abuocc                package:labdsv                R Documentation

_A_b_u_n_d_a_n_c_e/_O_c_c_u_r_r_e_n_c_e _G_r_a_p_h_i_c_a_l _A_n_a_l_y_s_i_s

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

     Calculates and plots summary statistics about species  occurrences
     in a data frame

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

     abuocc(veg,minabu=0)

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

     veg: a vegetation (or other taxon) dataframe with samples as rows 
          and species as columns

  minabu: a minimum abundance threshold species must exceed to be 
          included in the calculations (default=0)

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

     This functions calculates and plots four data summaries about the 
     occurrence of species:

     Plots

_1) the number of samples each species occurs in on a log scale, sorted
     from maximum to minimum

_2) the number of species in each sample plot (species richness) from
     highest to lowest

_3) the mean abundance of non-zero values (on a log scale) as a function
     of the number of plots a species occurs in

_4) the total abundance/sample as a function of the plot-level species
     richness

     The third plot allows you to identify individual species with the
     mouse; the fourth plot allows you to identify individual samples
     with the mouse.

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

     Returns an (invisible) list composed of: 

 spc.plt: number of species/sample

 plt.spc: number of samples each species occurs in

mean.abu: mean abundance of each species when present  (excluding
          values smaller then minabu)

_N_o_t_e:

     It's common in niche theory analyses to calculate the rank
     abundances  of taxa in a site.  This function is similar, but
     works on multiple samples simultaneously. The plt.spc vector in
     the returned list can be used to mask out rare species in 
     calculations of sample similarity using 'dsvdis' among other
     purposes.

_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:

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

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

     'fisherfit', 'prestonfit'

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

         ## Not run: data(bryceveg) # produces a data.frame called bryceveg
         ## Not run: abuocc(bryceveg)

