decostand               package:vegan               R Documentation

_S_t_a_n_d_a_r_d_i_z_a_t_o_n _M_e_t_h_o_d_s _f_o_r _C_o_m_m_u_n_i_t_y _E_c_o_l_o_g_y

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

     The function provides some popular (and effective) standardization
     methods for community ecologists.

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

     decostand(x, method, MARGIN)
     wisconsin(x)

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

       x: Community data matrix.

  method: Standardization method.

  MARGIN: Margin, if default is not acceptable.

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

     The function offers following standardization methods for
     community data:

        *  'total': divide by margin total (default 'MARGIN = 1').

        *  'max': divide by margin maximum (default 'MARGIN = 2').

        *  'freq': divide by margin maximum and multiply by number of
           non-zero items, so that the average of non-zero entries is
           one (Oksanen 1983; default 'MARGIN = 2').

        *  'normalize': make margin sum of squares equal to one
           (default 'MARGIN = 1').

        *  'range': standardize values into range 0 ... 1 (default
           'MARGIN = 2').

        *  'standardize': scale into zero mean and unit variance
           (default 'MARGIN = 2').

        *  'pa': scale into presence/absence scale (0/1).

        *  'chi.square': divide by row sums and square root of column
           sums, and adjust for square root of matrix total (Legendre &
           Gallagher 2001). When used with Euclidean distance, the
           matrix should be similar to the  the Chi-square distance
           used in correspondence analysis. However, the results from
           'cmdscale' would still differ, since CA is a weighted
           ordination method (default 'MARGIN = 1').

     Standardization, as contrasted to transformation, means that the
     entries are transformed relative to other entries.

     All methods have a default margin.  'MARGIN=1' means rows (sites
     in a normal data set) and 'MARGIN=2' means columns (species in a
     normal data set).

     Command 'wisconsin' is a shortcut to common Wisconsin double
     standardization where species ('MARGIN=2') are first standardized
     by maxima ('max') and then sites ('MARGIN=1') by site totals
     ('tot').

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

     Returns the standardized data frame.

_N_o_t_e:

     Common transformations can be made with standard R functions.

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

     Jari Oksanen

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

     Legendre, P. & Gallagher, E.D. (2001) Ecologically meaningful
     transformations for ordination of species data. _Oecologia_ 129:
     271-280.

     Oksanen, J. (1983) Ordination of boreal heath-like vegetation with
     principal component analysis, correspondence analysis and
     multidimensional scaling. _Vegetatio_ 52, 181-189.

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

     data(varespec)
     sptrans <- decostand(varespec, "max")
     apply(sptrans, 2, max)
     sptrans <- wisconsin(varespec)
     # Chi-square: Similar but not identical to Correspondence Analysis.
     sptrans <- decostand(varespec, "chi.square")
     plot(procrustes(rda(sptrans), cca(varespec)))
     # Hellinger transformation (Legendre & Callagher 2001):
     sptrans <- sqrt(decostand(varespec, "total"))

