relltest              package:scaleboot              R Documentation

_R_E_L_L _T_e_s_t _f_o_r _P_h_y_l_o_g_e_n_e_t_i_c _I_n_f_e_r_e_n_c_e

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

     Performs the RELL test for finding the largest item. This
     calculates AU p-values for each item via the multiscale bootstrap
     resampling. This is particularly useful for testing tree
     topologies in phylogenetic analysis.

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

     relltest(dat,nb=10000,sa=9^seq(-1,1,length=13),ass=NULL,
              cluster=NULL,nofit=FALSE,models=NULL,seed=100)

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

     dat: a matrix. Row vectors are to be resampled. Each column vector
          gives score values to be evaluated for an item. For the
          phylogenetic analysis, 'dat[i,j]' is the site-wise
          log-likelihood value at site-i for tree-j, and we are to find
          the tree with the largest expected value of 'sum(dat[,j])'.

      nb: Number of replicates for each scale.

      sa: Scales in sigma squared (sigma^2).

     ass: A list of association vectors for testing edges as well as
          trees. If 'ass=NULL', then only the results for trees are
          returned.

 cluster: 'snow' cluster object which may be generated by function
          'makeCluster'.

   nofit: logical. Passed to 'sbfit'.

  models: character vectors. Passed to 'sbfit'.

    seed: If non NULL, then a random seed is set. Specifying a seed is
          particularly important when 'cluster' is non NULL, in this
          case 'seed + seq(along=cluster)' are set to cluster nodes.

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

     'relltest' performs the resampling of estimated log-likelihoods
     (RELL) method of Kishino et al. (1990). For resampling indices
     stored in a vector 'i', the resampled log-likelihood for a tree-j
     is approximately calculated by 'sum(dat[i,j])'. This approximation
     avoids time-consuming recalculation of the maximum likelihood
     estimates of tree parameters, which are to be calculated by an
     external phylogenetic software such as PAML as described in
     'mam15'. In the implementation of 'relltest', the resampled
     log-likelihood is calculated by
     'sum(dat[i,j])''*nrow(dat)/length(i)' so that the statistic is
     comparable to the case when n'=n.

     'relltest' first calls 'scaleboot' internally for multiscale
     bootstrap resampling, and then 'scaleboot' calls 'sbfit' for
     fitting models to the bootstrap probabilities. The AU p-values
     (named "k.3") produced by the 'summary' method are improvements of
     the third-order p-values calculated by CONSEL software (Shimodaira
     and Hasegawa 2001).  In addition, 'relltest' calls 'scaleboot'
     with 'sa=1' for calculating p-values via the Shimodaira-Hasegawa
     test (SH-test) of Shimodaira and Hasegawa (1999).

     See 'mam15' for details through an example.

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

     'relltest' returns an object of class '"relltest"' that is
     inherited from the class '"scalebootv"' by adding two extra
     components called "stat" and "shtest". "stat" is a vector of the
     test statistics from the SH-test (i.e., the log-likelihood
     differences), and "shtest" is a list with two components: "pv", a
     vector of SH-test p-values, and "pe", a vector of standard errors
     of the p-values.  The results of multiscale bootstrap resampling
     are stored in the '"scalebootv"' components returned by a call to
     'sbfit'.

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

     Hidetoshi Shimodaira

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

     Kishino, H., Miyata, T. and Hasegawa, M. (1990). Maximum
     likelihood inference of  protein phylogeny and the origin of
     chloroplasts.,  _J. Mol. Evol._, 30, 151-160.

     Shimodaira, H. and Hasegawa, M. (1999). Multiple comparisons of
     log-likelihoods with applications to phylogenetic inference,
     _Molecular Biology and Evolution_, 16, 1114-1116.

     Shimodaira, H. and Hasegawa, M. (2001). CONSEL: for assessing the
     confidence of phylogenetic tree selection, _Bioinformatics_, 17,
     1246-1247 (software is available from <URL:
     http://www.is.titech.ac.jp/~shimo/prog/consel/>).

     Luke Tierney, A. J. Rossini, Na Li and H. Sevcikova. snow: Simple
     Network of Workstations. R package version 0.2-1.

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

     'sbfit', 'scaleboot', 'mam15'.

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

     ## Not run: 
     ## An example from data(mam15).
     ## It may take 20 mins to run relltest below.
     mam15.mt <- read.mt("mam15.mt") # site-wise log-likelihoods
     mam15.trees <- relltest(mam15.mt) # resampling and fitting
     summary(mam15.trees) # AU p-values
     ## End(Not run)

