corClasses                package:ape                R Documentation

_P_h_y_l_o_g_e_n_e_t_i_c _C_o_r_r_e_l_a_t_i_o_n _S_t_r_u_c_t_u_r_e_s

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

     Standard classes of phylogenetic correlation structures
     ('corPhyl') available in 'ape'.

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

     Available standard classes: 

corBrownian: Brownian model (Felsenstein 1985),

corMartins: The covariance matrix defined in Martins and Hansen (1997),

corGrafen: The covariance matrix defined in Grafen (1989).

     See classes documentation for reference and detailed description.

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

     Julien Dutheil julien.dutheil@univ-montp2.fr

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

     'corClasses' and 'gls' in the 'nlme' librarie, 'corBrownian',
     'corMartins', 'corGrafen'.

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

             library(ape)
             library(nlme)
             cat("((((Homo:0.21,Pongo:0.21):0.28,",
                             "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);",
                             file = "ex.tre", sep = "\n")
             tree.primates <- read.tree("ex.tre")
             X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
             Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
             unlink("ex.tre") # delete the file "ex.tre"
             m1 <- gls(Y~X, correlation=corBrownian(1, tree.primates))
             summary(m1)
             m2 <- gls(Y~X, correlation=corMartins(1, tree.primates))
             summary(m2)
             corMatrix(m2$modelStruct$corStruct)
             m3 <- gls(Y~X, correlation=corGrafen(1, tree.primates))
             summary(m3)
             corMatrix(m3$modelStruct$corStruct)

