mantel                 package:vegan                 R Documentation

_M_a_n_t_e_l _T_e_s_t _f_o_r _T_w_o _D_i_s_s_i_m_i_l_a_r_i_t_y _M_a_t_r_i_c_e_s

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

     Function 'mantel' finds the Mantel statistic as a matrix
     correlation between two dissimilarity matrices, and evaluates the
     significance of the statistic by permuting rows and columns of the
     dissimilarity matrix.  The statistic is evaluated either as a
     moment correlation or as a rank correlation.

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

     mantel(xdis, ydis, method="pearson", permutations=1000, strata)

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

    xdis: First dissimilarity matrix or a 'dist' object. 

    ydis: Second dissimilarity matrix or a 'dist' object. 

  method: Correlation method, as accepted by 'cor.test': 'pearson',
          'spearman' or 'kendall'. 

permutations: Number of permutations in assessing significance. 

  strata: An integer vector or factor specifying the strata for
          permutation. If supplied, observations are permuted only
          within the specified strata.

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

     Mantel statistic is simply a correlation between entries of two
     dissimilarity matrices (some use cross products, but these are
     linearly related).  However, the significance cannot be directly
     assessed, because there are N(N-1)/2 entries for just N
     observations. Mantel developed asymptotic test, but here we use
     permutations of N rows and columns of dissimilarity matrix.

     The function uses 'cor.test', which should accept alternatives
     'pearson' for product moment correlations and 'spearman' or
     'kendall' for rank correlations.

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

     The function returns a list of class 'mantel' with following
     components:  

   Call : Function call.

 method : Correlation method used, as returned by 'cor.test'.

statistic: The Mantel statistic.

  signif: Empirical significance level from permutations.

    perm: A vector of permuted values.

permutations: Number of permutations.

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

     Jari Oksanen

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

     The test is due to Mantel, of course, but the current
     implementation is based on Legendre and Legendre.

     Legendre, P. and Legendre, L. (1998) _Numerical Ecology_. 2nd
     English Edition. Elsevier.

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

     'cor.test' for correlation tests, 'protest' (``Procrustes test'')
     for an alternative with ordination diagrams, and 'anosim' for
     comparing dissimilarities against classification.  For
     dissimilarity matrices, see 'vegdist' or 'dist'.

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

     ## Is vegetation related to environment?
     data(varespec)
     data(varechem)
     veg.dist <- vegdist(varespec) # Bray-Curtis
     env.dist <- vegdist(scale(varechem), "euclid")
     mantel(veg.dist, env.dist)
     mantel(veg.dist, env.dist, method="spear")

