corBrownian               package:ape               R Documentation

_B_r_o_w_n_i_a_n _C_o_r_r_e_l_a_t_i_o_n _S_t_r_u_c_t_u_r_e

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

     Expected covariance under a Brownian model (Felsenstein 1985,
     Martins and Hansen 1997): 

                           Vij = gamma . ta

     where ta is the distance on the phylogeny between the root and the
     most recent common ancestor of taxa i and j and gamma is a
     constant.

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

             corBrownian(value=1, phy, form=~1)
             ## S3 method for class 'corBrownian':
             coef(object, unconstrained = TRUE, ...)
             ## S3 method for class 'corBrownian':
             corMatrix(object,
                             covariate = getCovariate(object), corr = TRUE, ...)

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

   value: The gamma parameter (default to 1)

     phy: An object of class 'phylo' representing the phylogeny (with
          branch lengths) to consider

  object: An (initialized) object of class 'corBrownian'

    corr: a logical value. If 'TRUE' the function returns the
          correlation matrix, otherwise it returns the
          variance/covariance matrix.

    form: ignored for now.

covariate: ignored for now.

unconstrained: a logical value. If 'TRUE' the coefficients are returned
          in unconstrained form (the same used in the optimization
          algorithm). If 'FALSE' the coefficients are returned in
          "natural", possibly constrained, form. Defaults to 'TRUE'

     ...: some methods for these generics require additional arguments.
          None are used in these methods.

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

     An object of class 'corBrownian' or coefficient from an object of
     this class (actually sends 'numeric(0)'!) or the correlation
     matrix of an initialized object of this class.

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

     Julien Dutheil julien.dutheil@univ-montp2.fr

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

     Felsenstein, J. (1985) Phylogenies and the comparative method.
     _American Naturalist_, *125*, 1-15.

     Martins, E. P. and Hansen, T. F. (1997) Phylogenies and the
     comparative method: a general approach to incorporating
     phylogenetic information into the analysis of interspecific data.
     _American Naturalist_, *149*, 646-667.

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

     'corClasses'.

