cherry                  package:ape                  R Documentation

_N_u_m_b_e_r _o_f _C_h_e_r_r_i_e_s _a_n_d _N_u_l_l _M_o_d_e_l_s _o_f _T_r_e_e_s

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

     This function calculates the number of cherries (see definition
     below) on a phylogenetic tree, and tests the null hypotheses
     whether this number agrees with those predicted from two null
     models of trees (the Yule model, and the uniform model).

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

     cherry(phy)

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

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

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

     A cherry is a pair of adjacent tips on a tree. The tree can be
     either rooted or unrooted, but the present function considers only
     rooted trees. The probability distribution function of the number
     of cherries on a tree depends on the speciation/extinction model
     that generated the tree.

     McKenzie and Steel (2000) derived the probability distribution
     function of the number of cherries for two models: the Yule model
     and the uniform model. Broadly, in the Yule model, each extant
     species is equally likely to split into two daughter-species; in
     the uniform model, a branch is added to tree on any of the already
     existing branches with a uniform probability.

     The probabilities are computed using recursive formulae; however,
     for both models, the probability density function converges to a
     normal law with increasing number of tips in the tree. The
     function uses these normal approximations for a number of tips
     greater than or equal to 20.

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

     A NULL value is returned, the results are simply printed.

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

     Emmanuel Paradis paradis@isem.univ-montp2.fr

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

     McKenzie, A. and Steel, M. (2000) Distributions of cherries for
     two models of trees. _Mathematical Biosciences_, *164*, 81-92.

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

     'gammaStat'

