The Rcmdr Package

January 8, 2009
Version 1.4-7

Date 2009/01/06

Title R Commander

Author John Fox <jfox@[Link]>, with contributions from Michael Ash, Theophilius Boye,
Stefano Calza, Andy Chang, Philippe Grosjean, Richard Heiberger, G. Jay Kerns, Renaud
Lancelot, Matthieu Lesnoff, Samir Messad, Martin Maechler, Duncan Murdoch, Erich Neuwirth,
Dan Putler, Brian Ripley, Miroslav Ristic, and Peter Wolf.

Maintainer John Fox <jfox@[Link]>

Depends R (>= 2.6.0), tcltk, grDevices, utils

Suggests abind, aplpack, car (>= 1.2-1), effects (>= 1.0-7), foreign, grid, lattice, lmtest, MASS, mgcv,
multcomp (>= 0.991-2), nlme, nnet, relimp, rgl, RODBC

LazyLoad no

Description A platform-independent basic-statistics GUI (graphical user interface) for R, based on the
tcltk package.

License GPL (>= 2)

URL [Link] [Link]

Revision 26

R topics documented:
Commander-es . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Commander . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Compute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Confint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Hist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
KMeans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Plugins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Rcmdr-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

1
2 Commander-es

[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
[Link]-specific . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
RcmdrPager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Recode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Scatter3DDialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
assignCluster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
colPercents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
generalizedLinearModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
hierarchicalCluster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
linearModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
numSummary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
[Link] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
plotMeans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
reliability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
scatter3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Index 40

Commander-es R Commander

Description
Inicia la GUI (Interfaz Gráfica de Usuario) de R Commander

Usage
Commander()

Details
Empezando
La interfaz por defecto de R Commander consiste en (de arriba a abajo) una barra de menús, una
barra de herramientas, una ventana de instrucciones, una ventana de salida y una ventana de men-
sajes.
Las instrucciones para leer, escribir, transformar y analizar datos se ejecutan usando la barra de
menú de la parte superior de la ventana de R Commander. La mayor parte de los items de este menú
le guiarán mediante ventanas de diálogo, preguntando más allá de la especificación. Es aconsejable
explorar el menú para ver las opciones disponibles.
Bajo la barra de menú se encuentra la barra de herramientas con (de izquierda a derecha) un campo
de información que muestra el nombre del conjunto de datos activos, botones para editar y mostrar
el conjunto de datos activos y un campo de información mostrando el modelo estadístico activo.
Bajo la ventana de instrucciones hay un botón Ejecutar para realizar las órdenes indicadas en la
ventana de instrucciones. Los campos de información para los datos y el modelo activo son botones
que pueden ser usados para seleccionar éstos entre, respectivamente, conjuntos de datos o modelos
disponibles en memoria.
Commander-es 3

La mayor parte de las órdenes requiere un conjunto de datos activos. Cuando se ejecuta R Comman-
der no hay conjunto de datos activos, como está indicado en el campo de información del conjunto
de datos activos. Un conjunto de datos llega a ser un conjunto de datos activos cuando éste es leído
en la memoria desde un paquete R o importado desde un archivo de texto, conjunto de datos SPSS,
conjunto de datos Minitab, conjunto de datos STATA, Excel, Access o dBase. Además el conjunto
de datos activos puede ser seleccionado desde conjuntos de datos R residentes en memoria. Los
datos pueden ser elegidos de entre todos los conjuntos para cada sesión.
Por defecto, las órdenes son registradas en la ventana de instrucciones (la ventana de texto vacía in-
mediatamente después de la barra de herramientas); las órdenes y las salidas aparecen en la ventana
de resultados (la ventana de texto vacía después de la ventana de instrucciones) y el conjunto de
datos activos es adjuntado a la ruta de búsqueda. Para alterar éstos y otros parámetros por defecto,
puede consultar la información pertinente en configuración.
Algunos diálogos de Rcmdr (éstos en Estadisticos -> Ajuste de modelos) generan
el modelo lineal, modelo lineal generalizado y otros modelos. Cuando un modelo es ajustado, se
convierte en el modelo activo, indicado en el campo de información de la barra de herramientas de
R Commander. Los items del menú Modelos se aplican al modelo activo. Inicialmente, no hay
modelo activo. Si hay varios modelos en memoria, puede elegir el modelo activo de entre ellos.
Si el registro de instrucciones está activo, las órdenes de R generadas desde los menús y los cuadros
de diálogos, son introducidas en la ventana de instrucciones de R Comander. Se pueden editar estas
órdenes de manera normal y se pueden escribir otras nuevas en la ventana de instrucciones. Las
órdenes individuales pueden ser continuadas en más de una línea, pero cada línea después de la
primera debe ser identada con uno o más espacios o tabuladores. El contenido de la ventana de
instrucciones puede ser almacenado durante o al final de la sesión y un conjunto de instrucciones
guardado puede ser cargado en la ventana de instrucciones. El contenido de la ventana de resultados
puede ser editado o guardado en un archivo de texto.
Para volver a ejecutar una orden o un conjunto de ellas, se seleccionan las líneas que se desean
ejecutar usando el ratón y se presiona el botón Ejecutar, situado a la derecha de la barra de
herramientas (o Control-R, para ejecutarlos). Si no hay texto seleccionado el botón Ejecutar
(o Control-R) envía el contenido de la línea que contiene el cursor de insercción. Observar que
se generará un error si la orden o las órdenes enviadas son incompletas.
Presionando Control-F se abre un cuadro de diálogo de búsqueda de texto (también es accesible
vía Editar -> Buscar) para buscar el texto en la ventana de instrucciones o la ventana de
resultados. Las búsquedas son realizadas en la ventana de instrucciones a menos que primero pulse
en la ventana de resultados para activarla.
Presionando Control-S se guardará el conjunto de instrucciones o la ventana de resultados.
Presionando Control-A se selecciona todo el texto del conjunto de instrucciones o de la ventana
de resultados.
Pulsando el botón derecho del ratón (el tercer botón en un ratón de tres botones) en el conjunto
de instrucciones o en la ventana de resultados se abre el menú contextual con los items del menú
Editar, más un item Ejecutar (en la ventana de instrucciones).
Cuando ejecute órdenes en la ventana de R Commander, debe asegurarse que la sentencia sea lógica.
Por ejemplo, no tiene sentido ajustar un modelo estadístico de un conjunto de datos que no ha sido
leído en memoria.
Presionando una letra (ej. "a") en un cuadro con una lista se recorrerá ésta hasta la siguiente entrada
que comience con esa letra desde el principio del cuadro.
4 Commander-es

Salir de R Commander se realiza mediante Fichero -> Salir o cerrando la ventana de R

