Commander               package:Rcmdr               R Documentation

_R _C_o_m_m_a_n_d_e_r

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

     Start the R Commander GUI (graphical user interface)

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

     Commander()

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

     *Getting Started*

     The default R Commander interface consists of (from top to bottom)
     a menu bar, a toolbar, a log/script window, and an output window.

     Commands to read, write, transform, and analyze data are entered
     using the menus in the menu bar at the top of the _Commander_
     window. Most menu items lead to dialog boxes requesting further
     specification. I suggest that you explore the menus to see what is
     available.

     Below the menu bar is a toolbar with (from left to right) an
     information field displaying the name of the active data set;
     buttons for editing and displaying the active data set; an
     information field showing the active statistical model; and a
     _Submit_ button for re-executing commands in the log/script
     window. The information fields for the active data set and active
     model are actually  buttons that can be used to select the active
     data set and model from among, respectively, data frames or linear
     and generalized linear model objects in memory.

     Almost all commands require an active data set. When the Commander
     starts, there is no active data set, as indicated in the data set
     information field. A data set becomes the active data set when it
     is read into memory from an R package or imported from a text
     file, SPSS data set, or Minitab data set. In addition, the active
     data set can be selected from among R data frames resident in
     memory. You can therefore switch among data sets during a session.

     By default, commands are logged to the log/script window (the
     initially empty text window immediately below the toolbar); 
     commands and output appear in the output window (the initially
     empty text window below the log/script window); and the active
     data set is attached to the search path. To alter these and other
     defaults, see the information below on configuration.

     Some 'Rcmdr' dialogs (those in the _Statistics -> Fit models_
     menu)  produce linear or generalized  linear models. When a model
     is fit, it becomes the active model, as indicated in the
     information field in the R Commander toolbar. Items in the
     _Models_ menu apply to the active model. Initially, there is no
     active model.  If there are several models in memory, you can
     select the active model from among them.

     If command logging in turned on, R commands that are generated
     from the menus and dialog boxes are entered into the log/script
     window in the Commander. You can edit these commands in the normal
     manner and can also type new commands into the log/script window.
     Individual commands can be continued over more than one line, but
     each line after the first must be indented with one or more spaces
     or tabs. The contents of the log/script window can be saved during
     or at the end of the session, and a saved script can be loaded
     into the log/script window. The contents of the output window can
     also be edited or saved to a text file.

     To re-execute a command or set of commands, select the lines to be
     executed using the mouse and press the _Submit_ button at the
     right of the toolbar (or _Control-R_, for "run"). If no text is
     selected, the _Submit_ button (or _Control-R_)  submits the line
     containing the text-insertion cursor. Note that an error will be
     generated if the submitted command or commands are incomplete.

     Pressing _Control-F_ brings up a find-text dialog box (which can
     also be accessed via  _Edit -> Find_) to search for text in the
     log/script window or the output window. Edit functions such as
     search are performed in the log/script window unless you first
     click in the output window to make it the active window.

     Pressing _Control-S_ will save the log/script or output window.

     Right-clicking the mouse (clicking button 3 on a three-button
     mouse) in the log/script or output window brings up a "context"
     menu with the _Edit_-menu items, plus (in the log/script window) a
     _Submit_ item.

     When you execute commands from the _Commander_ window, you must
     ensure that the sequence of commands is logical. For example, it
     makes no sense to fit a statistical model to a data set that has
     not been read into memory. 

     Exit from the Commander via the _File -> Exit_ menu or by closing
     the _Commander_ window.

     *Customization and Configuration*

     Configuration files reside in the 'etc' subdirectory of the
     package.

     The 'Rcmdr' menus can be customized by editing the file
     'Rcmdr-menus.txt'.

     Some functions (e.g., 'hist') that do not normally create visible
     printed output when executed from the _R Console_ command prompt
     will do so - unless prevented - when executed from the 
     _Commander_ log window. Such output can be suppressed by listing
     the names of these functions in the 'log-exceptions.txt' file.

