chronogram                package:ape                R Documentation

_C_h_r_o_n_o_g_r_a_m _C_o_m_p_u_t_e_d _b_y _N_o_n_p_a_r_a_m_e_t_r_i_c _R_a_t_e _S_m_o_o_t_h_i_n_g

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

     'chronogram' computes a chronogram from a phylogram by applying
     the NPRS (nonparametric rate smoothing) algorithm described in
     Sanderson (1997).

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

     chronogram(phy, scale = 1, expo = 2, minEdgeLength = 1e-06)

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

     phy: A phylogenetic tree (i.e. an object of class '"phylo"'),
          where the branch lengths are measured in substitutions.

   scale: Age of the root in the inferred chronogram (default value:
          0). 

    expo: Exponent in the objective function (default value: 2)

minEdgeLength: Minimum edge length in the phylogram (default value:
          1e-06). If any branch lengths are smaller then they will be
          set to this value.

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

     Please refer to Sanderson (1997) for mathematical details

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

     'chronogram' returns an object of class '"phylo"'. The branch
     lengths of this tree will be clock-like and scaled so that the
     root node has age 1 (or the value set by the option 'scale'

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

     Gangolf Jobb (<URL: http://www.treefinder.de>) and Korbinian
     Strimmer (<URL: http://www.stat.uni-muenchen.de/~strimmer/>)

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

     Sanderson, M. J. (1997) A nonparametric approach to estimating
     divergence times in the absence of rate constancy. _Molecular
     Biology and Evolution_, *14*, 1218-1231.

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

     'ratogram', 'NPRS.criterion'.

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

     library(ape)

     # get tree
     data("landplants.newick") # example tree in NH format
     tree.landplants <- read.tree(text = landplants.newick)

     # plot tree
     tree.landplants
     plot(tree.landplants, label.offset = 0.001)

     # estimate chronogram
     chrono.plants <- chronogram(tree.landplants)

     # plot and write to file
     plot(chrono.plants, label.offset = 0.001)
     write.tree(chrono.plants, file = "chronogram.phy")

     # value of NPRS function for our estimated chronogram
     NPRS.criterion(tree.landplants, chrono.plants)

