update docs

helske · Nov 8, 2024 · 36206c1 · 36206c1
1 parent 99d6883
commit 36206c1
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Showing 6 changed files with 19 additions and 9 deletions.
diff --git a/R/fit_nhmm.R b/R/fit_nhmm.R
@@ -243,7 +243,7 @@ fit_nhmm <- function(model, inits, init_sd, restarts, lambda, method,
 
       logliks <- unlist(lapply(out, "[[", "penalized_logLik")) * n_obs
       optimum <- out[[which.max(logliks)]]
-      init <- setNames(
+      init <- stats::setNames(
         optimum[c("eta_pi", "eta_A", "eta_B")], c("pi", "A", "B")
       )
       if (save_all_solutions) {

diff --git a/man/estimate_mnhmm.Rd b/man/estimate_mnhmm.Rd
diff --git a/man/estimate_nhmm.Rd b/man/estimate_nhmm.Rd
diff --git a/tests/testthat/test-build_hmm.R b/tests/testthat/test-build_hmm.R
@@ -83,11 +83,11 @@ test_that("build_hmm returns the correct probabilities", {
 
   expect_equal(
     rowSums(model$transition_probs),
-    setNames(rep(1, s), paste("State", 1:s))
+    stats::setNames(rep(1, s), paste("State", 1:s))
   )
   expect_equal(
     rowSums(model$emission_probs),
-    setNames(rep(1, s), paste("State", 1:s))
+    stats::setNames(rep(1, s), paste("State", 1:s))
   )
   expect_equal(colnames(model$emission_probs), letters[1:s])
   expect_true(all(model$transition_probs >= 0))

diff --git a/tests/testthat/test-build_mm.R b/tests/testthat/test-build_mm.R
@@ -86,11 +86,11 @@ test_that("build_mm returns the correct probabilities", {
   )
   expect_equal(
     rowSums(model$transition_probs),
-    setNames(rep(1, s), letters[1:s])
+    stats::setNames(rep(1, s), letters[1:s])
   )
   expect_equal(
     rowSums(model$emission_probs),
-    setNames(rep(1, s), letters[1:s])
+    stats::setNames(rep(1, s), letters[1:s])
   )
   expect_true(all(model$transition_probs >= 0))
   expect_true(all(model$emission_probs >= 0))

diff --git a/tests/testthat/test-build_mmm.R b/tests/testthat/test-build_mmm.R
@@ -68,6 +68,6 @@ test_that("build_mmm returns the correct number of states", {
   )
   expect_equal(
     lengths(model$initial_probs),
-    setNames(rep(s, k), paste("Cluster", 1:k))
+    stats::setNames(rep(s, k), paste("Cluster", 1:k))
   )
 })