Commander.
Personalización y configuración
Los archivos de configuración están en el subdirectorio etc de cada paquete o en la localización
dada por etc y en las opciones de etcMenus (mirar abajo).
Los menús de Rcmdr pueden ser personalizados editando el archivo [Link].
Algunas funciones (ej. histograma) que normalmente no crean salida visible cuando se ejecutan
desde la consola sí lo harán - a menos que se evite - cuando se ejecuten desde la ventana de instruc-
ciones de R Commander. Tal salida puede ser suprimida listando los nombres de estas funciones en
el archivo [Link].
Puede añadir código R al paquete, ej., para crear diálogos adicionales, colocando archivos con
extensión .R en el directorio etc, además puede editar [Link] para proporcionar
menús adicionales, submenús o items. Una demostración de esto se proporciona mediante el archivo
[Link]. Para activar la demo, renombre el archivo a BoxCox.R y descomente la corre-
spondiente línea del menú en [Link]. De forma alternativa, puede editar el código
del paquete y recompilarlo.
Algunas funciones son proporcionadas para ayudar a escribir diálogos y la información del estado
de Rcmdr en un emplazamiento separado. Mirar help("[Link]") y el manual
suministrado en el directorio doc del paquete de Rcmdr para mayor información.
Además, varias características son controladas mediante opciones, en tiempos de ejecución, es-
tablecidas por la orden options("Rcmdr"). Estas opciones deben ser establecidas antes de
cargar el paquete. Si las opciones no están establecidas, que es la situación normal, serán usados los
parámetros por defecto. Las opciones se especifican como una lista de pares name$=$values.
Puede no establecer, establecer una, varias, o todas las opciones. Las opciones disponibles son las
dadas a continuación:

[Link] Si es TRUE (por defecto FALSE), el conjunto de datos activo es fijado como
la ruta de búsqueda.
[Link] Si es TRUE (por defecto), al arranque, la presencia de todos los paquetes
recomendados de Rcmdr serán comprobados y si alguno no está instalado, Rcmdr preguntará
si deben instalarse.
[Link] El color de las órdenes en la ventana de resultados es, por defecto,
"red".
[Link] Si es TRUE la salida será dirigida a la consola de R y la ventana de salida de
R Commander no se mostrará. Por defecto es FALSE.
contrasts Ofrece la misma función que la opción general contrasts; por defecto es c("[Link]",
"[Link]"). Cuando se sale de Commander la opción contrasts vuelve a su valor
preexistente. Observe que [Link] es del paquete car.
[Link] Si es TRUE, los diálogos deben aparecer en la pantalla dibujada completa-
mente, más que acumular dispositivo a dispositivo. Esta opción debería afectar sólo a ver-
siones Windows de R, pero debe en cualquier caso ser inofensivo. Por defecto es TRUE bajo
versiones Windows de R 2.1.1 y superiores y FALSE si no. Si está trabajando en Windows
y encuentra que se incrementan los problemas de estabilidad, pruebe establecer esta opción a
FALSE.
Commander-es 5

[Link] La fuente por defecto, como la especificación de la fuente de X11, dada en

cadena de caracteres. Si está especificado, este valor toma precedencia sobre el tamaño de la
fuente por defecto (abajo). Esta opción es sólo para sistemas no-Windows.
[Link] Tamaño, en puntos, por defecto de la fuente. Por defecto es 10 para
sistemas Windows y 12 para otro sistemas, salvo especificación de lo contrario (mirar el item
anterior). La fuente por defecto es "*helvetica-medium-r-normal-*-xx*", donde
xx es por defecto el tamaño de la fuente. Esta opción es sólo para sistemas no-Windows.
[Link] Establecer a TRUE si quiere que un doble click con el botón izquierdo del ratón
sirva para pulsar el botón por defecto en todos los diálogos. Por defecto es FALSE.
[Link] Color de los mensajes de error; por defecto es "red".
etc Establece la ruta del directorio que contiene los archivos de configuración de Rcmdr; por
defecto el subdirectorio etc del paquete Rcmdr instalado.
[Link] Establecer a TRUE para "mantener" el enfoque en la ventana actual de Tk, esto es,
para prevenir que el enfoque sea cambiado a otra ventana Tk. En algunos sistemas, mantener
el enfoque de esta forma, puede causar problemas. Por defecto es TRUE. Si experimenta
problemas de enfoque, intente establecer esta opción a FALSE.
[Link] Vector de caracteres de nombres de los paquetes que deben ser cargados
cuando el paquete Rcmdr es cargado; por defecto se carga sólo el paquete car. Otros pa-
quetes requeridos serán cargados cuando se necesiten. Si esto está disponible, el paquete car
será cargado cuando Commander se inicie en cualquier caso.
[Link] Si es TRUE (por defecto), los comandos son repetidos en la ventana de instruc-
ciones; si es FALSE, la ventana de instrucciones no se muestra.
[Link] Tamaño de la fuente, en puntos, que es usado en la ventana de instrucciones, en
la ventana de resultados, en diálogos recodificados y en expresiones de cáculo, esto es, donde
es usada una fuente monoespacio. Por defecto es 10 para sistemas Windows y 12 para otros
sistemas.
[Link] La altura de la ventana de instrucciones, en líneas. Por defecto es 10. Estableciendo
[Link] a 0 tiene el mismo efecto que establer [Link] a FALSE.
[Link] Color del texto de la ventana de instrucciones; por defecto es "black".
[Link] La anchura de la ventana de instrucciones y la de salida, en caracteres. Por defecto
es 80.
[Link] Afecta a la forma en la que múltiples variables son seleccionadas
en una caja de listas de variables. Si se establece a "extended" (por defecto), el botón
izquierdo en una variable selecciona ésta y deselecciona cualquier otra variable que estuviera
seleccionada; Control+botón izquierdo acciona la selección (y puede ser usado para
seleccionar variables adicionales); Mayúsculas+botón izquierdo extiende la selec-
ción. éste es el convenio estándar de Windows. Si lo establece a "multiple", el botón
izquierdo acciona la selección de una variable y puede ser usado para seleccionar más de una
variable. éste es el comportamiento de Rcmdr antes de la versión 1.9-10.
[Link] Altura de la ventana de resultados, en líneas. Por defecto es dos veces la altura
de la ventana de instrucciones o 20 si la ventana de instrucciones es suprimida. Establecer
[Link] a 0 tiene el mismo efecto que [Link] a TRUE.
[Link] Color de la salida en la ventana de resultados, por defecto es "blue".
placement Emplazamiento de la ventana de R Commander, en píxeles; por defecto es "$-40+20$",
lo que pone la ventana cerca de la esquina superior derecha de la pantalla.
6 Commander-es

