procella                package:ade4                R Documentation

_P_h_y_l_o_g_e_n_y _a_n_d _q_u_a_n_t_i_t_a_t_i_v_e _t_r_a_i_t_s _o_f _b_i_r_d_s

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

     This data set describes the phylogeny of 19 birds as reported by
     Bried et al. (2002). It also gives 6 traits corresponding to these
     19 species.

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

     data(procella)

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

     'procella' 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 19 species and 6 traits    

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

     Variables of 'procella$traits' are the following ones: 
      site.fid: a numeric vector that describes the percentage of site
     fidelity
      mate.fid: a numeric vector that describes the percentage of mate
     fidelity
      mass: an integer vector that describes the adult body weight (g)
      ALE: a numeric vector that describes the adult life expectancy
     (years)
      BF: a numeric vector that describes the breeding frequencies
      col.size: an integer vector that describes the colony size (no
     nests monitored)

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

     Bried, J., Pontier, D. and Jouventin, P. (2002) Mate fidelity in
     monogamus birds: a re-examination of the Procellariiformes. 
     _Animal Behaviour_, *65*, 235-246.

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

     data(procella)
     pro.phy <- newick2phylog(procella$tre)
     plot(pro.phy,clabel.n = 1, clabel.l = 1)
     wt <- procella$traits
     wt$site.fid[is.na(wt$site.fid)] <- mean(wt$site.fid[!is.na(wt$site.fid)])
     wt$site.fid <- asin(sqrt(wt$site.fid/100))
     wt$ALE[is.na(wt$ALE)] <- mean(wt$ALE[!is.na(wt$ALE)])
     wt$ALE <- sqrt(wt$ALE)
     wt$BF[is.na(wt$BF)] <- mean(wt$BF[!is.na(wt$BF)])
     wt$mass <- log(wt$mass)
     wt <- wt[, -6]
     table.phylog(scalewt(wt), pro.phy)
     gearymoran(pro.phy$Amat,wt,9999)

