Allow different type for elementwise log

examples/basics.jl

@@ -259,5 +259,6 @@ hcat(initialization(hmm_est_concat), initialization(hmm))
 
 control_seq = fill(nothing, last(seq_ends));  #src
 test_identical_hmmbase(rng, hmm, 100; hmm_guess)  #src
+test_identical_hmmbase(rng, transpose_hmm(hmm), 100; transpose_hmm(hmm_guess))  #src
 test_coherent_algorithms(rng, hmm, control_seq; seq_ends, hmm_guess)  #src
 test_type_stability(rng, hmm, control_seq; seq_ends, hmm_guess)  #src

libs/HMMTest/src/HMMTest.jl

@@ -9,11 +9,13 @@ using Random: AbstractRNG
 using Statistics: mean
 using Test: @test, @testset, @test_broken
 
+export transpose_hmm
 export test_equal_hmms, test_coherent_algorithms
 export test_identical_hmmbase
 export test_allocations
 export test_type_stability
 
+include("utils.jl")
 include("coherence.jl")
 include("allocations.jl")
 include("hmmbase.jl")

libs/HMMTest/src/utils.jl

@@ -0,0 +1,8 @@
+function transpose_hmm(hmm::HMM)
+    init = initial_distribution(hmm)
+    trans = transition_matrix(hmm)
+    dists = obs_distributions(hmm)
+    trans_transpose = transpose(convert(typeof(trans), transpose(trans)))
+    @assert trans_transpose == trans
+    return HMM(init, trans_transpose, dists)
+end

src/types/hmm.jl

@@ -7,21 +7,31 @@ Basic implementation of an HMM.
 
 $(TYPEDFIELDS)
 """
-struct HMM{V<:AbstractVector,M<:AbstractMatrix,VD<:AbstractVector} <: AbstractHMM
+struct HMM{
+    V<:AbstractVector,
+    M<:AbstractMatrix,
+    VD<:AbstractVector,
+    Vl<:AbstractVector,
+    Ml<:AbstractMatrix,
+} <: AbstractHMM
     "initial state probabilities"
     init::V
     "state transition probabilities"
     trans::M
     "observation distributions"
     dists::VD
     "logarithms of initial state probabilities"
-    loginit::V
+    loginit::Vl
     "logarithms of state transition probabilities"
-    logtrans::M
+    logtrans::Ml
 
     function HMM(init::AbstractVector, trans::AbstractMatrix, dists::AbstractVector)
-        hmm = new{typeof(init),typeof(trans),typeof(dists)}(
-            init, trans, dists, elementwise_log(init), elementwise_log(trans)
+        log_init = elementwise_log(init)
+        log_trans = elementwise_log(trans)
+        hmm = new{
+            typeof(init),typeof(trans),typeof(dists),typeof(log_init),typeof(log_trans)
+        }(
+            init, trans, dists, log_init, log_trans
         )
         @argcheck valid_hmm(hmm)
         return hmm