pedigree-class             package:lme4             R Documentation

_C_l_a_s_s "_p_e_d_i_g_r_e_e"

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

     Objects of class '"pedigree"' represent a set of individuals that
     can have two parents including their parent-child relations.  The
     terminology has been taken from cattle breeding.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("pedigree",
     ...)', or more conveniently, 'pedigree(sire= ., dam = ., label =
     .)'.

_S_l_o_t_s:

     '_s_i_r_e': integer vector (with some 'NA' entries), denoting a
          _previous_ entry in the pedigree corresponding to the current
          entry's "father".

     '_d_a_m': similarly as 'sire' for the "mother" of each entry.

     '_l_a_b_e_l': a '"character"' vector of the same length as 'sire' and
          'dam' giving a unique ID for the corresponding entry.

_M_e_t_h_o_d_s:

     _c_h_o_l 'signature(x = "pedigree"': returns the lower-triangular,
          sparse matrix (a 'dtCMatrix' object) that is the left
          Cholesky factor of the relationship matrix of the pedigree.
          .in -5

     _c_o_e_r_c_e 'signature(from = "pedigree", to = "dtCMatrix")': ... 

     _c_o_e_r_c_e 'signature(from = "pedigree", to = "data.frame")': ... 

     _h_e_a_d 'signature(x = "pedigree")': ... 

     _s_h_o_w 'signature(object = "pedigree")': ... 

     _t_a_i_l 'signature(x = "pedigree")': ... 

_R_e_f_e_r_e_n_c_e_s:

     R. A. Mrode, _Linear Models for the Prediction of Animal Breeding
     Values, 2nd ed_, CABI Publishing, 2005.

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

     'pedigree'

_E_x_a_m_p_l_e_s:

     ## Rather use, pedigree()!   The following is "raw code":
     ## Example from chapter 2 of Mrode (2005)
     p1 <- new("pedigree",
               sire = as.integer(c(NA,NA,1, 1,4,5)),
               dam  = as.integer(c(NA,NA,2,NA,3,2)),
               label = as.character(1:6))
     p1
     (dtc <- as(p1, "dtCMatrix"))   # T-inverse in Mrode's notation
     solve(dtc)
     chol(p1)  # (left) Cholesky factor of A, the relationship matrix

