ade4TkGUI             package:ade4TkGUI             R Documentation

_T_c_l/_T_k _G_U_I _f_o_r _t_h_e _a_d_e_4 _p_a_c_k_a_g_e

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

     A Tcl/Tk GUI for some basic functions in the 'ade4' package.

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

     ade4TkGUI(show = FALSE, history = FALSE)

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

    show: a logical value. If 'TRUE', R commands executed in the GUI
          are echoed to the console.

 history: a logical value. If 'TRUE', R commands executed in the GUI
          are stored in the R session history.

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

     Right-click on ade4 function buttons to get help on these
     functions. You can also click on the questionhead icon in the
     dialog windows. This displays the R help for the corresponding
     function.

     In all dialog windows, entries can either be filled with a "'set'"
     button, or typed directly in the entry field. The "'set'" button
     displays a listbox with a list of available objects in the global
     environment. This list is restricted to objects with an adequate
     type (dataframe, dudi, factor, etc). Entries can also be filled
     directly by typing the desired value. In this case, R expressions
     can also be entered, for example 'c("red", "green", "blue")',
     'doubs$mil[1:20,1:5]', 'meau$plan$dat' , or '1:20'.

_B_u_t_t_o_n_s:

     The first row of buttons ('- Data sets -') is used to load data
     sets, either from a tab-delimited text file exported from Excel
     ('Read data file' button), or from the 'ade4' package built-in
     datasets ('Load a data set' button;  right-click to get help on
     the selected dataset).

     The second block of buttons ('- One table analyses -') gives
     access to simple analyses (like 'pca'), in which only one table is
     analysed. 

     The third block ('- One table with groups -') is for analyses in
     which the rows of the table belong to several groups. This is the
     case for example  for  discriminant analysis ('discrimin') and for
     the 'within' and 'between' analyses (see 'ade4' documentation).

     The fourth block ('- Two tables analyses -') gives access to three
     analyses in which the relationships between two data tables are
     analysed. 'cca' is the well known (at least in ecology) canonical
     correspondence analysis, 'coinertia' can be seen as a robust
     alternative to 'cca' when the number of samples is low, and
     'pcaiv' is principal components analyses with respect to
     instrumental variables (see 'ade4' documentation).

     The fifth block ('- Graphic functions -') contains three buttons
     that launch the dialog windows for three basic graphic functions
     in 'ade4' : 's.label' (scatter diagram of a factor map), 's.class'
     (scatter diagram with groups),  's.value' (scatter diagram with
     squares proportional to one variable).

     Other graphic functions are available in the 'Graphics' menu :
     's.corcircle' (correlation circle in normed pca), 's.chull'
     (scatter diagram with convex hulls), and 's.match' (scatter
     diagram of two paired clouds of points)

     The sixth block ('- Advanced graphics -') can be used for several
     things:

     - 'Display dudi' displays a dialog window grouping all the
     components of a 'dudi'. Each of these components is represented by
     a button which action is to draw a graphical display of the
     corresponding component. The axes used to draw theses graphics can
     be set by the user. The last row of buttons gives access to
     particular graphic functions that can be used according to the
     dudi type.

     - 'Graph explore' is a dynamic graphic exploration of factor maps
     (it needs the 'tkrplot' package). It allows dynamic operations
     like zooming, panning, and identifying points. This is
     particularly usefull when many points are superimposed.

     - 'Monte-Carlo tests' displays a dialog window for computing
     Monte-Carlo tests after (e.g.) a 'between' or 'coinertia'
     analysis.

_M_e_n_u _b_a_r:

     The menu bar at the top of the window can be used to launch the
     same functions, plus several others. All theses menus are
     tear-off.

     The 'File' menu can be used to read and load files and datasets,
     to edit a dataframe, and to quit R :

     - 'Read text file' allows to read a data file and store the result
     in a dataframe. It can be used to read standard Excel
     tab-delimited text files (with variable names on the first row and
     sample names in the first column, leaving the first cell empty).
     The name "clipboard" can be used to read a data table just copied
     from an Excel data sheet (so it is not necessary to save the data
     in a text file).

     - 'Load data set' allows to load a data set from the 'ade4'
     package.

     - 'Edit data frame' can be used to edit a dataframe.

     - 'Quit R' opens a dialog window to ask if the environment should
     be saved before quitting R.

     The 'Windows' menu allows to manage several graphical windows :

     - 'New graphic window' opens a new graphic window and makes it the
     active window. This is usefull to compare easily several graphics.

     - 'Change graphic window' changes the active window (i.e., the one
     into which the next graphic will be drawn).

     - 'Save graphic window' saves the graphic drawn in the active
     window into a disk file in several formats (postscript, pdf, etc).

     The '1table', '1table+groups', '2tables', and 'Graphics' menus
     give access to several other analysis methods and graphics.

_H_i_s_t_o_r_y _a_n_d _c_o_m_m_a_n_d _l_i_n_e _e_c_h_o_i_n_g:

     If the 'show' argument is set to TRUE, then all the commands
     executed in the GUI are echoed to the console. This is handy for
     complex commands, as it allows to check the exact syntax of the
     command that was executed.

     If the 'history' argument is set to TRUE, then the commands
     executed in the GUI (the same as the commands which are echoed to
     the console) are stored in the R session history buffer. For each
     command, the history buffer is written to a temporary disk file
     with 'savehistory()', the command is appended to this file, and
     the file is reread in memory with 'loadhistory()'.

     The value (T/F) of both arguments is recalled in the title of the
     window (ade4TkGUI), so that different instances of the GUI
     launched simultaneously with different values for these arguments
     can be easily recognized.

_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
     ade4TkGUI()
     ## End(Not run)

