indspc                package:labdsv                R Documentation

_C_o_m_p_o_s_i_t_i_o_n_a_l _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 mean similarity of all plots in which a species
     occurs.

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

     indspc(taxa, dis, numitr=100)
     ## S3 method for class 'indspc':
     plot(x, ...)

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

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

     dis: an object of class 'dist' from  'dist', 'vegist', or 
          'dsvdis'

  numitr: the number of iterations to use to establish the quantiles 
          of the distribution

       x: an object of class indspc

     ...: additional arguments to the plot function

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

     a list with two dataframes: vals with species name, mean
     similarity, and number of occurrences, and quantiles with the
     distribution of the quantiles

_N_o_t_e:

     One measure of the habitat specificity of a species is the  degree
     to which a species only occurs in communities that are similar to
     each other.  This function calculates the mean similarity of  all
     samples in which each species occurs.  The mean similarity of
     species which only occur once is set to 0, rather than NA.

     The calculated values can be compared to random samples of plots
     with the  same number of occurrences.

_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','duarm'

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

     data(bryceveg) # returns a vegetation dataframe
     dis.bc <- dsvdis(bryceveg,'bray/curtis')
         # returns a Bray/Curtis dissimilarity matrix
     indspc(bryceveg,dis.bc)

