R: R Commander

Commander {Rcmdr}

R Documentation

R Commander

Description

Start the R Commander GUI (graphical user interface)

Usage

Commander()

Details

Getting Started

For more detailed information about getting started, see Help -> Introduction to the R Commander from the R Commander menus or Fox (2017).

The default R Commander interface consists of (from top to bottom) a menu bar, a toolbar, a code window with script and R Markdown tabs, 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 tab. 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, STATA data set, SAS XPORT data set; or an Excel spreadsheet. 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 tab (the initially empty text window immediately below the toolbar), and commands and output appear in the Output window (the initially empty text window below the Script tab). Commands that don't require direct user interaction (such as interactive identification of points on a graph) are also used to create an R Markdown document in the tab of the same name. When the R Markdown tab is in front, pressing the "Generate HTML report" button compiles the document to create an html page with input and output, which opens in a web browser. To alter these and other defaults, see the information below on configuration. Note, for example, that the knitr package can be used to create a LaTeX document to be compiled to a PDF report, as an alternative to — or in addition to — an R Markdown document (see the use.knitr option below).

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 and R Markdown tabs in the Commander. You can edit these commands in the normal manner and can also type new commands. You can also type explanatory text in the R Markdown tab. Individual commands in the Script tab can be continued over more than one line, but the several lines of a multi-line command must be submitted simultaneously. (It is not necessary, as in earlier versions of the R Commander, to begin continuation lines with white space.) The contents of the Script and R Markdown tabs can be saved during or at the end of the session, and a saved script or R Markdown document can be loaded into the respective tabs. The contents of the Output window can also be edited or saved to a text file. Finally, editing operations also work in the Messages window.

To re-execute a command or set of commands in the Script tab, 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", or Control-Tab). If no text is selected, the Submit button (or Control-R or Control-Tab) 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 tab, R Markdown tab, knitr tab, Output window, or Messages window. Edit functions such as search are performed in the Script tab unless you first click in another tab or window to make it active.

Pressing Control-S will save the Script tab, R Markdown tab, knitr tab, or Output window.

Pressing Control-A selects all of the text in the Script tab, R Markdown tab, knitr tab, Output window, or Messages window.

In addition, the following Control-key combinations work in these tabs and windows: Control-X, cut; Control-C, copy; Control-V, insert; Control-Z or Alt-Backspace, undo; and Control-W, redo.

Under Mac OS X, the command key may be used in place of the Control key, though the latter works as well.

Right-clicking the mouse (clicking button 3 on a three-button mouse, or Control-left-clicking) in the tabs or windows brings up a "context" menu with the Edit-menu items, plus (in the Script, R Markdown, and knitr tabs) a Submit item.

You can open a larger editor window with the document in the Markdown or knitr tab by making the corresponding selection from the Edit menu, the right-click context menu when the cursor is in the tab, or by pressing Control-E when the cursor is in the tab.

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.

Pressing a letter key (e.g., "a") in a list box will scroll the list box to bring the next entry starting with that letter to the top of the box.

You can cancel an R Commander dialog box by pressing the Esc key.

Most R Commander dialogs remember their state when this is appropriate, and can be restored to pristine state by pressing the Reset button.

Some R Commander dialogs have an Apply button that will execute the command generated by the dialog and then re-open the dialog in its previous state.

Exit from the Commander via the File -> Exit menu or by closing the Commander window.

Customization and Configuration

The preferred way of customizing the R Commander is to write a plug-in package: see help("Plugins").

Alternatively, configuration files reside in the etc subdirectory of the package, or in the locations given by the etc and etcMenus options (see below).

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

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. Alternatively, you can edit the source package and recompile it.

To reiterate, however, the preferred procedure is to write an R Commander plug-in package.

