transitionScale          package:VanillaICE          R Documentation

_S_c_a_l_e_s _t_h_e _t_r_a_n_s_i_t_i_o_n _p_r_o_b_a_b_i_l_i_t_i_e_s _o_f _t_h_e _h_i_d_d_e_n _M_a_r_k_o_v _m_o_d_e_l

_D_e_s_c_r_i_p_t_i_o_n:

     Accessor and replacement methods for scaling the transition
     probabilities

_U_s_a_g_e:

     transitionScale(object)
     transitionScale(object) <- value

_A_r_g_u_m_e_n_t_s:

  object: An object of class 'HmmParameter'

   value: 

     {A matrix of dimension STATES x STATES, where STATES is the number
     of hidden states.}

_D_e_t_a_i_l_s:

     The probability of remaining in the same state, $P(S_t = S_{t+1})$
     (the diagonal of the transition probability matrix) is a function
     of the distance between SNPs.  The probability of transitioning to
     some other state is epsilon, where epsilon = 1 - $P(S_t =
     S_{t+1})$.  The epsilon is split among STATES-1 states.  By
     default, the probability of transitioning from an altered state
     back to the normal state is twice as likely as the probability of
     transitioning between two altered states. The weights for epsilon
     are provided in the 'transitionScale' matrix in objects of class
     'HmmParameter'.

_V_a_l_u_e:

     A matrix

_A_u_t_h_o_r(_s):

     R. Scharpf

_S_e_e _A_l_s_o:

     'scaleTransitionProbability'

