R Commander

Description

Start the R Commander GUI (graphical user interface)

Usage

Commander()

Details

Getting Started

The default R Commander interface consists of (from top to bottom) a menu bar, a toolbar, a script window, an output window, and a messages 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; and an information field showing the active statistical model. There is also a Submit button for re-executing commands in the 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 suitable 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, Minitab data set, or STATA 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 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 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, generalized linear, or other 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 script window in the Commander. You can edit these commands in the normal manner and can also type new commands into the 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 script window can be saved during or at the end of the session, and a saved script can be loaded into the 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 script window or the output window. Edit functions such as search are performed in the script window unless you first click in the output window to make it the active window.

Pressing Control-S will save the script or output window.

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

A number of functions are provided to assist in writing dialogs, and Rcmdr state information is stored in a separate environment. See help("Rcmdr.Utilities") and the manual supplied in the doc 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:

attach.data.set

if TRUE (the default is FALSE), the active data set is attached to the search path.

check.packages

if TRUE (the default), on start-up, the presence of all of the Rcmdr recommended packages will be checked, and if any are absent, the Rcmdr will offer to install them.

command.text.color

Color for commands in the output window; the default is "red".

console.output

If TRUE, output is directed to the R Console, and the R Commander output window is not displayed. The default is FALSE.

contrasts

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.

crisp.dialogs

If TRUE, dialogs should appear on the screen fully drawn, rather than built up widget by widget. This option should affect the Windows version of R only, but should in any event be harmless. The default is TRUE under Windows for R versions 2.1.1 and above, and FALSE otherwise. If you're working on Windows and encounter increased stability problems, trying setting this option to FALSE.

default.font

The default font, as an X11 font specification, given in a character string. If specified, this value takes precedence over the default font size (below). This option is only for non-Windows systems.

default.font.size

The size, in points, of the default font. The default is 10 for Windows systems and 12 for other systems Unless otherwise specified (see the previous 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.

double.click

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.

error.text.color

Color for error messages; the default is "red".

grab.focus

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.

load.at.startup

A character vector of names of packages to be loaded when the Rcmdr package is loaded; the default is to load only the car package. Other required packages will be loaded as needed. If it is available, the car package will be loaded at when the Commander starts in any event.

log.commands

If TRUE (the default), commands are echoed to the script window; if FALSE, the script window is not displayed.

log.font.size

The font size, in points, to be used in the 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 for Windows systems and 12 for other systems.

log.height

The height of the script window, in lines. The default is 10. Setting log.height to 0 has the same effect as setting log.commands to FALSE.

log.text.color

Color for text in the script window; the default is "black".

log.width

The width of the script and output windows, in characters. The default is 80.

multiple.select.mode

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.

output.height

The height of the output window, in lines. The default is twice the height of the script window, or 20 if the script window is suppressed. Setting output.height to 0 has the same effect as setting console.output to TRUE.

output.text.color

Color for output in the output window; the default is "blue".

placement

Placement of the R Commander window, in pixels; the default is "-40+20", which puts the window near the upper-right corner of the screen.

suppress.X11.warnings

On (some?) Linux systems, multiple X11 warnings are generated by Rcmdr commands after a graphics-device window has been opened. Set this option to TRUE (the default when running under X11) to suppress reporting of these warnings. An undesirable side effect is that then all warnings and error messages are intercepted by the Rcmdr, even those for commands entered at the R command prompt. Messages produced by such commands will be printed in the Commander Messages window after the next Rcmdr-generated command. Some X11 warnings may be printed when you exit from the Commander.

retain.messages

If TRUE (the default is code{FALSE}), the contents of the message window are not erased between messages. In any event, a "NOTE" message will not erase a preceding "WARNING" or "ERROR".

scale.factor

A scaling factor to be applied to all Tk elements, such as fonts. This works well only in Windows. The default is NULL.

showData.threshold

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; setting the threshold to 0 suppresses the use of showData altogether.

show.edit.button

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 (though I believe that this problem as been solved).

sort.names

Set to TRUE (the default) if you want variable names to be sorted alphabetically in variable lists.

tkwait

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 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 when output is directed to the R console.

use.rgl

If TRUE (the default), the rgl package will be loaded if it is present in an accessible library; if FALSE, the rgl package will be ignored even if it is available. The rgl package can sometimes cause problems when running R under X11.

warning.text.color

Color for warning messages; the default is "darkgreen".

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

Note

This version is compatible with SciViews, which currently runs only under Windows systems: http://www.sciviews.org/SciViews-R; see Rcmdr.sciviews-specific. Under Windows, the Rcmdr package can also be run under the Rgui in SDI (single-document interface) mode, or under rterm.exe; you might experience problems running the Rcmdr under ESS withNTEmacs or XEmacs.

Author(s)

John Fox jfox@mcmaster.ca

Examples

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