plugins Vector de caracteres con los nombres de paquetes de plugins de Rcmdr a cargar cuando
Commander arranque. Los paquetes plugins también pueden ser cargados desde el menú
Herramientas -> Cargar paquete(s).
[Link] Si es TRUE, la barra de menús y de herramientas de R Commander son
suprimidas, permitiendo que otro programa (como Excel) asuma esas funciones. Por defecto
(por supuesto) es FALSE.
[Link] En (algunos) sistemas Linux X11 se generan múltiples adverten-
cias por las órdenes de Rcmdr, después de abrir la ventana del dispositivo gráfico. Establecer
esta opción a TRUE (por defecto cuando arranca interactivamente bajo X11 antes de la versión
de R 2.4.0) suprime la aparición de estas advertencias. Un efecto secundario indeseable es que
entonces todas las advertencias y mensajes de error son interceptados por Rcmdr, incluso para
las instrucciones introducidas en los avisos de R. Los mensajes producidos por tales órdenes
serán impresos en la ventana de mensajes de R Commander después de la siguiente orden gen-
erada en Rcmdr. Algunas advertencias de X11 puede ser impresas al salir de R Commander.
Este problema sólo se aplica a versiones de R anteriores a 2.4.0 y el valor por defecto de la
opción es establecido por consiguiente.
[Link] Si es TRUE (por defecto FALSE), el contenido de la ventana de mensajes
no es borrado entre mensajes. En cualquier caso, un mensaje "NOTE" no borrará un anterior
"WARNING" o "ERROR".
RExcelSupport Establecido como TRUE (por defecto es FALSE), los menús y salidas son di-
rigidas a Excel.
[Link] Factor de escala aplicado a todos los elementos Tk, como las fuentes. Esto
funciona bien sólo en Windows. Por defecto es NULL.
[Link] Si el número de variables en el conjunto de datos activos excede este
valor (por defecto, 100), entonces edit(), más que showData(), es utilizado para exhibir
el conjunto de datos. Un inconveniente es que el control no se devuelve a Commander hasta
que la ventana de edición sea cerrada. La razón de esta opción es que showData() es
muy lento cuando el número de variables es grande; fijando el umbral a 0 suprime el uso en
conjunto de showData.
[Link] Fijar a TRUE (por defecto) si quiere un botón Editar en la ventana de
Commander, que permita editar el conjunto activo de datos. Los usuarios de Windows pueden
desear establecer esta opción a FALSE para suprimir el botón Editar porque cambiando
los nombres de las variables en el editor de datos se puede causar que R falle (aunque este
problema se cree solucionado).
[Link] Fijar a TRUE (por defecto) si se quiere ordenar alfabéticamente el nombre de las
variables en una lista de variables.
tkwait Esta opción trata un problema que, en mi conocimiento, es raro y puede ocurrir en algunos
sistemas no Windows. Si R Commander causa que se cuelgue R, entonces establezca la opción
tkwait a TRUE; o conserve la opción en FALSE e ignórelo. Un indeseable efecto secundario
de establecer la opción tkwait a TRUE es que el aviso de órdenes de la sesión de R es
suprimido hasta salir de R Commander. Uno sin embargo todavía puede introducir órdenes por
la ventana de instrucciones. En particular, no hay razón para usar esta opción bajo Windows
y no se debería usar con la GUI de R en Windows con salida protegida cuando la salida esté
dirigida a la consola de R.
[Link] Si es TRUE (por defecto), el paquete rgl será cargado si está presente en una librería
accesible, si es FALSE, el paquete rgl será ignorado aunque esté disponible. El paquete rgl
puede a veces causar problemas cuando se arranca R bajo X11.
Commander-es 7

[Link] Color de los mensajes de advertencia; por defecto es "darkgreen".

Muchas opciones pueden también ser establecidas mediante el menú Archivo -> Opciones, que
reiniciará R Commander después de que las opciones sean establecidas.
Si quiere lanzar R Commander cuando inicie R, puede incluir la siguiente instrucción en uno de los
ficheros de inicio de R (por ejemplo, en el fichero [Link] de la carpeta etc de R):

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

Las opciones de R Commander puede ser establecidas de forma permanente de la misma forma.
Para más información sobre el inicio de R, véase ?Startup.

Avisos
La ventana de instrucciones de R Commander no proporciona una verdadera consola a R y tiene
ciertas limitaciones. No se recomienda usar R Commander para la programación sería o el análisis
de datos que confíe primordialmente en instrucciones - usar un editor de programación en su lugar.
Por ejemplo, para declaraciones de composiciones de R incluidas entre llaves "{ }", incluyendo
definición de funciones, no serían analizadas ni ejecutadas correctamente, aunque si las líneas de-
spués de las primeras que estén identandas. Puede ejecutar declaraciones de composiciones desde
la ventana de instrucciones separando los comandos dentro de las llaves por puntos y comas.

Problemas Conocidos
Ocasionalmente, bajo Windows, después de teclear algún texto en un cuadro de diálogo (ej. subcon-
junto de expresiones en el diálogo de subconjunto de conjunto de datos), algunos botones en el diál-
ogo (ej. el botón Aceptar) pueden no tener efecto cuando sean presionados. Pulsando en cualquier
sitio, dentro o fuera del cuadro de diálogo, debería restaurarse las funciones de los botones. Por lo
que se ha podido comprobar, éste es un problema con Tcl/Tk de Windows.

Note
Esta versión debe ser compatible con SciViews, que actualmente sólo funciona bajo sistemas Win-
dows: [Link] mirar [Link]-specific.
Bajo Windows, el paquete Rcmdr puede también funcionar bajo de Rgui en modo SDI (interfaz de
único documento) o bajo [Link]; puede ser que experimente problemas ejecutando Rcmdr
bajo ESS con NTEmacs o XEmacs.

Author(s)
John Fox hjfox@[Link] (de la versión inglesa)
Manuel González (traductor) hgonzalezperezmanuel@[Link]
Manuel Muñoz Márquez (traductor–revisor) [Link]@[Link]
Véase [Link]
La última versión de este fichero la puede encontrar en [Link]
R-contribuciones
8 Commander

See Also
Plugins

Examples
options(Rcmdr=list([Link]=12, contrasts=c("[Link]", "[Link]")))

Commander 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, STATA data set, or an Excel, Access, or dBase 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,
Commander 9

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, 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 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", 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 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.
Pressing Control-A selects all of the text in the script or output window.
In addition, the following Control-key combinations work in the script and output windows: Control-
X, cut; Control-C, copy; Control-V, insert; Control-Z, undo; and Control-W, redo.
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.
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.
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 [Link].
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 [Link] to provide additional menus, sub-
menus, or menu-items. A demo addition is provided in the file [Link]. To activate the
demo, rename this file to BoxCox.R, and uncomment the corresponding menu line in Rcmdr-
[Link]. 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("[Link]") and the manual supplied
in the doc directory of the Rcmdr package for more information.
10 Commander

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:

[Link] if TRUE (the default), then the user is asked whether to save the script file and the
output file when the Rcmdr exits.
[Link] if TRUE (the default is FALSE), the active data set is attached to the search
path.
[Link] if TRUE (the default), on start-up, the presence of all of the Rcmdr recom-
mended packages will be checked, and if any are absent, the Rcmdr will offer to install them.
[Link] Color for commands in the output window; the default is "red".
[Link] If TRUE, messages are directed to the R Console, and the R Commander
output window is not displayed. The default is FALSE.
[Link] If TRUE, output is directed to the R Console, and the R Commander output
window is not displayed. The default is FALSE.
[Link] Serves the same function as the general contrasts option; the default
is
c("[Link]", "[Link]"). When the Commander exits, the contrasts
option is returned to its pre-existing value. Note that [Link] is from the car
package.
[Link] 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.
[Link] 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.
[Link] 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 de-
fault font is "*helvetica-medium-r-normal-*-xx*", where xx is the default font
size. This option is only for non-Windows systems.
[Link] 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.
[Link] 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.
[Link] 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.
[Link] If TRUE, the Commander window is minimized on startup; the default is
FALSE.
Commander 11

[Link] The R Commander maintains a list of output objects, by default in-

cluding 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”).
[Link] 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.
[Link] If TRUE (the default), commands are echoed to the script window; if FALSE,
the script window is not displayed.
[Link] 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.
[Link] The height of the script window, in lines. The default is 10. Setting [Link]
to 0 has the same effect as setting [Link] to FALSE.
[Link] Color for text in the script window; the default is "black".
[Link] The width of the script and output windows, in characters. The default is 80.
[Link] 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 Win-
dows 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.
[Link] 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 [Link] to 0
has the same effect as setting [Link] to TRUE.
[Link] 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.
plugins A character vector giving the names of Rcmdr plug-in packages to load when the Com-
mander starts up. Plug-in packages can also be loaded from the Tools -> Load Rcmdr plug-
in(s) menu. See Plugins.
[Link] if TRUE, the Commander menu bar and tool bar are suppressed, allowing an-
other program (such as Excel) to take over these functions. The default (of course) is FALSE.
[Link] 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 interactively under X11 prior to R version 2.4.0) 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. This problem only applies to R versions before 2.4.0, and the
default value of the option is set accordingly.
12 Commander

[Link] If TRUE (the default is 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".
RExcelSupport If TRUE (the default is FALSE), menus and output are handled by Excel.
[Link] A scaling factor to be applied to all Tk elements, such as fonts. This works well
only in Windows. The default is NULL.
[Link] If the number of variables in the active data set exceeds this value (de-
fault, 100), then edit() rather than showData() is used to display the data set. A disad-
vantage 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.
[Link] 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).
[Link] 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 partic-
ular, 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.
[Link] 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.
[Link] the number of variables to display in variable-list boxes; longer lists
may be viewed by scrolling. The default is 4.
[Link] 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.
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 [Link] 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.
Compute 13

Warning
The R Commander Script window does not provide a true console to R, and may have certain lim-
itations. 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 window, however, I’d appreciate it if you brought them to my attention.

