corMartins                package:ape                R Documentation

_M_a_r_t_i_n_s'_s (_1_9_9_7) _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:

     Martins and Hansen's (1997) covariance structure: 

                   Vij = gamma . exp(-alpha . tij)

     where tij is the phylogenetic distance between taxa i and j and
     gamma is a constant.

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

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

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

   value: The alpha parameter

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

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

    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, ok 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 'corMartins' or the alpha 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:

     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'.