     You can add R code to the package, e.g., for creating additional
     dialogs, by placing files with file type '.R' in the 'etc'
     directory, also editing 'Rcmdr-menus.txt' to provide additional
     menus, sub-menus, or menu-items. A demo addition is provided in
     the file  'BoxCox.demo'. To activate the demo, rename this file to
     'BoxCox.R', and uncomment the corresponding menu line in
     'Rcmdr-menus.txt'. Alternatively, you can edit  the source package
     and recompile it.

     The following functions are provided to assist in writing dialogs:
     'activeDataSet',  'activeModel', 'doItAndPrint', 'justDoIt',
     'listDataSets',  'listGeneralizedLinearModels',
     'listLinearModels', 'logger'. The following global variables
     contain information about variables in the active data set:
     '.factors', '.numeric', '.twoLevelFactors', '.variables'. See
     'help("Rcmdr.Utilities")' and the manual supplied in the 'etc'
     directory of the 'Rcmdr' package for more information.

     In addition, several features are controlled by run-time options,
     set via the 'options("Rcmdr")' command. These options should be
     set before the package is loaded. If the options are unset, which
     is the usual situation, defaults are used. Specify options as a
     list of _name=value_ pairs. You can set none, one, several, or all
     options. The available options are as follows:

     '_a_t_t_a_c_h._d_a_t_a._s_e_t' if 'TRUE' (the default), the active data set is
          attached to the search path.

     '_l_o_g._c_o_m_m_a_n_d_s' If 'TRUE' (the default), commands are echoed to the
          log/script window; if 'FALSE', the log/script window is not
          displayed.

     '_l_o_g._t_e_x_t._c_o_l_o_r' Color for text in the log/script window; the
          default is '"black"'.

     '_l_o_g._f_o_n_t._s_i_z_e' The font size, in points, to be used in the
          log/script window, in the output window, in recode dialogs,
          and in compute expressions - that is, where a monospaced font
          is used.  The default is 10.

     '_l_o_g._w_i_d_t_h' The width of the log/script and output windows, in
          characters. The default is 80.

     '_l_o_g._h_e_i_g_h_t' The height of the log/script window, in lines. The
          default is 10. Setting 'log.height' to 0 has the same effect
          as setting 'log.commands' to 'FALSE'.

     '_c_o_n_s_o_l_e._o_u_t_p_u_t' If 'TRUE', output is directed to the _R Console_,
          and the  _R Commander_ output window is not displayed. The
          default is 'FALSE'.

     '_o_u_t_p_u_t._h_e_i_g_h_t' The height of the output window, in lines. The
          default is twice the height of the log/script window, or 20
          if the log/script window is suppressed. Setting
          'output.height' to 0 has the same effect as setting
          'console.output' to 'TRUE'.

     '_c_o_m_m_a_n_d._t_e_x_t._c_o_l_o_r' Color for commands in the output window; the
          default is '"red"'.

     '_o_u_t_p_u_t._t_e_x_t._c_o_l_o_r' Color for output in the output window; the
          default is '"blue"'.

     '_p_l_a_c_e_m_e_n_t' Placement of the _R Commander_ window, in pixels; the
          default is '"-40+40"', which puts the window near the
          upper-right corner of the screen.

     '_c_o_n_t_r_a_s_t_s' Serves the same function as the general 'contrasts'
          option; the default is  'c("contr.Treatment", "contr.poly")'.
          When the Commander exits, the 'contrasts' option is returned
          to its pre-existing value. Note that 'contr.Treatment' is
          from the 'car' package.

     '_g_r_a_b._f_o_c_u_s' Set to 'TRUE' for the current Tk window to  "grab"
          the focus - that is, to prevent the focus from being changed
          to another Tk window. On some systems, grabbing the focus in
          this manner apparently causes problems. The default is
          'TRUE'.  If you experience focus problems, try setting this
          option to 'FALSE'.