Known Problem
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.

Note
This version may be compatible with SciViews, which currently runs only under Windows systems:
[Link] see [Link]-specific. Under
Windows, the Rcmdr package can also be run under the Rgui in SDI (single-document interface)
mode, or under [Link]; you might experience problems running the Rcmdr under ESS with-
NTEmacs or XEmacs.

Author(s)
John Fox hjfox@[Link]

See Also
Plugins, [Link]

Examples
options(Rcmdr=list([Link]=12, [Link]=c("[Link]", "[Link]")))

Compute Rcmdr Compute Dialog

Description
The compute dialog is used to compute new variables.

Details
The name of the new variable must be a valid R object name (consisting only of upper and lower-
case letters, numerals, and periods, and not starting with a numeral).
Enter an R expression in the box at the right. The expression is evaluated using the active data
set. You can double-click in the variable-list box to enter variable names in the expression. The
expression must evaluate to a valid variable, which is added to the active data set.
14 Confint

Author(s)
John Fox hjfox@[Link]

See Also
Arithmetic

Confint Confidence Intervals for Model Coefficients

Description
Except for glm objects, where a method is provided that provides intervals optionally based on the
Wald statistic, this generic function simply calls confint in the stats package via its default
method.

Usage
Confint(object, parm, level = 0.95, ...)

## S3 method for class 'glm':

Confint(object, parm, level=0.95, type=c("LR", "Wald"), ...)

Arguments
object a model object.
parm which parameters to use, defaults to all.
level level of confidence, defaulting to 0.95.
type for a glm object, confidence interval based on the profile likelihood (the default)
or the Wald statistic.
... arguments to be passed down to methods.

Value
dependent upon the method called.

Author(s)
John Fox hjfox@[Link]

See Also
confint
Hist 15

Hist Plot a Histogram

Description

This function is a wrapper for the hist function in the base package, permitting percentage
scaling of the vertical axis in addition to frequency and density scaling.

Usage

Hist(x, scale=c("frequency", "percent", "density"), xlab=deparse(substitute(x)),

ylab=scale, main="", ...)

Arguments

x a vector of values for which a histogram is to be plotted.

scale the scaling of the vertical axis: "frequency" (the default), "percent", or
"density".
xlab x-axis label, defaults to name of variable.
ylab y-axis label, defaults to value of scale.
main main title for graph, defaults to empty.
... arguments to be passed to hist.

Value

This function returns NULL, and is called for its side effect — plotting a histogram.

Author(s)

John Fox hjfox@[Link]

See Also

hist

Examples
library(car)
data(Prestige)
Hist(Prestige$income, scale="percent")
16 KMeans

KMeans K-Means Clustering Using Multiple Random Seeds

Description
Finds a number of k-means clusting solutions using R’s kmeans function, and selects as the final
solution the one that has the minimum total within-cluster sum of squared distances.

Usage
KMeans(x, centers, [Link]=10, [Link]=10)

Arguments
x A numeric matrix of data, or an object that can be coerced to such a matrix (such
as a numeric vector or a dataframe with all numeric columns).
centers The number of clusters in the solution.
[Link] The maximum number of iterations allowed.
[Link] The number of different starting random seeds to use. Each random seed results
in a different k-means solution.

Value
A list with components:

cluster A vector of integers indicating the cluster to which each point is allocated.
centers A matrix of cluster centres (centroids).
withinss The within-cluster sum of squares for each cluster.
[Link] The within-cluster sum of squares summed across clusters.
betweenss The between-cluster sum of squared distances.
size The number of points in each cluster.

Author(s)
Dan Putler

See Also
kmeans

Examples
data(USArrests)
KMeans(USArrests, centers=3, [Link]=5, [Link]=5)
Plugins 17

Plugins R Commander Plug-in Packages

Description
Plug-ins are R packages that extend the R Command interface.

Details
An R Commander plug-in is an ordinary R package that (1) provides extensions to the R Com-
mander menus is a file named [Link] located in the package’s etc directory; (2) pro-
vides call-back functions required by these menus; and (3) in an Models: field in the package’s
DESCRIPTION file, augments the list of model objects recognized by the R Commander. The
menus provided by a plug-in package are merged with the standard Commander menus. It is also
possible to remove menus and menu items from the standard Commander menu file or from the
files of plug-ins installed before the current one.
Plug-in packages given in the R Commander plugins option (see Commander) are automatically
loaded when the Commander starts up. Plug-in packages may also be loaded via the Commander
Tools -> Load Rcmdr plug-in(s) menu; a restart of the Commander is required to install the new
menus. Finally, loading a plug-in package when the Rcmdr is not loaded will load the Rcmdr and
activate the plug-in.
An illustrative R Commander plug-in package, [Link], is available on
CRAN.
For more details, see my (slightly out-of-date) article on “Extending the Rcmdr by Plug-in Pack-
ages” in the December 2007 issue of R News <[Link]
Rnews_2007-[Link]>.

See Also
Commander

Rcmdr-package R Commander

Description
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk
package.
18 [Link]

Details

Package: Rcmdr
Version: 1.4-7
Date: 2009/01/06
Depends: R (>= 2.1.0), tcltk, grDevices, utils
Suggests: abind, aplpack, car (>= 1.1-1), effects (>= 1.0-7), foreign, grid, lattice, lmtest, MASS, mgcv, multcomp, nlme, nn
LazyLoad: no
License: GPL (>= 2)
URL: [Link] [Link]

Translations
The R Commander comes with translations from English into several other languages. I am grate-
ful to the following individuals and groups for preparing these translations: Brazilian Portuguese,
Adriano Azevedo-Filho and Marilia Sa Carvalho; Catalan, Manel Salamero; French, Philippe Gros-
jean; German: Gerhard Schoen; Indonesian, I Made Tirta; Italian, Stefano Calza; Japanese, Taka-
haru Araki; Romanian, Adrian Dusa; Russian, Alexey Shipunov; Slovenian, Jaro Lajovic; Spanish,
Spanish R-UCA Project, [Link]

Author(s)
John Fox <jfox@[Link]>, with contributions from Michael Ash, Theophilius Boye, Ste-
fano Calza, Andy Chang, Philippe Grosjean, Richard Heiberger, G. Jay Kerns, Renaud Lancelot,
Matthieu Lesnoff, Samir Messad, Martin Maechler, Duncan Murdoch, Erich Neuwirth, Dan Putler,
Brian Ripley, Miroslav Ristic, and Peter Wolf.
Maintainer: John Fox <jfox@[Link]>

[Link] Rcmdr Utility Functions

Description
These functions support writing additions to the Rcmdr package. Additional R code can be placed
in files with file type .R in the etc subdirectory of the package. Add menus, submenus, and menu
items by editing the file [Link] in the same directory.

