gsi.merge2signary        package:compositions        R Documentation

_A_u_x_i_l_i_a_r_y _f_u_n_c_t_i_o_n_s _t_o _c_o_m_p_u_t_e _u_s_e_r-_d_e_f_i_n_e_d _i_l_r _a_n_d _i_p_t _t_r_a_n_s_f_o_r_m_s.

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

     Compute the basis of a clr-plane, to use with isometric log-ratio
     or planar transform of a (dataset of) compositions.

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

               gsi.merge2signary( M )
               gsi.ilrBase2signary( V )
               gsi.optimalilrBase( x )
               gsi.buildilrBase( W=c(1,-1) )
               gsi.signary2ilrBase( W=c(1,-1) )
               gsi.OrderIlr( V )
               

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

       M: a merge structure (as explained in 'hclust') 

       x: a compositional data set 

       W: a signary matrix (as explained below) defining a partition 

       V: a matrix of change of basis from clr/cpt to ilr/ipt 

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

     A signary matrix is a matrix with the same shape as an ilr matrix,
      but containing only +1, 0 or -1 values (thus, it is a kind of
     "extended  binary"). If the value W[i,j]= +1, then part "i" is
     involved in  coordinate "j" in the numerator; if W[i,j]=-1, it is
     involed in the denominator, and if W[i,j]=0 then part "i" does not
     take  part in coordinate "j".

     Functions 'gsi.merge2signary' and 'gsi.buildilrBase' are  intended
     to compute 'ilrBase' matrices associated to user-defined 
     partition structures. Function 'gsi.ilrBase2signary' offers the 
     inverse functionality.

     Function 'gsi.OrderIlr' returns a list with two elements: 
     "ilrBase" and "order". The first one contains the ilr basis with 
     coordinates reordered in decreasing number of involved parts (so, 
     all parts are involved in the first coordinate, and only two in
     the  last). The second one gives a permutation of the parts so
     that  involved parts in each coordinate are always together.  Note
     that ilrBase does not have its parts permuted!

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

     These functions will not be usually called on themselves, but 
     through their wrappers, mainly 'ilrBase'. Functions
     'gsi.merge2signary' and 'gsi.ilrBase2signary' return  a signary
     matrix (as explained in "details"), code{gsi.optimalilrBase} 
     returns a merge structure (as epxlained in 'hclust'), and
     'gsi.buildilrBase' (and its alias 'gsi.signary2ilrBase')  returns
     an ilr matrix. These functions are thought to be called 
     sequentially. 
      Apart, 'gsi.OrderIlr' reorders both parts and coordinates to 
     ease dendrogram-like representations (see 'CoDaDendrogram').

_N_o_t_e:

     It is better not to use gsi.* functions directly since they are
     internal functions of the package. Use their wrappers.

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

     Raimon Tolosana-Delgado, K.Gerald v.d. Boogaart <URL:
     http://www.stat.boogaart.de>

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

     Egozcue J.J., V. Pawlowsky-Glahn, G. Mateu-Figueras and C.
     Barcel'o-Vidal (2003) Isometric logratio transformations for
     compositional data analysis. _Mathematical Geology_, *35*(3)
     279-300

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

     'ilrBase','ipt','ilr', <URL:
     http://ima.udg.es/Activitats/CoDaWork03>

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

     m <- matrix(data=c(-1,-2,
                       -3,-4,
                        1, 2),ncol=2,nrow=3,byrow=TRUE)
     w <- gsi.merge2signary(m)
     w
     V=gsi.buildilrBase(w)
     V
     gsi.ilrBase2signary(V)
     gsi.OrderIlr(V)

