ordihull                package:vegan                R Documentation

_A_d_d _G_r_a_p_h_i_c_a_l _I_t_e_m_s _t_o _O_r_d_i_n_a_t_i_o_n _D_i_a_g_r_a_m_s

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

     Functions to add convex hulls, arrows, line segments, regular
     grids of points, `spider' graphs, ellipses, cluster dendrogram or
     spanning trees to ordination diagrams. The ordination diagrams can
     be produced by 'vegan' 'plot.cca', 'plot.decorana' or 'ordiplot'.

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

     ordihull(ord, groups, display = "sites", draw = c("lines","polygon"), ...)
     ordiarrows(ord, groups, levels, replicates, display = "sites", ...)
     ordisegments(ord, groups, levels, replicates, display = "sites", ...)
     ordigrid(ord, levels, replicates, display = "sites",  ...)
     ordispider(ord, groups, display="sites", w = weights(ord, display), ...)
     ordiellipse(ord, groups, display="sites", kind = c("sd","se"), conf,
                 draw = c("lines","polygon"), w = weights(ord, display), ...)
     ordicluster(ord, cluster, prune = 0, display = "sites",
                 w = weights(ord, display), ...)
     ordispantree(ord, tree, display = "sites", ...)

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

     ord: An ordination object or an 'ordiplot' object. 

  groups: Factor giving the groups for which the graphical item is
          drawn. 

levels, replicates: Alternatively, regular groups can be defined with
          arguments 'levels' and 'replicates', where 'levels' gives the
          number of groups, and 'replicates' the number of successive
          items at the same group.

 display: Item to displayed. 

    draw: Use either 'lines' or 'polygon' to draw the line. Graphical
          parameters are passed to both. The main difference is that
          'polygon's may be filled and non-transparent.

       w: Weights used to find the average within group. Weights are
          used automatically for 'cca' and 'decorana' results, unless
          undone by the user. 'w=NULL' sets equal weights to all
          points. 

    kind: Whether standard deviations of points ('sd') or standard
          deviations of their (weighted) averages ('se') are used.

    conf: Confidence limit for ellipses, e.g. 0.95. If given, the
          corresponding 'sd' or 'se' is multiplied with the
          corresponding value found from the Chi-squared distribution
          with 2df. 

 cluster: Result of hierarchic cluster analysis, such as 'hclust' or
          'agnes'.

   prune: Number of upper level hierarchies removed from the
          dendrogram. If 'prune' >0, dendrogram will be disconnected.

    tree: Structure defining a spanning tree. This can be a result of
          'spantree' or a vector giving the child node of each parent
          omitting the first point. Values 'NA' means that there is no
          link from the corresponding parent.

     ...: Parameters passed to graphical functions such as 'lines',
          'segments', 'arrows', 'polygon' or to 'scores' to select axes
          and scaling etc. 

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

     Function 'ordihull' draws 'lines' or 'polygon's for the convex
     hulls found by function 'chull' encircling the items in the
     groups.

     Function 'ordiarrows' draws 'arrows' and 'ordisegments' draws line
     'segments' between successive items in the groups. Function
     'ordigrid' draws line 'segments' both within the groups and for
     the corresponding items among the groups.

     Function 'ordispider' draws a `spider' diagram where each point is
     connected to the group centroid with 'segments'. Weighted
     centroids are used in the correspondence analysis  methods 'cca'
     and 'decorana' or if the user gives the weights in the call. If
     'ordispider' is called with 'cca' or 'rda' result without 'groups'
     argument, the function connects each `WA' scores to the
     correspoding `LC' score.

     Function 'ordiellipse' draws 'lines' or 'polygon's for dispersion
     'ellipse' using either standard deviation of point scores or
     standard error of the (weighted) average of scores, and the
     (weighted) correlation defines the direction of the principal axis
     of the ellipse. The function requires library 'ellipse'. An
     ellipsoid hull can be drawn with function 'ellipsoidhull' of
     package 'cluster'.

     Function 'ordicluster' overlays a cluster dendrogram onto
     ordination. It needs the result from a hierarchic clustering such
     as 'hclust' or 'agnes', or other with a similar structure.
     Function 'ordicluster' connects cluster centroids to each other
     with line 'segments'. Function uses centroids of all points in the
      clusters, and is therefore similar to average linkage methods.

     Function 'ordispantree' overlays a (minimum) spanning tree onto
     ordination. It needs a result from 'spantree' or a vector listing
     children of each parent, starting from second (i.e., omitting the
     first: the number of links is one less number of points). Missing
     links are denoted as 'NA'. For an example, see 'spantree'.

_N_o_t_e:

     These functions add graphical items to ordination graph: You must
     draw a graph first.

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

     Jari Oksanen

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

     The function pass parameters to basic graphical functions, and you
     may wish to change the default values in 'arrows', 'lines',
     'segments' and 'polygon'. You can pass parameters to 'scores' as
     well. Other underlying functions are 'chull' and 'ellipse'.

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

     data(dune)
     data(dune.env)
     mod <- cca(dune ~ Moisture, dune.env)
     attach(dune.env)
     plot(mod, type="n")
     ordihull(mod, Moisture)
     ordispider(mod, col="red")
     plot(mod, type = "p", display="sites")
     ordicluster(mod, hclust(vegdist(dune)), prune=3, col = "blue")
     # The following is not executed automatically because it needs
     # a non-standard library `ellipse'. 
     ## Not run: ordiellipse(mod, Moisture, kind="se", level=0.95, lwd=2, col="blue")