Usage
activateMenus()
activeDataSet(dsname, flushModel=TRUE)
ActiveDataSet(name)
activeDataSetP()
activeModel(model)
ActiveModel(name)
[Link] 19

activeModelP()
checkActiveDataSet()
checkActiveModel()
checkBoxes(window=top, frame, boxes, initialValues=NULL, labels, title=NULL) # mac
checkClass(object, class, message=NULL) # macro
checkFactors(n=1)
checkMethod(generic, object, message=NULL, default=FALSE, strict=FALSE,
reportError=TRUE) # macro
checkNumeric(n=1)
checkReplace(name, type=gettextRcmdr("Variable"))
checkTwoLevelFactors(n=1)
checkVariables(n=1)
closeCommander(ask=TRUE, [Link]=ask)
closeDialog(window, release=TRUE) # macro
CommanderWindow()
dataSetsP()
defmacro(..., expr)
dialogSuffix(window=top, onOK=onOK, rows=1, columns=1, focus=top, bindReturn=TRUE,
preventGrabFocus=FALSE, preventDoubleClick=FALSE, preventCrisp=FALSE) # macro
doItAndPrint(command, log=TRUE)
errorCondition(window=top, recall=NULL, message, model=FALSE) # macro
[Link](generic, object, default=TRUE, strict=FALSE)
Factors(names)
factorsP(n=1)
formulaFields(model, hasLhs=TRUE, glm=FALSE)
## S3 method for class 'listbox':
getFrame(object)
## S3 method for class 'listbox':
getSelection(object)
getRcmdr(x, mode="any")
gettextRcmdr(...)
glmP()
GrabFocus(value)
groupsBox(recall=NULL, label=gettextRcmdr("Plot by:"),
initialLabel=gettextRcmdr("Plot by groups"),
plotLinesByGroup=FALSE, positionLegend=FALSE,
plotLinesByGroupsText=gettextRcmdr("Plot lines by group")) # macro
groupsLabel(frame=top, groupsBox=groupsBox, columnspan=1) # macro
hclustSolutionsP()
initializeDialog(window=top, title="", offset=10, preventCrisp=FALSE) # macro
[Link](x)
justDoIt(command)
listAllModels(envir=.GlobalEnv, ...)
listAOVModels(envir=.GlobalEnv, ...)
listDataSets(envir=.GlobalEnv, ...)
listFactors(dataSet=ActiveDataSet())
listGeneralizedLinearModels(envir=.GlobalEnv, ...)
listLinearModels(envir=.GlobalEnv, ...)
20 [Link]

listMultinomialLogitModels(envir=.GlobalEnv, ...)
listNumeric(dataSet=ActiveDataSet())
listPlugins(loaded=FALSE)
listProportionalOddsModels(envir=.GlobalEnv, ...)
listTwoLevelFactors(dataSet=ActiveDataSet())
listVariables(dataSet=ActiveDataSet())
lmP()
logger(command)
LogWindow()
MacOSXP()
Message(message, type=c("note", "error", "warning"))
MessagesWindow()
modelFormula(frame=top, hasLhs=TRUE) # macro
modelsP(n=1)
multinomP()
nobs(model)
Numeric(names)
numericP(n=1)
OKCancelHelp(window=top, helpSubject=NULL, model=FALSE) # macro
OutputWindow()
packageAvailable(name)
polrP()
popOutput()
putRcmdr(x, value)
radioButtons(window=top, name, buttons, values=NULL, initialValue=..values[1],
labels, title) # macro
RcmdrTclSet(name, value)
RcmdrTkmessageBox(message, icon=c("info", "question", "warning",
"error"), type=c("okcancel", "yesno", "ok"), default, title="")
rglLoaded()
sortVarNames(x)
subOKCancelHelp(window=subdialog, helpSubject=NULL) # macro
subsetBox(window=top, model=FALSE) # macro
tclvalue(x)
[Link](text)
TwoLevelFactors(names)
twoLevelFactorsP(n=1)
UpdateModelNumber(increment=1)
variableListBox(parentWindow, variableList=Variables(), bg="white",
selectmode="single", export="FALSE", initialSelection=NULL,
listHeight=getRcmdr("[Link]"), title)
Variables(names)

# the following function is exported for technical reasons,

# but is not meant to be called directly

commanderPosition()
[Link] 21

Arguments
ask ask for confirmation.
[Link] ask whether to save contents of script and output windows.
bg background color.
bindReturn if TRUE, the Return key is bound to the onOK function in the dialog.
boxes vector of quoted names for check boxes, used to generate each box and its asso-
ciated variable.
buttons vector of quoted names for buttons in a set of related radio buttons.
class quoted name of class.
columnspan number of dialog-box columns to be spanned by frame.
command a character string that evaluates to an R command.
dataSet, dsname
the quoted name of a data frame in memory.
default default button: if not specified, "ok" for "okcancel", "yes" for "yesno", and "ok"
for "ok"; or look for a default method.
envir the environment to be searched; should generally be left at the default.
export export selection?
expr expression constituting the body of the macro; typically a compound expression.
flushModel set (or reset) the active model to NULL? Should normally be TRUE when the
active data set is changed; an exception is when variables are simply added to,
deleted from, or modified in the data set set.
focus Tk window to get the focus.
frame frame or quoted name for frame depending upon the function.
generic quoted name of generic function.
glm TRUE if the model is a glm object, FALSE otherwise.
groupsBox listbox object for selecting groups variable.
hasLhs does the model formula have a left-hand side?
helpSubject the quoted name of a help subject, to be called as help(helpSubject) when
the dialog Help button is pressed.
icon Message-box icon.
increment increment to model number; -1 to set back after error.
initialLabel label for groups button before a selection is made.
initialSelection
index of item initially selected, 0-base indexing.
initialValue for a set of related radio buttons.
initialValues
for a set of related check boxes.
label label prefix for groups button after a selection is made.
labels a vector of character strings to label a set of radio buttons or check boxes.
22 [Link]

listHeight Maximum number of elements displayed simultaneously in list box.

loaded if TRUE, plug-in packages that are loaded are included in the vector of names
returned.
log echo command to the log window, as well as executing it and printing its output.
message error (or other) message.
mode mode of object to retrieve.
model the name of a model, as a character string, or a model object, or TRUE or FALSE,
depending upon the function.
name quoted name.
names optional names to be stored.
n number of items to check for.
object an object (depends on context).
offset in pixels, from top-left of Commander window.
onOK function to execute when the OK button is pressed.
plotLinesByGroup
include a check box for plotting lines by group?
plotLinesByGroupsText
the label for the plot-lines-by-group check box.
positionLegend
include a check box for a legend?
preventGrabFocus
prevent the dialog box from grabbing the focus.
preventDoubleClick
prevent double-clicking from pressing the OK button, even when the [Link]
option is set; necessary for statistical modelling dialogs, which use double-
clicking to build the model formula.
preventCrisp prevent call to tclServiceMode, which (rarely) causes problems with some
dialogs.
recall function to call after error — usually the function that initiates the dialog.
release release the focus if the [Link] option has been set.
reportError if TRUE, report an error message.
rows, columns
numbers of rows and columns of widgets in the dialog box.
values vector of quoted values associated with radio buttons or check boxes.
selectmode "single" or "multiple".
strict if TRUE, only use first element of class vector.
text a text string.
title Window or dialog-box-element title.
type quoted type of object to check; used to generate check-replace dialog box; or
type of message to print in Message window.
value an object to be stored.
[Link] 23

variableList a vector of variable names.

window, parentWindow
a Tk window.
x an R object name, as a character string, or a tcl variable or object, or a vector of
variable names to be sorted.
... For gettextRcmdr, text string or vector of text strings to translate; for defmacro,
arguments for the macro; otherwise disregard.

