phylog                 package:ade4                 R Documentation

_P_h_y_l_o_g_e_n_y

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

     Create and use objects of class 'phylog'. 
      'phylog.extract' returns objects of class 'phylog'. It extracts
     sub-trees from a tree. 
      'phylog.permut' returns objects of class 'phylog'. It creates the
     different representations compatible with tree topology.

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

     print.phylog(x, ...)
     phylog.extract(phylog, node, distance = TRUE)
     phylog.permut(phylog, list.nodes = NULL, distance = TRUE))

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

x, phylog: : an object of class 'phylog'

     ...: : further arguments passed to or from other methods

    node: : a string of characters giving a node name. The functions
          extracts the tree rooted at this node.

distance: : if TRUE, both functions retain branch lengths. If FALSE,
          they returns tree with arbitrary branch lengths (each branch
          length equals one)

list.nodes: : a list which elements are vectors of string of character
          corresponding to direct descendants of nodes. This list
          defines one representation compatible with tree topology
          among the set of possibilities.

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

     Returns a list of class 'phylog' : 

     tre: : a character string of the phylogenetic tree in Newick
          format whithout branch length values

  leaves: : a vector which names corresponds to leaves and values gives
          the distance between leaves and nodes closest to these leaves

   nodes: : a vector which names corresponds to nodes and values gives
          the distance between nodes and nodes closest to these leaves

   parts: : a list which elements gives the direct descendants of each
          nodes

   paths: : a list which elements gives the path leading from the root
          to taxonomic units (leaves and nodes)

   droot: : a vector which names corresponds to taxonomic units and
          values gives distance between taxonomic units and the root

    call: : call

    Wmat: : a phylogenetic link matrix, generally called the covariance
          matrix. Matrix values Wmat_ij correspond to path length that
          lead from root to the first common ancestor of the two leaves
          i and j

   Wdist: : a phylogenetic distance matrix of class ''dist''. Matrix
          values Wdist_ij correspond to $\sqrt{d_{ij}}$ where d_ij is
          the classical distance between two leaves i and j

 Wvalues: : a vector with the eigen values of Wmat

 Wscores: : a data frame with eigen vectors of Wmat. This data frame
          defines an orthobasis that could be used to calculate the
          orthonormal decomposition of a biological trait on a tree.

    Amat: : a phylogenetic link matrix stemed from Abouheif's test and
          defined in Ollier et al. (submited)

 Avalues: : a vector with the eigen values of Amat

    Adim: : number of positive eigen values

 Ascores: : a data frame with eigen vectors of Amat. This data frame
          defines an orthobasis that could be used to calculate the
          orthonormal decomposition of a biological trait on a tree.

  Aparam: : a data frame with attributes associated to nodes.

 Bindica: : a data frame giving for some taxonomic units the partition
          of leaves that is associated to its

 Bscores: : a data frame giving an orthobasis defined by Ollier et al.
          (submited) that could be used to calculate the orthonormal
          decomposition of a biological trait on a tree.

 Bvalues: : a vector giving the degree of phylogenetic autocorrelation
          for each vectors of Bscores (Moran's form calculated with the
          matrix Wmat)

 Blabels: : a vector giving for each nodes the name of the vector of
          Bscores that is associated to its

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

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

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

     Ollier, S., Pontier, D. and Chessel, D. (submitted) Comments on
     Abouheif's test. _Evolutionary Ecology Research_.

     Ollier, S., Couteron, P. and Chessel, D. (submitted) Orthonormal
     transforms to detect and describe phylogenetic autocorrelation.
     _Biometrics_.

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

     'newick2phylog', 'plot.phylog'

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

     marthans.tre <- NULL
     marthans.tre[1] <-"((((1:4,2:4)a:5,(3:7,4:7)b:2)c:2,5:11)d:2,"
     marthans.tre[2] <- "((6:5,7:5)e:4,(8:4,9:4)f:5)g:4);"
     marthans.phylog <- newick2phylog(marthans.tre)
     marthans.phylog

     if (require(ape, quietly=TRUE)) {
     marthans.phylo <- read.tree(text = marthans.tre)
     marthans.phylo

     par(mfrow =c (1,2))
     plot.phylog(marthans.phylog, cnode = 3, f = 0.8, cle = 3)
     plot.phylo(marthans.phylo)
     par(mfrow = c(1,1))
     }

