mjrochet                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 _t_e_l_e_o_s _f_i_s_h_e_s

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

     This data set describes the phylogeny of 49 teleos fishes as
     reported by Rochet et al. (2000). It also gives life-history
     traits corresponding to these 49 species.

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

     data(mjrochet)

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

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

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

     _t_a_b is a data frame with 49 rows and 7 traits.  

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

     Variables of 'mjrochet$tab' are the following ones : tm (age at
     maturity (years)),  lm (length at maturity (cm)), l05 (length at 5
     per cent survival (cm)), t05 (time to 5 per cent survival
     (years)), fb (slope of the log-log fecundity-length relationship),
     fm (fecundity the year of maturity), egg (volume of eggs (mm^3)).

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

     Data taken from: 
      Summary of data - Clupeiformes : <URL:
     http://www.ifremer.fr/maerha/clupe.html> 
      Summary of data - Argentiniformes : <URL:
     http://www.ifremer.fr/maerha/argentin.html> 
      Summary of data - Salmoniformes : <URL:
     http://www.ifremer.fr/maerha/salmon.html> 
      Summary of data - Gadiformes : <URL:
     http://www.ifremer.fr/maerha/gadi.html> 
      Summary of data - Lophiiformes : <URL:
     http://www.ifremer.fr/maerha/loph.html> 
      Summary of data - Atheriniformes : <URL:
     http://www.ifremer.fr/maerha/ather.html> 
      Summary of data - Perciformes : <URL:
     http://www.ifremer.fr/maerha/perci.html> 
      Summary of data - Pleuronectiformes : <URL:
     http://www.ifremer.fr/maerha/pleuro.html> 
      Summary of data - Scorpaeniformes : <URL:
     http://www.ifremer.fr/maerha/scorpa.html> 
      Phylogenetic tree : <URL:
     http://www.ifremer.fr/maerha/life_history.html>

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

     Rochet, M. J., Cornillon, P-A., Sabatier, R. and Pontier, D.
     (2000)  Comparative analysis of phylogenic and fishing effects in
     life history patterns of teleos fishes. _Okos_, *91*, 255-270.

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

     data(mjrochet)
     mjrochet.phy <- newick2phylog(mjrochet$tre)
     tab <- log((mjrochet$tab))
     tab0 <- data.frame(scalewt(tab))
     table.phylog(tab0, mjrochet.phy, csi = 2, clabel.r = 0.75)
     orthogram(tab0[,1], ortho = mjrochet.phy$Bscores)