Details
There are several groups of functions exported by the Rcmdr package and documented briefly here.
To see how these functions work, it is simplest to examine the dialog-generating functions in the
Rcmdr package.
Executing and logging commands: The functions doItAndPrint, justDoIt, and logger
control the execution, logging, and printing of commands generated by menus and dialogs. logger(command)
adds command to the log/script window and to the output window. justDoIt(command)
causes command to be executed. doItAndPrint(command) does both of these operations,
and also prints the output produced by the command. The R Commander maintains a list of output
objects, by default including the last 10 outputs. 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”).
Checking for errors: The function [Link] checks whether a character string specifies
a valid name for an R object. The functions checkActiveDataSet, checkActiveModel,
checkFactors, checkNumeric, checkTwoLevelFactors, and checkVariables check
for the existence of objects and write an error message to the log if they are absent (or insufficiently
numerous, in the case of different kinds of variables). The function checkReplace opens a dia-
log to query whether an existing object should be replaced. The function checkMethod, checks
whether a method exists for a particular generic that is appropriate for a particular object. The func-
tion checkClass checks whether an object is of a specific class. Both of these functions write
error messages to the log if the condition fails. The function errorCondition reports an error
to the user and (optionally) re-starts a dialog.
Information: Several functions return vectors of object names: listAllModels,
listAOVModels, listDataSets, listGeneralizedLinearModels, listFactors,
listLinearModels, listMultinomialLogitModels, listNumeric, listProportionalOddsModels,
listTwoLevelFactors, listVariables. The functions activeDataSet and activeModel
respectively report or set the active data set and model. The function packageAvailable re-
ports whether the named package is available to be loaded (or has possibly already been loaded).
The function [Link] checks whether a method exists for a particular generic that is
appropriate for a particular object, and returns TRUE or FALSE.
Building dialog boxes: Several functions simplify the process of constructing Tk dialogs: ini-
tializing a dialog box, initializeDialog, and completing the definition of a dialog box,
dialogSuffix; a set of check boxes, checkBoxes; a set of radio buttons, radioButtons;
a list box with associated scrollbars and state variable, variableListBox (and the associated
functions getFrame and getSelection); a button and subdialog for selecting a "grouping"
variable, groupsBox; displaying the currently defined groups in a dialog, groupsLabel; a
dialog-box structure for entering a model formula, modelFormula; a text box for entering a sub-
setting expression, subsetBox; OK, Cancel, and Help buttons for dialogs, OKCancelHelp, and
subdialogs, subOKCancelHelp.
24 [Link]-specific

“Themed” Tk widgets: Tk 8.5 introduced so-called “themed” widgets, which look better than the
traditional Tk widgets. Several functions, contributed by Brian Ripley, are written to access the
new widgets by switching automatically between the new and old widget sets depending upon
the availability of the former: buttonRcmdr, to access either ttkbutton or tkbutton;
labelRcmdr, to access either ttklabel or tklabel; ttkentry, to access either ttkentry
or tkentry; ttkframe, to access either ttkframe or tkframe; ttkradiobutton, to
access either ttkradiobutton or tkradiobutton; and ttkscrollbar, to access either
ttkscrollbar or tkscrollbar. Note that the last four functions mask functions of the same
names in the tcltk package.
Translating text: The gettextRcmdr function simply passes its argument(s) to gettext, adding
the argument domain="R-Rcmdr".
Miscellaneous: The function [Link] removes spaces from the beginning and end of a
character string. The function installPlugin installs an Rcmdr plug-in from a ZIP file or
directory; this function may be used to create self-installing plug-ins in the form of packages. The
function nobs returns the number of observations on which a statistical model is based. The
function formulaFields returns information about the left-hand side, right-hand side, data,
subject, and (for GLMs) family and link, of a model object. The function sortVarNames sorts
variable names, including those containing numerals, into a more "natural" order than does the
standard sort function.
Some of these functions, marked # macro under Usage, are "macro-like" in their behaviour, in
that they execute in the environment from which they are called. These were defined with an
adaptation (used with permission) of Thomas Lumley’s defmacro function, described in Lumley
(2001).

Author(s)

John Fox hjfox@[Link]

References

T. Lumley (2001) Programmer’s niche: Macros in R. R News, 1(3), 11–13.

[Link]-specific
Rcmdr SciViews-specific Functions

Description

These functions provide compatibility with SciViews ([Link] Thanks

to them, Rcmdr is totally integrated into SciViews Insider. In this environment, the main ’R Com-
mander’ window is replaced by an ’R Commander menu’ and log files are replaced by special R
code editing windows with syntax highlighting. Most of these functions are not intended for direct
use.
RcmdrPager 25

Usage

[Link]()
[Link]()
svlogger(command)
optionLogCommand()
optionAttachDataSet()
optionSortVariables()
refreshStatus()

Arguments

command a character string that evaluates to an R command.

Details

The functions [Link] tests if R is running under SciViews. If not, most of the other
SciViews-specific functions do nothing. [Link] test if the SciViews client com-
municates with R through Tcl/Tk (otherwise, it probably uses SciViews plugs). The function
svlogger is similar to logger, but it records Rcmdr commands in the specific SciViews R script
window and in the SciViews command history, instead of the log window and the default R com-
mand history. optionLogCommand, optionAttachDataSet and optionSortVariables
allow to change the command logging, automatic attachment of the active data set and sorting of
variable names (equivalent options than those accessible by check boxes in the ’R Commander’
window of Rcmdr outside of SciViews, or in the Options dialog box). In SciViews insider, the state
of these options, as well as the names of the active data set and model are displayed in the status
bar. refreshStatus make sure that this information in the status bar is updated according to the
current internal state of Rcmdr.

Author(s)

Philippe Grosjean hphgrosjean@[Link]

RcmdrPager Pager for Text Files

Description

This is a slightly modified version of the tkpager, changed to use the Rcmdr monospaced font and
a white background.

Usage

RcmdrPager(file, header, title, [Link])

26 Recode

Arguments
file character vector of file(s) to be displayed.
header for the beginning of each file.
title for window
[Link] delete file(s) on close.

See Also
tkpager

Recode Rcmdr Recode Dialog

Description
The recode dialog is normally used to recode numeric variables and factors into factors, for example
by combining values of numeric variables or levels of factors. It may also be used to produce new
numeric variables. The Rcmdr recode dialog is based on the recode function in the car package.

Details
The name of each new variable must be a valid R object name (consisting only of upper and lower-
case letters, numerals, and periods, and not starting with a numeral).
Enter recode directives in the box near the bottom of the dialog. Directives are normally entered
one per line, but may also be separated by semicolons. Each directive is of the form input =
output (see the examples below). If an input value satisfies more than one specification, then the
first (from top to bottom, and left to right) applies. If no specification is satisfied, then the input
value is carried over to the result. NA is allowed on input and output. Factor levels are enclosed in
double-quotes on both input and output.
Several recode specifications are supported:

a single value For example, "missing" = NA.

several values separated by commas For example, 7,8,9 = "high".
a range of values indicated by a colon For example, 7:9 = "high". The special values low
and high may appear in a range. For example, low:10=1. Note that these values are
unquoted.
the special value else everything that does not fit a previous specification. For example, else=NA.
Note that else matches all otherwise unspecified values on input, including NA.