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:

ask.to.exit: if TRUE (the default), then the user is asked whether he or she wants to exit the Rcmdr; if this option is set to FALSE, then the subsequent option is also set to FALSE.
ask.on.exit: if TRUE (the default), then the user is asked whether to save the script file, R Markdown file, and output file when the Rcmdr exits.
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, unless the R Commander is running under RStudio, in which case the default is TRUE.
crisp.dialogs: If TRUE, dialogs should appear on the screen fully drawn, rather than built up widget by widget. Prior to R 2.6.1, this option only works on the Windows version of R, but should in any event be harmless. The default is TRUE. If you encounter stability problems, try setting this option to FALSE.
default.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.
default.font.family: The default font for GUI elements such as menus and text labels, in the form of a Tk font family specification, given in a character string. For example, "Helvetica" specifies the sans-serif Helvetica font family. The default is taken from the TkDefaultFont. Normally a sans-serif font should be used.
default.font.size: The size, in points, of the default font. The default is 10 on non-Windows system and the size of the system font on Windows. To set the font size for R input and output, see the log.font.size option. The Rcmdr scale.factor option may also be used to control font size.
discreteness.theshold: should be a positive integer; if greater than 0 (which is the default), the maximum number of distinct values for a numeric variable to be considered discrete; if 0 (or smaller), the threshold is taken as the smallest of 100, twice the squareroot of the number of cases in the active data set (n), and 10 times log10(n).
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.
editDataset.threshold: If the number of values in the current data set exceed this value (the default is 10000), then the standard R data editor is used in preference to the R Commander editDataset editor.
error.text.color: Color for error messages; the default is "red".
etc: Set to the path of the directory containing the Rcmdr configuration files; defaults to the etc subdirectory of the installed Rcmdr package.
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.
help_type: This Rcmdr option takes precedence over the global R help_type option (see options and help), and by default is set to "html".
iconify.commander: If TRUE, the Commander window is minimized on startup; the default is FALSE.
length.output.stack: The R Commander maintains a list of output objects, by default including the last several outputs; the default length of the output stack is 10. popOutput() “pops” (i.e., returns and removes) the first entry of the output stack. Note that, as a stack, the queue is LIFO (“last in, first out”).
length.command.stack: The R Commander also maintains a list of commands that is managed similarly; the default length of this stack is also 10.
log.commands: If TRUE (the default), commands are echoed to the script window; if FALSE, the script window is not displayed.
log.font.family: The font family to be used for text in the script window, output window, messages window, etc., specified as a character vector giving a Tk font family. This should normally be a monospaced font like "Courier". The default is taken from the TkFixedFont.
log.font.size: The font size, in points, to be used in the script window, in the output window, messages window, in recode dialogs, and in compute expressions — that is, where a monospaced font is used. The default is 10. Alternatively the Rcmdr scale factor option may also be used to control font size.
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.
messages.height: The height of the messages window, in lines. The default is 4.
model.case.deletion: if TRUE (the default is FALSE), include a text box for case deletion in statistical-model dialog boxes (e.g., for linear models).
minimum.width: The minimum width, in pixels, for the main R Commander windows; the default is 1000.
minimum.height: The minimum height, in pixels, for the main R Commander windows; the default is 400.
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.
number.messages: If TRUE, the default, messages in the messages window are numbered.
open.graphics.devices: If TRUE (the default is FALSE), open the system graphics device and (if 3D RGL graphics are used) the RGL graphics device when the R Commander starts.
open.markdown.editor: If TRUE (the default is FALSE), open the R Markdown editor when the R Commander starts.
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 "", which lets the Tk window manager decide where to place the window; for example, "+20+20" should put the window near the upper-left corner of the screen, "-20+20" near the upper-right corner, though this doesn't appear to work reliably on Windows systems.
plugins: A character vector giving the names of Rcmdr plug-in packages to load when the Commander starts up. Plug-in packages can also be loaded from the Tools -> Load Rcmdr plug-in(s) menu. See Plugins.
prefixes: A four-item character vector to specify the prefixes used when output is directed to the R console; the default is c("Rcmdr> ", "Rcmdr+ ", "RcmdrMsg: ", "RcmdrMsg+ ").
quit.R.on.close: if TRUE, both the Commander and R are exited when the Commander window is closed. The default is FALSE, in which case only the Commander is exited (and can be restarted by the command Commander()).
RcmdrEnv.on.path: If TRUE (the default is FALSE), the environment in which R Commander state information is stored is placed on the search path. Some plug-ins, at least until they are updated, may require this setting.
