corGrafen                package:ape                R Documentation

_G_r_a_f_e_n'_s (_1_9_8_9) _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:

     rafen's (1989) covariance structure. Branch lengths are computed
     using Grafen's method (see 'compute.brlen'). The covariance
     matrice is then the traditional variance-covariance matrix for a
     phylogeny.

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

     corGrafen(value=numeric(0), phy, form=~1, fixed = FALSE)
     ## S3 method for class 'corGrafen':
     coef(object, unconstrained = TRUE, ...)
     ## S3 method for class 'corGrafen':
     corMatrix(object,
                       covariate = getCovariate(object), corr = TRUE, ...)

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

   value: The rho parameter

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

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

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

   fixed: an optional logical value indicating whether the coefficients
          should be allowed to vary in the optimization, or kept fixed
          at their initial value. Defaults to 'FALSE', in which case
          the coefficients are allowed to vary.

    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 'corGrafen' or the rho coefficient from an
     object of this class 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:

     Grafen, A. (1989) The phylogenetic regression. _Philosophical
     Transactions of the Royal society of London. Series B. Biological
     Sciences_, *326*, 119-157.

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

     'corClasses', 'compute.brlen', 'vcv.phylo'.