If all of the output values are numeric, and the "Make new variable a factor" check box is unchecked,
then a numeric result is returned.
If several variables are selected for recoding, then each is recoded using the same recode directives.
In this case, the name entered in the box labelled "New variable name or prefix for multiple recodes"
will be prefixed to the name of each variable being recoded. Setting an empty prefix (i.e., "") will
cause the recoded variables to replace the original variables.
Scatter3DDialog 27

Author(s)
John Fox hjfox@[Link]

See Also
recode

Scatter3DDialog Rcmdr 3D Scatterplot Dialog

Description
This dialog sets up a call to the scatter3d function to draw a three-dimensional scatterplot, and
optionally to identify3d to label points interactively with the mouse.

Details
The explanatory variables provide the "horizontal" and "out-of-screen" axes of the scatterplot, the
response variable provides the "vertical" axis.
Data points are represented as spheres or points, depending upon the number of observations.
Several regression surfaces can be plotted: a linear least-squares surface; a full quadratic least-
squares surface with squared and cross-product terms; a "smooth" regression surface — either a
smoothing spline, if no degrees of freedom are specified (in which case the gam function selects the
df by generalized cross validation), or a fixed-df regression spline; an additive-regression surface
(also fit by gam), with either smoothing spline or regression spline components (again selected
according to the specification of degrees of freedom). If only one surface is fit, then residuals are
plotted as red (negative) and green (positive) lines from the surface to the points.
You can specify a factor defining groups by pressing the Plot by groups button. A separate surface
or set of surfaces is plotted for each level of the groups factor. These surfaces can be constrained to
be parallel.
The completed plot can be manipulated with the mouse: Click, hold, drag the left mouse button to
rotate the display; click, hold, and drag the right button (or centre button on a three-button mouse)
to zoom in and out.
If the box labelled Identify observations with mouse is checked, you may use the mouse to identify
points interactively: Press the right mouse button (or the centre button on a three-button mouse),
drag a rectangle around the points to be identified, and release the button. Repeat this procedure
for each point or set of "nearby" points to be identified. To exit from point-identification mode,
right-click (or centre-click) in an empty region of the plot.
Points may also be identified subsequently by selecting Identify observations with mouse from the
R Commander 3D graph menu: As above, click and drag the left mouse button to rotate the display,
and click and drag the right (or centre) button to identify points.

Author(s)
John Fox hjfox@[Link]
28 assignCluster

See Also
scatter3d, identify3d, [Link], gam

assignCluster Append a Cluster Membership Variable to a Dataframe

Description
Correctly creates a cluster membership variable that can be attached to a dataframe when only a
subset of the observations in that dataframe were used to create the clustering solution. NAs are
assigned to the observations of the original dataframe not used in creating the clustering solution.

Usage
assignCluster(clusterData, origData, clusterVec)

Arguments
clusterData The data matrix used in the clustering solution. The data matrix may have have
only a subset of the observations contained in the original dataframe.
origData The original dataframe from which the data used in the clustering solution were
taken.
clusterVec An integer variable containing the cluster membership assignments for the ob-
servations used in creating the clustering solution. This vector can be created
using cutree for clustering solutions generated by hclust or the cluster
component of a list object created by kmeans or KMeans.

Value
A factor (with integer labels) that indicate the cluster assignment for each observation, with an NA
value given to observations not used in the clustering solution.

Author(s)
Dan Putler

See Also
hclust, cutree, kmeans, KMeans

Examples
data(USArrests)
USArrkm3 <- KMeans(USArrests[USArrests$UrbanPop<66, ], centers=3)
assignCluster(USArrests[USArrests$UrbanPop<66, ], USArrests, USArrkm3$cluster)
[Link] 29

[Link] Bin a Numeric Varisible

Description

Create a factor dissecting the range of a numeric variable into bins of equal width, (roughly) equal
frequency, or at "natural" cut points. The cut function is used to create the factor.

Usage

[Link](x, bins = 4, method = c("intervals", "proportions", "natural"),

labels = FALSE)

Arguments

x numeric variable to be binned.

bins number of bins.
method one of "intervals" for equal-width bins; "proportions" for equal-
count bins; "natural" for cut points between bins to be determined by a
k-means clustering.
labels if FALSE, numeric labels will be used for the factor levels; if NULL, the cut
points are used to define labels; otherwise a character vector of level names.

Value

A factor.

Author(s)

Dan Putler, slightly modified by John Fox hjfox@[Link] with the original author’s permis-
sion.

See Also

cut, kmeans.

Examples
summary([Link](rnorm(100), method="prop", labels=letters[1:4]))
30 generalizedLinearModel

colPercents Row, Column, and Total Percentage Tables

Description
Percentage a matrix or higher-dimensional array of frequency counts by rows, columns, or total
frequency.

Usage
colPercents(tab, digits=1)
rowPercents(tab, digits=1)
totPercents(tab, digits=1)

Arguments
tab a matrix or higher-dimensional array of frequency counts.
digits number of places to the right of the decimal place for percentages.

Value
Returns an array of the same size and shape as tab percentaged by rows or columns, plus rows or
columns of totals and counts, or by the table total.

Author(s)
John Fox hjfox@[Link]

generalizedLinearModel
Rcmdr Generalized Linear Model Dialog

Description
This dialog is used to specify a generalized linear model to be fit by the glm function.

Details
The left model-formula box specifies the response variable to be used in the model; it may be a vari-
able name or an expression evaluating to the response variable, such as working == "Fulltime".
The right model-formula box specifies the right-hand (i.e., predictor) side of the model. See glm
for details.
You can type directly in the model formula boxes. Alternatively, double-clicking the left mouse
button on a variable in the variable-list transfers it to the left-hand side of the model (if it is empty)
hierarchicalCluster 31

or to the right-hand side. Factors are indicated in the variable list; all other variables are numeric.
You can also enter operators and parentheses using the buttons above the formula.
Double-click the left mouse button to select a family in the "Family" box and the corresponding
permissible link functions appear in the "Link function" box to the right. Initially, the canonical
link for the family is selected. See family for details.
Specifying a subset expression allows you to fit the model to a subset of observations in the active
data set. For example, assuming that gender is a variable in the active data set, entering gender
== "Male" would restrict the model to males.
If the active model is a generalized linear model, and the active data set has not changed, then the
initial values of the left-hand-side, right-hand-side, family, link, and subset fields are retained from
the active model.

Author(s)
John Fox hjfox@[Link]

See Also
glm, family, Comparison

hierarchicalCluster
Rcmdr Hierarchical Clustering Dialog

Description
This dialog is used to specify a hierarchical cluster analysis solution using hclust, with the dis-
tance matrix calculated using dist.

Details
Enter a name for the hierarchical clustering solution to be created if you want to retain more than
one solution. The solution name must be a valid R object name (consisting only of upper- and
lower-case letters, numerials, and periods, and not starting with a number).
Select the variables to be included in the solution using the variable selection box on the left side
of the dialog box. A non-contiguous set of variables can be selected by pressing your control key
(ctrl) while selecting variables.
Specifying a subset expression (the field below the variable selection box) allows you to obtain a
clustering solution for a subset of observations in the active data set. For example, assuming that
gener is a variable in the active data set, entering gender == "Male" would restrict the solution
to males.
Select a clustering method and a distance measure if you are working with raw data. There is often
a relationship between the selection of these two items. For example, squared-euclidian distance is
appropriate for Ward’s method of cluster analysis. If your data is a distance matrix, then select "No
Transformation" as the distance measure.
The "Plot Dendrogram" option results in the dendrogram of the solution being display by using the
plot function.
32 linearModel

Author(s)

Dan Putler

See Also

hclust, dist

linearModel Rcmdr Linear Model Dialog

Description

This dialog is used to specify a linear model to be fit by the lm function.

