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'

