palm                  package:ade4                  R Documentation

_P_h_y_l_o_g_e_n_e_t_i_c _a_n_d _q_u_a_n_t_i_t_a_t_i_v_e _t_r_a_i_t_s _o_f _a_m_a_z_o_n_i_a_n _p_a_l_m _t_r_e_e_s

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

     This data set describes the phylogeny of 66 amazonian palm trees.
     It also gives 7 traits corresponding to these 66 species.

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

     data(palm)

_F_o_r_m_a_t:

     'palm' is a list containing the 2 following objects: 

     _t_r_e is a character string giving the phylogenetic tree in Newick
          format. 

     _t_r_a_i_t_s is a data frame with 66 species (rows) and 7 traits
          (columns).

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

     Variables of 'palm$traits' are the following ones: 
      rord: specific richness with five ordered levels
      h: height in meter (squared transform)
      dqual: diameter at breast height in centimeter with five levels
     'sout : subterranean', ' d1(0, 5 cm)', ' d2(5, 15 cm)', ' d3(15,
     30 cm)' and ' d4(30, 100 cm)'
      vfruit: fruit volume in mm^3 (logged transform)
      vgrain: seed volume in mm^3 (logged transform)
      aire: spatial distribution area (km^2)
      alti: maximum altitude in meter (logged transform)

_S_o_u_r_c_e:

     This data set was obtained by Clmentine Gimaret-Carpentier
      gimaret@biomserv.univ-lyon1.fr.

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

     ## Not run: 
     data(palm)
     palm.phy <- newick2phylog(palm$tre)
     radial.phylog(palm.phy,clabel.l=1.25)

     orthogram(palm$traits[,4],palm.phy$Bscores)
     dotchart.phylog(palm.phy,palm$traits[,4], clabel.l = 1,
      labels.n = palm.phy$Blabels, clabel.n = 0.75)
     w <- cbind.data.frame(palm.phy$Bscores[,c(3,4,6,13,21)],
      scalewt((palm$traits[,4])))
     names(w)[6] <- names(palm$traits[4])
     table.phylog(w, palm.phy, clabel.r = 0.75, f = 0.5)

     gearymoran(palm.phy$Amat, palm$traits[,-c(1,3)])
     ## End(Not run)

