vegemite                package:vegan                R Documentation

_P_r_i_n_t_s _a _C_o_m_p_a_c_t, _O_r_d_e_r_e_d _V_e_g_e_t_a_t_i_o_n _T_a_b_l_e

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

     The function prints a compact vegetation table, where species are
     rows, and each site takes only one column without spaces.  The
     vegetation table can be ordered by explicit indexing, by
     environmental variables or results from an ordination or cluster
     analysis.

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

     vegemite(x, use, scale, sp.ind, site.ind, zero=".")
     coverscale(x, scale=c("Braun.Blanquet", "Domin", "Hult", "Hill", "fix", "log"))

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

       x: Vegetation data. 

     use: Either a vector or an object from 'cca', 'decorana' _etc._ or
          'hclust' for ordering sites and species.

  sp.ind: Species indices. 

site.ind: Site indices. 

    zero: Character used for zeros. 

   scale: Cover scale used (can be abbreviated).

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

     The function prints a traditional vegetation table. Unlike in
     ordinary data matrices, species are used as rows and sites as
     columns.  The table is printed in compact form:  only one
     character can be used for abundance, and there are no spaces
     between columns.

     The parameter 'use' can be a vector or an object from 'hclust', a
     'dendrogram' or any ordination result recognized by 'scores'.  If
     'use' is a vector, it is used for ordering sites.  If 'use' is an
     object from ordination, both sites and species are arranged by the
     first axis.   When 'use' is an object from 'hclust', the sites are
     ordered similarly as in the cluster dendrogram. If ordination
     methods provide species scores, these are used for ordering
     species.  In all cases where species scores are missing, species
     are ordered by their weighted averages ('wascores') on site
     scores. There is no natural, unique ordering in hierarchic
     clustering, but in some cases species are still nicely ordered.
     Alternatively, species and sites can be ordered explicitly giving
     their indices or names in parameters 'sp.ind' and 'site.ind'.  If
     these are given, they take precedence over 'use'. 

     If 'scale' is given, 'vegemite' calls 'coverscale' to transform
     percent cover scale or some other scales into traditional class
     scales used in vegetation science ('coverscale' can be called
     directly, too). Braun-Blanquet and Domin scales are actually not
     strict cover scales, and the limits used for codes 'r' and '+' are
     arbitrary.  Scale 'Hill' may be inappropriately named, since Mark
     O. Hill probably never intended this as a cover scale.  However,
     it is used as default `cut levels' in his 'TWINSPAN', and
     surprisingly many users stick to this default, and so this is a
     _de facto_ standard in publications.  All traditional scales
     assume that values are cover percentages with maximum 100.
     However, non-traditional alternative 'log' can be used with any
     scale range.  Its class limits are integer powers of 1/2 of the
     observed maximum in the data, with '+' used for non-zero entries
     less than 1/512 of data maximum ('log' stands alternatively for
     logarithmic or logical).  Scale 'fix' is intended for `fixing'
     10-point scales: it truncates scale values to integers, and
     replaces 10 with 'X' and positive values below 1 with '+'.

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

     The function is used mainly to print a table, but it returns
     (invisibly) a list with items: 

    spec: Ordered species indices.

   sites: Ordered site indices.

_N_o_t_e:

     This function was called 'vegetab' in older versions of 'vegan'. 
     The new name was chosen  because the output is so compact (and to
     avoid confusion with the 'vegtab' function in the 'labdsv'
     package).

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

     Jari Oksanen

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

     The cover scales are presented in many textbooks of vegetation
     science; I used:

     Shimwell, D.W. (1971) _The Description and Classification of
     Vegetation_. Sidgwick & Jackson.

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

     'cut' and 'approx' for making your own `cover scales', 'wascores'
     for weighted averages.

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

     data(varespec)
     ## Print only more common species 
     freq <- apply(varespec > 0, 2, sum)
     vegemite(varespec, scale="Hult", sp.ind = freq > 10)
     ## Order by correspondence analysis, use Hill scaling and layout:
     dca <- decorana(varespec)
     vegemite(varespec, dca, "Hill", zero="-")