retain.messages: If TRUE (the default), 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".
retain.selections: If TRUE (the default), dialogs remember their previous state, where appropriate, as long as the data set isn't changed; some dialogs, e.g., for probabilities, retain selections even when the data set chanages.
RExcelSupport: If TRUE (the default is FALSE), menus and output are handled by Excel.
rmarkdown.output: Values of several options for converting R Markdown to a document file. The default for this option is TRUE, which corresponds to markdown.output=list(command.sections=TRUE, section.level=3, toc=TRUE, toc_float=TRUE, toc_depth=3, number_sections=FALSE, translate.rmd.headers=TRUE). The sub-option command.sections controls whether most R commands produce sections in the R Markdown document; the sub-option section.level controls the level of the sections that are created; the sub-option translate.rmd.headers controls whether the headers are translated from English into another language, if a translation is available; and the other sub-options are standard for rmarkdown. The toc_float, toc_depth, and number_sections sub-options are only effective if Pandoc is installed.
rmd.output.format: The output file type for R Markdown documents if pandoc is installed; one of "html" (the default), "pdf" (requires LaTeX), "docx" (Word), or "rtf" (rich text file).
rmd.template: The quoted path to a .Rmd file to serve as a template for R code and output. The default is to use a template included with the package.
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.
scientific.notation: Higher numbers cause ordinary (decimal) notation to be increasingly preferred to scientific notation for representing very small and very large numbers; correspond to the scipen option in R: see options. The default is 5, while the standard default in R is 0 (where 0 means that scientific notation is used whenever the resulting printed representation of a number is smaller in scientific than in standard notation).
showData.threshold: a vector with 2 entries, defaulting to c(20000, 100). If the number of cases in the active data set exceeds the first number (default, 20,000) or the number of variables exceeds the second number (default, 100), then View() rather than showData() is used to display the data set. The reason for the option is that showData() is very slow when the number of cases or variables is large; setting the threshold to c(0, 0) suppresses the use of showData altogether. It's necessary to use showData however for the view of the active data set to be updated dynamically when, e.g., a variable is added.
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.
suppress.icon.images: Set to TRUE to suppress the icon images in dialog OK, Cancel, Reset, and Help buttons; the default is FALSE.
suppress.menus: if TRUE, the Commander menu bar and tool bar are suppressed, allowing another program (such as Excel) to take over these functions. The default (of course) is FALSE.
suppress.X11.warnings: On (some?) Linux and Mac OS X 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 interactively 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.
theme: A ttk theme to control the overall style of the Commander GUI; should be one of the themes returned by tcltk2::tk2theme.list(). The default theme varies by operating system, and can be discovered by entering the command tcltk2::tk2theme() in a fresh R session.
title.color: Color for the titles of some widgets, such as variable-list boxes; can be given as a color name, such as "blue" or as an RGB value, such as "#0000FF". The default is the standard color for ttk label frames, unless that is "#000000" or "black", in which case "blue" is used instead.
tkwait.commander: 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.commander 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.
tkwait.dialog: If TRUE (the default is FALSE), R will wait until an R Commander dialog is closed. This has the disadvantage of preventing help pages from being displayed until a dialog is closed in the Mac OS X R.app and in RStudio. This was also the standard behavior of the R Commander in earlier versions and is provided for compatibility with previous behavior. If this option is TRUE, then the R Commander data editor is disabled in favor of the standard R platform-specific data editor, and the new-data-set menu item is suppressed.
use.knitr: If TRUE (the default is FALSE), a knitr .Rnw LaTeX document is created in a tab of the main Commander window; this document can be compiled into .tex and .pdf reports via the knit2pdf function in the knitr package.
use.markdown: If TRUE (the default is the negation of the use.knitr argument), an R Markdown document is created, which can be compiled into an HTML, PDF, Word, or rich text file report.
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.
"valid.classes": The classes of variables that the R Commander recognizes, in addition to numeric data; other variables in a data set will be suppressed. The default is "factor", "ordered", "character", "logical", "POSIXct", "POSIXlt", "Date", "chron", "yearmon", "yearqtr", "zoo", "zooreg", "timeDate", "xts", "its", "ti", "jul", "timeSeries", "fts", "Period", "hms", "difftime").
variable.list.height: the number of items (typically variables) to display in list boxes; longer lists may be viewed by scrolling. The default is 6.
variable.list.width: a two-item vector controlling the width of list boxes, in characters, giving the minimum and maximum width to display; the default is c(20, Inf). If the widest item name falls in this range, then its number of characters determines the width of the box. Note: This specification works only approximately.
warning.text.color: Color for warning messages; the default is "darkgreen".

