clo               package:compositions               R Documentation

_C_l_o_s_u_r_e _o_f _a _c_o_m_p_o_s_i_t_i_o_n

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

     Closes compositions to sum up to one (or an optional total), by
     dividing each part by the sum.

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

               clo( X, parts=1:NCOL(oneOrDataset(X)),total=1,
                    detectionlimit=attr(X,"detectionlimit"),
                    BDL=NULL,MAR=NULL,MNAR=NULL,SZ=NULL,
                    storelimit=!is.null(attr(X,"detectionlimit"))
                    )
               

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

       X: composition or dataset of compositions

   parts: vector containing the indices xor names of the columns to be
          used

   total: the total amount to which the compositions should be closed;
          either  a single number, or a numeric vector of length
          'gsi.getN(X)' specifying a different total for each
          compositional vector in the dataset.

detectionlimit: a number, vector or matrix of positive numbers giving
          the detection limit of all values, all variables, or each
          value

     BDL: the code for values below detection limit in X

      SZ: the code for structural zeroes in X

     MAR: the code for values missed at random in X

    MNAR: the code for values missed not at random in X

storelimit: a boolean indicating wether to store the detection limit as
          an attribute in the data. It defaults to FALSE if the
          detection limit is not already stored in the dataset. The
          attribute is only needed for very advanced analysis. Most
          times, this  will not be used.

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

     The closure operation is given by

                    clo(x) := ( _x_i_ / sum(x_j))

     'clo' generates a composition without assigning one of the
     compositional classes 'acomp' or 'rcomp'.  Note that after
     computing the closed-to-one version, obtaining a  version closed
     to any other value is done by simple multiplication.  

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

     a composition or a data matrix of compositions, maybe without
     compositional class. The individual compositions are forced to sum
     to 1 (or to  the optionally-specified total). The result should
     have the same shape as the input (vector, row, matrix).

_M_i_s_s_i_n_g _P_o_l_i_c_y:

     How missing values are coded in the output always follows the
     general rules described in 'compositions.missing'. The BDL values
     are accordingly scaled during the scaling operations but not taken
     into acount for the calculation of the total sum.

_N_o_t_e:

     'clo' can be used to unclass compositions.

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

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

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

     Aitchison, J. (1986) _The Statistical Analysis of Compositional
     Data_ Monographs on Statistics and Applied Probability. Chapman &
     Hall Ltd., London (UK). 416p.

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

     'clr','acomp','rcomp'

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

     (tmp <- clo(c(1,2,3)))
     clo(tmp,total=100)
     data(Hydrochem)
     cdata <- Hydrochem[,6:19]
     plot( clo(Hydrochem,8:9) ) # Giving points on a line 

