API Reference
=============

.. toctree::
   :maxdepth: 1

   modules/combine_states
   modules/cutpoints
   modules/deepest_ti
   modules/expm
   modules/get_emission_prob_mat
   modules/get_joint_prob_mat
   modules/get_tab
   modules/get_trans_emiss
   modules/helper_omegas
   modules/int_combine_states
   modules/int_get_emission_prob_mat
   modules/int_get_joint_prob_mat
   modules/int_get_ordered
   modules/int_get_tab
   modules/int_get_times
   modules/int_get_trans_emiss
   modules/int_load_trans_mat
   modules/int_optimizer
   modules/int_shared_data
   modules/int_vanloan
   modules/ncpu
   modules/optimizer
   modules/read_data
   modules/run_markov_chain_AB
   modules/run_markov_chain_ABC
   modules/trans_mat
   modules/vanloan
   modules/workflow_int_optimize
   modules/workflow_int_posterior
   modules/workflow_int_viterbi
   modules/workflow_optimize
   modules/workflow_posterior
   modules/workflow_viterbi
   modules/yaml_helpers