     '_d_o_u_b_l_e._c_l_i_c_k' Set to 'TRUE' if you want a double-click of the
          left mouse button to press the default button in all dialogs.
          The default is 'FALSE'.

     '_m_u_l_t_i_p_l_e._s_e_l_e_c_t._m_o_d_e' Affects the way multiple variables are
          selected in variable-list boxes. If set to '"extended"' (the
          default), left-clicking on a variable selects it and
          deselects any other variables that are selected;
          Control-left-click toggles the selection (and may be used to
          select additional variables); Shift-left-click extends the
          selection. This is the standard Windows convention. If set to
          '"multiple"', left-clicking toggles the selection of a
          variable and may be used to select more than one variable.
          This is the behaviour in the Rcmdr prior to version 1.9-10.

     '_r_e_p_o_r_t._X_1_1._w_a_r_n_i_n_g_s' On (some?) Linux systems, multiple X11
          warnings are generated by Rcmdr commands after a
          graphics-device window has been opened. Set this option to
          'FALSE' (the default) to suppress reporting of these
          warnings. Some warnings will be printed when you exit from
          the Commander.

     '_s_o_r_t._n_a_m_e_s' Set to 'TRUE' (the default) if you want variable
          names to be sorted alphabetically in variable lists.

     '_s_h_o_w._e_d_i_t._b_u_t_t_o_n' Set to 'TRUE' (the default) if you want an
          _Edit_ button in the Commander window, permitting you to edit
          the active data set. Windows users may wish to set this
          option to 'FALSE' to suppress the _Edit_ button because
          changing variable names in the data editor can cause R to
          crash.

     '_s_c_a_l_e._f_a_c_t_o_r' A scaling factor to be applied to all Tk elements,
          such as fonts. This works well only in Windows. The default
          is 'NULL'.

     '_d_e_f_a_u_l_t._f_o_n_t._s_i_z_e' The size, in points, of the default font. The
          default is 10. Unless otherwise  specified (see the next
          item), the default font is
          '"*helvetica-medium-r-normal-*-xx*"', where 'xx' is the
          default font size. This option is only for non-Windows
          systems.

     '_d_e_f_a_u_l_t._f_o_n_t' The default font, as an X11 font specification,
          given in a character string.  If specified, this value takes
          precedence over the default font size (above). This option is
          only for non-Windows systems.

     '_t_k_w_a_i_t' This option addresses a problem that, to my knowledge, is
          rare,  and may occur on some non-Windows systems. If the
          Commander causes R to hang,  then set the 'tkwait' option to
          'TRUE'; otherwise set the option to 'FALSE' or ignore it.  An
          undesirable side effect of setting the 'tkwait' option to
          'TRUE' is that the R session command prompt is suppressed
          until the Commander exits. One can still enter commands via
          the log/script window, however. In particular, there is no
          reason to use this option under Windows, and it should not be
          used with the Windows R GUI with buffered output.

     '_s_h_o_w_D_a_t_a._t_h_r_e_s_h_o_l_d' If the number of variables in the active data
          set exceeds this value (default, 100), then 'edit()' rather
          than 'showData()' is used to display the data set. A
          disadvantage is that control doesn't return to the Commander
          until the edit window is closed. The reason for the option is
          that 'showData()' is very slow when the number of variables
          is large.

     Many options can also be set via the _File -> Options_ menu, which
     will restart the Commander after options are set.

_N_o_t_e:

     This version is compatible with SciViews, which currently runs
     only under Windows systems: <URL:
     http://www.sciviews.org/SciViews-R>; see
     'Rcmdr.sciviews-specific'.

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

     John Fox jfox@mcmaster.ca

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

         options(Rcmdr=list(log.font.size=12, contrasts=c("contr.Sum", "contr.poly")))
         

