duarm                 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 _P_a_r_t_i_a_l _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:

     duarm(taxa,clustering,sort=FALSE)

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

    taxa: a matrix or dataframe 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 dataframe of species indicator values

_N_o_t_e:

     The name duarm is a horrible pun on the name duleg, which is an
     abbreviation for Dufrene and Legendre who defined an alternative
     indicator species algorithm.

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

     David W. Roberts droberts@montana.edu <URL:
     http://ecology.msu.montana.edu/droberts>

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

     <URL: http://ecology.msu.montana.edu/labdsv/R>

_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)
         duarm(bryceveg,clust)

