X_pi, "icpt_only")) {

R/get_probs.R

@@ -97,10 +97,10 @@ get_transition_probs.nhmm <- function(model, probs, remove_voids = TRUE, ...) {
   model$X_A[attr(model$X_A, "missing")] <- NA
   if (model$n_channels == 1L) {
     ids <- rownames(model$observations)
-    times <- colnames(model$observations)
+    times <- as.numeric(colnames(model$observations))
   } else {
     ids <- rownames(model$observations[[1]])
-    times <- colnames(model$observations[[1]])
+    times <- as.numeric(colnames(model$observations[[1]]))
   }
   if (!attr(model$X_A, "iv")) {
     X <- model$X_A[, , 1L, drop = FALSE]
@@ -182,12 +182,12 @@ get_emission_probs.nhmm <- function(model, probs, remove_voids = TRUE, ...) {
   model$X_B[attr(model$X_B, "missing")] <- NA
   if (C == 1L) {
     ids <- rownames(model$observations)
-    times <- colnames(model$observations)
+    times <- as.numeric(colnames(model$observations))
     symbol_names <- list(model$symbol_names)
     model$gammas$B <- list(model$gammas$B)
   } else {
     ids <- rownames(model$observations[[1]])
-    times <- colnames(model$observations[[1]])
+    times <- as.numeric(colnames(model$observations[[1]]))
     symbol_names <- model$symbol_names
   }
   if (!attr(model$X_B, "iv")) {

R/simulate_mnhmm.R

@@ -53,7 +53,11 @@ simulate_mnhmm <- function(
   )
   sequence_lengths <- rep(sequence_lengths, length.out = n_sequences)
   n_channels <- length(n_symbols)
-  symbol_names <- lapply(seq_len(n_channels), function(i) seq_len(n_symbols[i]))
+  symbol_names <- lapply(
+    seq_len(n_channels), function(i) {
+      as.character(seq_len(n_symbols[i]))
+    }
+  )
   T_ <- max(sequence_lengths)
   obs <- lapply(seq_len(n_channels), function(i) {
     suppressWarnings(suppressMessages(
@@ -98,7 +102,7 @@ simulate_mnhmm <- function(
     gamma_B <- c(eta_to_gamma_cube_field(unlist(model$etas$B, recursive = FALSE)))
     model$gammas$B <- split(gamma_B, rep(seq_along(l), l))
   }
-
+  
   model$gammas$omega <- eta_to_gamma_mat(
     model$etas$omega
   )
@@ -120,7 +124,7 @@ simulate_mnhmm <- function(
       model$n_symbols
     )
   }
-
+  
   for (i in seq_len(model$n_sequences)) {
     Ti <- sequence_lengths[i]
     if (Ti < T_) {
@@ -143,7 +147,7 @@ simulate_mnhmm <- function(
       alphabet = state_names, cnames = seq_len(T_)
     )
   ))
-
+  
   if (n_channels == 1) {
     dim(out$observations) <- dim(out$observations)[2:3]
     out$observations[] <- symbol_names[c(out$observations) + 1]

R/simulate_nhmm.R

@@ -47,7 +47,11 @@ simulate_nhmm <- function(
   )
   sequence_lengths <- rep(sequence_lengths, length.out = n_sequences)
   n_channels <- length(n_symbols)
-  symbol_names <- lapply(seq_len(n_channels), function(i) seq_len(n_symbols[i]))
+  symbol_names <- lapply(
+    seq_len(n_channels), function(i) {
+      as.character(seq_len(n_symbols[i]))
+    }
+  )
   T_ <- max(sequence_lengths)
   obs <- lapply(seq_len(n_channels), function(i) {
     suppressWarnings(suppressMessages(