gammaStat                package:ape                R Documentation

_G_a_m_m_a-_S_t_a_t_i_s_t_i_c _o_f _P_y_b_u_s _a_n_d _H_a_r_v_e_y

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

     This function computes the gamma-statistic which summarizes the
     information contained in the inter-node intervals of a phylogeny.
     It is assumed that the tree is ultrametric. Note that the function
     does not check that the tree is effectively ultrametric, so if it
     is not, the returned result may not be meaningful.

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

     gammaStat(phy)

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

     phy: an object of class '"phylo"'.

_D_e_t_a_i_l_s:

     The gamma-statistic is a summary of the information contained in
     the inter-node intervals of a phylogeny; it follows, under the
     assumption that the clade diversified with constant rates, a
     normal distribution with mean zero and standard-deviation unity
     (Pybus and Harvey 2000). Thus, the null hypothesis that the clade
     diversified with constant rates may be tested with '1 -
     2*pnorm(abs(gammaStat(phy)))' for a two-tailed test, or '1 -
     pnorm(abs(gammaStat(phy)))' for a one-tailed test, both returning
     the corresponding P-value.

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

     a numeric vector of length one.

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

     Emmanuel Paradis paradis@isem.univ-montp2.fr

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

     Pybus, O. G. and Harvey, P. H. (2000) Testing macro-evolutionary
     models using incomplete molecular phylogenies. _Proceedings of the
     Royal Society of London. Series B. Biological Sciences_, *267*,
     2267-2272.

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

     'branching.times', 'ltt.plot', 'skyline'

