lagtime                package:PhySim                R Documentation

_C_o_r_r_e_c_t_i_o_n _f_o_r _l_a_g-_t_i_m_e _t_o _s_p_e_c_i_a_t_i_o_n _a_l_o_n_g _a _p_h_y_l_o_g_e_n_y

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

     Each node is classified as an interspecific or intraspecific
     phylogenetic split  by drawing a lag-time to speciaton randomly
     from a exponential distribution of lag-times.  Beginning from the
     root, once a node is classified as a intraspecific split all of
     its  daughter lineages keep the same classification in order to
     maintain species as monophyletic. All nodes classified as
     intra-specific splits are pruned.

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

     lagtime(phy, rate)

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

     phy: a phylogenetic tree of class phylo

    rate: the average lag-time to speciation. 1 / rate is the rate
          parameter  of the exponential distribution used to model
          speciation along a phylogenetic tree.

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

     returns a phylogenetic tree of class phylo, possessing only
     inter-specific splits.

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

     Jason T. Weir

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

     Weir, J. T. and Schluter, D. 2007. Science in press

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

     'lagtime.batch', to model a lag-time to speciation for a batch of
     phylogenetic trees

_E_x_a_m_p_l_e_s:

      #Apply an average lag-time of 1
      tree <- birthdeath.tree(b=0.3, d=0, T=10)
      tree2 <- lagtime(phy=tree, rate = 1)

