birthdeath                package:ape                R Documentation

_E_s_t_i_m_a_t_i_o_n _o_f _S_p_e_c_i_a_t_i_o_n _a_n_d _E_x_t_i_n_c_t_i_o_n _R_a_t_e_s _W_i_t_h _B_i_r_t_h-_D_e_a_t_h _M_o_d_e_l_s

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

     This function fits by maximum likelihood a birth-death model to
     the branching times computed from a phylogenetic tree using the
     method of Nee et al. (1994).

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

     birthdeath(phy)
     ## S3 method for class 'birthdeath':
     print(x, ...)

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

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

       x: an object of class '"birthdeath"'.

     ...: further arguments passed to the 'print' function.

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

     Nee et al. (1994) used a re-parametrization of the birth-death
     model studied by Kendall (1948) so that the likelihood has to be
     maximized over _d/b_ and _b - d_, where _b_ is the birth rate, and
     _d_ the death rate. This is the approach used by the present
     function.

     This function computes the standard-errors of the estimated
     parameters using a normal approximations of the maximum likelihood
     estimates: this is likely to be inaccurate because of asymmetries
     of the likelihood function (Nee et al. 1995). In addition, 95 
     intervals of both parameters are computed using profile
     likelihood: they are particularly useful if the estimate of _d/b_
     is at the boundary of the parameter space (i.e. 0, which is often
     the case).

     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.

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

     An object of class '"birthdeath"' which is a list with the
     following components: 

    tree: the name of the tree analysed.

       N: the number of species.

     dev: the deviance (= -2 log lik) at its minimum.

    para: the estimated parameters.

      se: the corresponding standard-errors.

      CI: the 95% profile-likelihood confidence intervals.

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

     Emmanuel Paradis paradis@isem.univ-montp2.fr

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

     Kendall, D. G. (1948) On the generalized ``birth-and-death''
     process. _Annals of Mathematical Statistics_, *19*, 1-15.

     Nee, S., May, R. M. and Harvey, P. H. (1994) The reconstructed
     evolutionary process. _Philosophical Transactions of the Royal
     Society of London. Series B. Biological Sciences_, *344*, 305-311.

     Nee, S., Holmes, E. C., May, R. M. and Harvey, P. H. (1995)
     Estimating extinctions from molecular phylogenies. in _Extinction
     Rates_, eds. Lawton, J. H. and May, R. M., pp. 164-182, Oxford
     University Press.

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

     'branching.times', 'diversi.gof', 'diversi.time', 'ltt.plot',
     'yule', 'bd.ext', 'yule.cov'