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

If you want always to launch the R Commander when R starts up, you can include the following code in one of R's start-up files (e.g., in the Rprofile.site file in R's etc subdirectory):

local({
old <- getOption("defaultPackages")
options(defaultPackages = c(old, "Rcmdr"))
})

R Commander options can also be permanently set in the same manner. For more information about R initialization, see ?Startup.

Warning

The R Commander Script window does not provide a true console to R, and may have certain limitations. I don't recommend using the R Commander for serious programming or for data analysis that relies primarily on scripts — use a programming editor instead. If you encounter any problems with the Script tab, however, I'd appreciate it if you brought them to my attention.

Platform-Specific Issues

Under Windows, the Rcmdr package can be run under the Rgui in the SDI (single-document interface) mode, or under rterm.exe. You might experience problems running the Rcmdr under ESS with NTEmacs or XEmacs, or under other R consoles. The R Commander can be run under the Rgui in MDI (multiple-document interface) mode but it is relatively inconvenient to do so and isn't recommended.

Occasionally, under Windows, after typing some text into a dialog box (e.g., a subsetting expression in the Subset Data Set dialog), buttons in the dialog (e.g., the OK button) will have no effect when they are pressed. Clicking anywhere inside or outside of the dialog box should restore the function of the buttons. As far as I have been able to ascertain, this is a problem with Tcl/Tk for Windows. I have not seen this behavior in some time and the problem may have been solved.

Under Mac OS X Mavericks and later, the R Commander may appear to freeze or hesitate when run under R.app if the R.app window is hidden and "app nap" is turned on. It is recommended that app nap be turned off for R.app, which can be most conveniently done via the R Commander Tools menu. The app nap setting is permanent until changed and so the current setting will apply whether or not the R Commander is used. When R is first installed, app nap will be on for R.app. The tcltk package requires that X Windows is installed under Mac OS X, and as a consequence the Rcmdr package, which depends on tcltk, will not load if X Windows is absent. X Windows for Mac OS X may be obtained from https://www.xquartz.org/.

Note

On startup, the R Commander sets options(na.action=na.exclude); this is done so that observation statistics such as residuals can be properly added to the active data set when there are missing values. The option is reset to its pre-existing value when the Commander exits. Some functions may not work properly when the default na.action is set to na.exclude.

This version should be compatiable with the RExcel package, which can use the R Commander menus.

Author(s)

John Fox jfox@mcmaster.ca

References

Fox, J. (2017) Using the R Commander: A Point-and-Click Interface for R. Chapman and Hall/CRC Press.

Fox, J. (2005) The R Commander: A Basic Statistics Graphical User Interface to R. Journal of Statistical Software, 14(9): 1–42.

Fox, J. (2007) Extending the R Commander by "plug in" packages. R News, 7(3): 46–52.

Examples

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

[Package Rcmdr version 2.9-2 Index]