stopifnot to stopifnot_

R/estimate_coef.R

@@ -9,7 +9,7 @@
 #' @param threads Number of threads to use in parallel computing. 
 #' The default is 1.
 estimate_coef <- function(model, threads = 1) {
-  stopifnot(
+  stopifnot_(
     inherits(model, "mhmm"),
     "{.arg model} must be a {.cls mhmm} object."
   )

R/simulate_mnhmm.R

@@ -92,7 +92,9 @@ simulate_mnhmm <- function(
   times <- sort(unique(data[[time]]))
   clusters <- character(n_sequences)
   cluster_names <- model$cluster_names
-  state_names <- paste0(rep(cluster_names, each = S), ": ", model$state_names)
+  state_names <- paste0(
+    rep(cluster_names, each = model$n_states), ": ", model$state_names
+  )
   for (i in seq_len(n_sequences)) {
     p_cluster <- probs$cluster[
       probs$cluster[[time]] == time[1] & probs$cluster[[id]] == ids[i],
@@ -115,7 +117,7 @@ simulate_mnhmm <- function(
       obs[1, k, i] <- sample(symbol_names[[k]], 1, prob = p_emission)
     }
   }
-
+  
   for (i in seq_len(n_sequences)) {
     for (t in 2:sequence_lengths[i]) {
       p_transition <- probs$transition[
@@ -147,7 +149,7 @@ simulate_mnhmm <- function(
   obs <- lapply(seq_len(n_channels), function(i) {
     suppressWarnings(suppressMessages(
       seqdef(t(obs[, i, ]), alphabet = symbol_names[[i]])
-      ))
+    ))
   })
   names(obs) <- model$channel_names
   if (n_channels == 1) obs <- obs[[1]]

tests/testthat/test-estimate_coef.R

@@ -1,6 +1,7 @@
 
 test_that("'estimate_coef' works for 'mhmm'", {
   set.seed(123)
+  data("mhmm_biofam")
   expect_error(
     out <- estimate_coef(mhmm_biofam),
     NA
@@ -10,13 +11,14 @@ test_that("'estimate_coef' works for 'mhmm'", {
 
 test_that("'estimate_coef' errors for 'hmm'", {
   set.seed(123)
+  data("hmm_biofam")
   expect_error(
     out <- estimate_coef(hmm_biofam),
     "`model` must be a `mhmm` object."
   )
 })
 test_that("'estimate_coef' errors for incorrect 'threads'", {
-  set.seed(123)
+  data("mhmm_biofam")
   expect_error(
     out <- estimate_coef(mhmm_biofam, threads = "a"),
     "Argument `threads` must be a single positive integer"

tests/testthat/test-fit_model.R

@@ -31,7 +31,6 @@ test_that("'fit_model' works for 'hmm'", {
     ),
     NA
   )
-  expect_error(print(fit$model), NA)
 })
 
 test_that("'fit_model' works for 'mhmm'", {
@@ -94,5 +93,4 @@ test_that("'fit_model' works for 'mhmm'", {
     ),
     NA
   )
-  expect_error(print(fit$model), NA)
 })

tests/testthat/test-forward_backward.R

@@ -50,7 +50,7 @@ test_that("'forward_backward' works for multichannel 'nhmm'", {
   )
   expect_gte(min(fb$forward_probs), -200)
   expect_gte(min(fb$backward_probs), -200)
-  expect_lte(max(fb$forward_probs), -5)
+  expect_lte(max(fb$forward_probs), 0)
   expect_lte(max(fb$backward_probs), 0)
 
   expect_error(