PI2newick                package:ade4                R Documentation

_I_m_p_o_r_t _d_a_t_a _f_i_l_e_s _f_r_o_m _P_h_y_l_o_g_e_n_e_t_i_c _I_n_d_e_p_e_n_d_a_n_c_e _P_a_c_k_a_g_e

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

     This function ensures to transform a data set written for the
     Phylogenetic Independance package of Abouheif (1999) in a data set
     formatting for the functions of ade4.

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

     PI2newick(x)

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

       x: is a data frame that contains information on phylogeny
          topology and trait values

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

     Returns a list containing : 

     tre: : a character string giving the phylogenetic tree in Newick
          format

   trait: : a vector containing values of the trait

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

     Sbastien Ollier ollier@biomserv.univ-lyon1.fr 
      Daniel Chessel chessel@biomserv.univ-lyon1.fr

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

     Abouheif, E. (1999) A method for testing the assumption of
     phylogenetic independence in comparative data. _Evolutionary
     Ecology Research_, *1*, 895-909.

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

     x <- c(2.0266, 0.5832, 0.2460, 1.2963, 0.2460, 0.1565, -99.0000,
             -99.0000, 10.1000, -99.0000,  20.2000,  28.2000, -99.0000, 
             14.1000, 11.2000, -99.0000, 21.3000, 27.5000, 1.0000, 2.0000,
             -1.0000, 4.0000, -1.0000, -1.0000, 3.0000, -1.0000, -1.0000,
             5.0000, -1.0000, -1.0000, 0.0000, 0.0000, 0.0000, 0.0000,
             0.0000, 0.0000)
     x <- matrix(x, nrow = 6)
     x <- as.data.frame(x)
     res <- PI2newick(x)
     dotchart.phylog(newick2phylog(res$tre), res$trait)

