duleg                 package:labdsv                 R Documentation

_D_u_f_r_e_n_e-_L_e_g_e_n_d_r_e _I_n_d_i_c_a_t_o_r _S_p_e_c_i_e_s _A_n_a_l_y_s_i_s

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

     Calculates the indicator value (fidelity and relative abundance)
     of species in clusters or types.

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

     duleg(taxa,clustering,numitr=1000)
     ## S3 method for class 'duleg':
     summary(object, ...)

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

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

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

  numitr: the number of randomizations to iterate to calculate
          probabilities

  object: an object of class 'duleg'

     ...: additional arguments to the summary function

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

     Calculates the indicator value d of species as the product of the 
     relative frequency and relative average abundance in clusters. 
     Specifically,

     where:
      p_{i,j} =  presence/absence (1/0) of species i in  sample j; 
      x_{i,j} =  abundance of species i in sample j; 
      n_c =  number of samples in cluster c;
      for cluster c in set K; 



              f_{i,c} = {sum_{j in c} p_{i,j} over n_c}


 a_{i,c} = {(sum_{j in c} x_{i,j}) / n_c over sum_{k=1}^K ((sum_{j in k} x_{i,j}) / n_k)}


                   d_{i,c} = f_{i,c} times a_{i,c}


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

     a list with components: 

  relfrq: relative frequency of species in classes

  relabu: relative abundance of species in classes

  indval: the indicator value for each species

  maxcls: the class each species has maximum indicator value for

  indcls: the indicator value for each species to its maximum class

    pval: the probability of obtaining as high an indicator values as
          observed over the specified iterations


     The 'summary' function simply returns the sum of probabilities for
     the species.

_N_o_t_e:

     Indicator value analysis was proposed by Dufrene and Legendre
     (1997) as a source of possible stopping rules for clustering, but
     has been used by ecologists for a variety of analyses.  Dufrene
     and Legendre's nomenclature in the paper is somewhat ambiguous,
     but the equations above are taken from the  worked example in the
     paper, not the equations on page 350 which  appear to be in error.
      Dufrene and Legendre, however, multiply d  by 100; this function
     does not.

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

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

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

     Dufrene, M. and Legendre, P.  1997.  Species assemblages and
     indicator species: the need for a flexible asymmetrical approach. 
     Ecol. Monogr. 67(3):345-366.

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

     'duarm'

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

         data(bryceveg) # returns a vegetation dataframe
         dis.bc <- dsvdis(bryceveg,'bray/curtis') # returns a dissimilarity matrix
         clust <- sample(1:5,nrow(bryceveg),replace=TRUE)
         duleg(bryceveg,clust)

