isamic                package:labdsv                R Documentation

_I_n_d_i_c_a_t_o_r _S_p_e_c_i_e_s _A_n_a_l_y_s_i_s _M_i_n_i_m_i_z_i_n_g _I_n_t_e_r_m_e_d_i_a_t_e _O_c_c_u_r_r_e_n_c_e_s

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

     Calculates the degree to which species are either always present
     or always absent within clusters or types.

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

     isamic(taxa,clustering,sort=FALSE)

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

    taxa: a matrix or data.frame of samples, species as columns,
          samples as rows

clustering: a vector of numeric cluster memberships for samples, or a
          classification object returned from 'pam',  or 'partana'

    sort: if TRUE, return in order of highest value to lowest rather
          than input order

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

     Calculates the constancy (fractional occurrence of each species in
     every type), and then calculates twice the the sum of the absolute
     values of the constancy - 0.5, normalized to the number of
     clusters (columns).

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

     a data.frame of species indicator values

_N_o_t_e:

     This function was previously called 'duarm', a horrible pun on the
      name 'duleg', which is an abbreviation for Dufrene and Legendre
     who defined an alternative indicator species algorithm.  Following
     publication of Aho et al. 2008, it was renamed 'isamic' as
     decribed in that paper.

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

     David W. Roberts droberts@montana.edu

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

     <URL: http://ecology.msu.montana.edu/labdsv/R/labdsv> Aho, K.,
     D.W. Roberts, and T.W.Weaver.  2008. Using geometric and
     non-geometric internal evaluators to compare eight vegetation
     classification methods.  J. Veg. Sci. In press.

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

     'duleg'

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

         data(bryceveg)
         dis.bc <- dsvdis(bryceveg,'bray/curtis')
         clust <- sample(1:5,nrow(bryceveg),replace=TRUE)
         isamic(bryceveg,clust)

