interface             package:scaleboot             R Documentation

_I_n_t_e_r_f_a_c_e _t_o _E_x_t_e_r_n_a_l _P_a_c_k_a_g_e_s

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

     Interface for other packages such as CONSEL (phylogenetic
     inference), and pvclust (hierarchical clustering)

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

     read.mt(file,tlab="t")

     read.ass(file,identity=TRUE,tlab="t",elab="e") 

     read.cnt(file)

     ## S3 method for class 'pvclust':
     sbfit(x,...)

     sbpvclust(x,mbs,k=3,k.bp=1,...)

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

    file: character of a file name to be read.

identity: logical. Should the identity association be included?

    tlab: character for basename of tree labels.

    elab: character for basename of edge labels.

       x: an object of class '"pvclust"'.

     mbs: an object of class '"scalebootv"'.

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

       k: numeric of k for a AU p-value.

    k.bp: numeric of k for a BP p-value.

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

     CONSEL is a program package consisting of small programs written
     in the C language for assessing the confidence of phylogenetic
     tree selection. Some functions for interfacing with CONSEL are:
     'read.mt',   'read.ass',  and 'read.cnt' for reading,
     respectively, 'mt', 'ass', and 'cnt' format. Once 'mt' file is
     read, we can calculate improved versions of approximately unbiased
     p-values by 'relltest'in 'scaleboot' instead of CONSEL.

     pvclust is a R package for hierarchical clustering with p-values.
     Functions for interface to pvclust are: 'sbfit' method for an
     object of class '"pvclust"' to convert it to '"scalebootv"' class,
     and 'sbpvclust' for writing back the result to a '"pvclust"'
     object.

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

     'read.mt' returns a matrix of dimension sequence-length by
     tree-number. If 'identity=FALSE', then 'read.ass' returns a list
     containing components 'x' for edge->tree associations and 'y' for
     tree$\to$edge associations. If 'identity=TRUE', 'read.ass' returns
     a list vector of edge$\to$tree associations, where the identity
     associations for tree$\to$tree are included. 'read.cnt' returns a
     list containing components 'bps', 'nb', and 'sa' to be used for
     'sbfit'. The list also contains components 'cnt', 'id', and 'val'.

     'sbfit.pvclust' returns an object of class '"scalebootv"'.
     'sbpvclust' returns an object of class '"pvclust"'.

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

     Hidetoshi Shimodaira

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

     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/>).

     Suzuki, R. and Shimodaira, H. (2006). pvclust: An R package for
     hierarchical clustering with p-values, _Bioinformatics_, 22,
     1540-1542 (software is available from CRAN or <URL:
     http://www.is.titech.ac.jp/~shimo/prog/pvclust/>).

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

     'relltest'

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

     ## Not run: 
     ## reading CONSEL files
     ## sample files are found in mam15 subdirectory
     ## see help(mam15) for details
     mam15.mt <- read.mt("mam15.mt")
     mam15.ass <- read.mt("mam15.ass")
     mam15.cnt <- read.mt("mam15.cnt")
     ## End(Not run)

     ## Not run: 
     ## see help(lung73) for details
     data(lung73)
     lung73.sb <- sbfit(lung73.pvclust,cluster=cl) # model fitting
     lung73.new <- sbpvclust(lung73.pvclust,lung73.sb) # au <- k.3
     ## End(Not run)

