ordiClust             package:ade4TkGUI             R Documentation

_O_r_d_i_n_a_t_i_o_n _a_n_d _C_l_u_s_t_e_r _a_n_a_l_y_s_i_s

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

     This function does cluster analysis on ordination scores,
     providing a dynamic exploration of the clusters on the factor
     maps. As a first step, an ordination method computes the row
     scores of the input data table. In a second step, cluster analysis
     is used on these row scores to obtain groups. The dudi and the
     factor are available in the global environment under the names
     'ordiClust.dudi' and 'ordiClust.factor'.

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

     ordiClust(datatab=NULL, hscalef=1.2, vscalef=1.2, maxgr=20)

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

 datatab: a dataframe containing the data table to analyse, or directly
          a dudi.

 hscalef: horizontal scale factor used to resize the drawing in the
          tkrplot window.

 vscalef: vertical scale factor used to resize the drawing in the
          tkrplot window.

   maxgr: maximum number of groups displayed on the ordination factor
          map.

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

     The GUI is divided in a graph panel on the right and several
     dialog panels on the left.

      Under the graph panel, a scale widget can be used to set the
     number of groups, and  three buttons allow to change the graphical
     parameters (ellipses or convex hulls, and color or black & white).
     The 'Submit' button under the graph (or the return key) draws the
     groups on the factor map. 'Up arrow' and 'Down arrow' keys (or the
     scale widget) can be used to increase or decrease the number of
     groups. Choosing another clustering algorithm or another distance
     automatically updates the graph, allowing easy comparisons. The
     'Dismiss' button at the bottom of the window closes the ordiClust
     window.

      From top to bottom the left panels are :

      'Input data frame' : this is the data table that will be
     analysed. The user can set it with the 'Set' button.

      'Input dudi' : this is directly the dudi that will be analysed.
     The user can set it with the 'Set' button. No ordination method
     should be used when a dudi is selected here: cluster analysis will
     be done on the row scores of this dudi.

      'Ordination method' : the user can choose between principal
     component analysis (centered or normed), correspondence analysis,
     and multiple correspondence analysis. After computations are
     finished, the eigenvalues bar chart is displayed in the right
     panel. The user can then set the number of principal components
     (axes) on which cluster analysis will be done with the 'Set'
     button (defaults to 2). If no number is chosen, then all axes are
     kept.

      'Ordination graph' : draw the factor maps for rows or columns.
     Axis numbers can be chosen (default is 1 for X axis and 2 for Y
     axis).

      'Cluster analysis - Distance' : choose the way distances are
     computed among rows. See help("dist"). The 'dudi' option is a
     special case: computations are done with the 'dist.dudi' function
     of the 'ade4' package (i.e., for a normed PCA this is the
     Euclidean distance computed on normed variables).

      'Cluster analysis - Cluster method' : choose the clustering
     algorithm. See help("hclust"). The 'Submit' button starts the
     computations and the hierarchical tree is displayed in the right
     panel. Choosing another algorithm or another distance
     automatically updates the graph, allowing easy comparisons.

      'Number of groups' : this is the number of groups used to cut the
     tree computed by cluster analysis. The 'Cut tree' button cuts the
     tree and draws a red line on the right panel. 'Up arrow' and 'Down
     arrow' keyboard keys (or the scale widget) can be used to increase
     or decrease this value respectively.

      'Level height' : height of the cut level in the tree computed by
     cluster analysis. The 'Cut tree' button cuts the tree and draws a
     red line on the right panel.

      'Inertia ratio' : this is the between group to total inertia
     ratio (percentage of explained variance). The 'Draw curve' button
     draws the curve of this ratio as a function of the number of
     groups. Steps on this curve can be used to choose the number of
     groups. The red cross on this graph gives the number of groups and
     the corresponding percentage of between-groups inertia. 'Up arrow'
     and 'Down arrow' keys (or the scale widget) can be used to
     increase or decrease the number of groups. Choosing another
     clustering algorithm or another distance automatically updates the
     graph, allowing easy comparisons.

      'BGA MCTest p-value' : p-value of the Between Groups Analysis
     Monte-Carlo test (BGA, ade4 'between' function).

      The dudi and the factor used to draw the graphs are available in
     the global environment, withe the names 'ordiClust.dudi' and
     'ordiClust.factor'.

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

     Jean Thioulouse jthioulouse@biomserv.univ-lyon1.fr 
      Stephane Dray dray@biomserv.univ-lyon1.fr

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

     ## Not run: 
     ## Start the GUI form the console
     data(meau) 
     ordiClust(dudi.pca(meau$mil,scan=F))
     ## End(Not run)