Details

The left model-formula box specifies the response variable to be used in the model; it may be a
variable name or an expression evaluating to the response variable, such as log(income).
The right model-formula box specifies the right-hand (i.e., predictor) side of the model. See lm for
details.
You can type directly in the model formula boxes. Alternatively, double-clicking the left mouse
button on a variable in the variable-list transfers it to the left-hand side of the model (if it is empty)
or to the right-hand side. You can also enter operators and parentheses using the buttons above the
formula.
Specifying a subset expression allows you to fit the model to a subset of observations in the active
data set. For example, assuming that gender is a variable in the active data set, entering gender
== "Male" would restrict the model to males.
If the active model is a linear model and the active data set has not changed, then the initial values
of the left-hand-side, right-hand-side, and subset fields are retained from the previous model.

Author(s)

John Fox hjfox@[Link]

See Also

lm, Comparison
numSummary 33

numSummary Mean, Standard Deviation, and Quantiles for Numeric Variables

Description
numSummary creates neatly formatted tables of means, standard deviations, and quantiles of nu-
meric variables.

Usage
numSummary(data, statistics=c("mean", "sd", "quantiles"),
quantiles=c(0, .25, .5, .75, 1), groups)

## S3 method for class 'numSummary':

print(x, ...)

Arguments
data a numeric vector, matrix, or data frame.
statistics any of "mean", "sd", or "quantiles", defaulting to all three.
quantiles quantiles to report; default is c(0, 0.25, 0.5, 0.75, 1).
groups optional variable, typically a factor, to be used to partition the data.
x object of class "numSummary" to print.
... arguments to pass down from the print method.

Value
numSummary returns an object of class "numSummary" containing the table of statistics to be
reported along with information on missing data, if there are any.

Author(s)
John Fox hjfox@[Link]

See Also
mean, sd, quantile.

Examples
library(car)
Prestige[1, "income"] <- NA
numSummary(Prestige[,c("income", "education")])
numSummary(Prestige[,c("income", "education")], groups=Prestige$type)
remove(Prestige)
34 plotMeans

[Link] Partial Correlations

Description
Computes a matrix of partial correlations between each pair of variables controlling for the others.

Usage
[Link](X, ...)

Arguments
X data matrix.
... arguments to be passed to cor.

Value
Returns a matrix of partial correlations.

Author(s)
John Fox hjfox@[Link]

See Also
cor

Examples
library(car)
data(DavisThin)
[Link](DavisThin)

plotMeans Plot Means for One or Two-Way Layout

Description
Plots cell means for a numeric variable in each category of a factor or in each combination of
categories of two factors, optionally along with error bars based on cell standard errors or standard
deviations.
plotMeans 35

Usage

plotMeans(response, factor1, factor2,

[Link] = c("se", "sd", "[Link]", "none"), level=0.95,
xlab = deparse(substitute(factor1)),
ylab = paste("mean of", deparse(substitute(response))),
[Link] = deparse(substitute(factor2)), main = "Plot of Means",
pch = 1:[Link].2, lty = 1:[Link].2, col = palette())

Arguments

response Numeric variable for which means are to be computed.

factor1 Factor defining horizontal axis of the plot.
factor2 If present, factor defining profiles of means
[Link] If "se", the default, error bars around means give plus or minus one standard
error of the mean; if "sd", error bars give plus or minus one standard deviation;
if "[Link]", error bars give a confidence interval around each mean; if
"none", error bars are suppressed.
level level of confidence for confidence intervals; default is .95
xlab Label for horizontal axis.
ylab Label for vertical axis.
[Link] Label for legend.
main Label for the graph.
pch Plotting characters for profiles of means.
lty Line types for profiles of means.
col Colours for profiles of means

Value

The function invisibly returns NULL.

Author(s)

John Fox hjfox@[Link]

See Also

[Link]
36 reliability

reliability Reliability of a Composite Scale

Description
Calculates Cronbach’s alpha and standardized alpha (lower bounds on reliability) for a composite
(summated-rating) scale. Standardized alpha is for the sum of the standardized items. In addition,
the function calculates alpha and standardized alpha for the scale with each item deleted in turn,
and computes the correlation between each item and the sum of the other items.

Usage
reliability(S)

## S3 method for class 'reliability':

print(x, digits=4, ...)

Arguments
S the covariance matrix of the items; normally, there should be at least 3 items and
certainly no fewer than 2.
x reliability object to be printed.
digits number of decimal places.
... not used: for compatibility with the print generic."

Value
an object of class reliability, which normally would be printed.

Author(s)
John Fox hjfox@[Link]

References
N. Cliff (1986) Psychological testing theory. Pp. 343–349 in S. Kotz and N. Johnson, eds., Ency-
clopedia of Statistical Sciences, Vol. 7. Wiley.

See Also
cov

Examples
library(car)
data(DavisThin)
reliability(cov(DavisThin))
scatter3d 37

scatter3d Three-Dimensional Scatterplots and Point Identification

Description
The scatter3d function uses the rgl package to draw 3D scatterplots with various regression
surfaces. The function identify3d allows you to label points interactively with the mouse: Press
the right mouse button (on a two-button mouse) or the centre button (on a three-button mouse), drag
a rectangle around the points to be identified, and release the button. Repeat this procedure for each
point or set of “nearby” points to be identified. To exit from point-identification mode, click the
right (or centre) button an empty region of the plot.

Usage
scatter3d(x, y, z,
xlab=deparse(substitute(x)), ylab=deparse(substitute(y)),
[Link]=TRUE,
zlab=deparse(substitute(z)), revolutions=0, [Link]=c("white", "black"),
[Link]=if ([Link] == "white") c("darkmagenta", "black", "darkcyan")
else c("darkmagenta", "white", "darkcyan"),
[Link]=c("blue", "green", "orange", "magenta", "cyan", "red", "yellow"
[Link]="red", [Link]="green",
[Link]=if ([Link] == "white") "black" else "gray", [Link]="yellow",
[Link]=[Link], [Link]=if ([Link] == "white") "black" else "gray",
fogtype=c("exp2", "linear", "exp", "none"),
residuals=(length(fit) == 1), surface=TRUE, fill=TRUE, grid=TRUE, [Link]
[Link]=NULL, [Link]=NULL,
[Link]=1, threshold=0.01, speed=1, fov=60,
fit="linear", groups=NULL, parallel=TRUE, ellipsoid=FALSE, level=0.5,
[Link]=FALSE)

identify3d(x, y, z, [Link]=TRUE, groups=NULL, labels=1:length(x),

col=c("blue", "green", "orange", "magenta", "cyan", "red", "yellow", "gray"),
offset = ((100/length(x))^(1/3)) * 0.02)

Arguments
x variable for horizontal axis.
y variable for vertical axis (response).
z variable for out-of-screen axis.
xlab, ylab, zlab
axis labels.
[Link] if TRUE, label the values of the ends of the axes. Note: For identify3d to
work properly, the value of this argument must be the same as in scatter3d.
revolutions number of full revolutions of the display.
38 scatter3d

[Link] background colour; one of "white", "black".

[Link] colours for axes; if [Link] is FALSE, then the second colour is used
for all three axes.
[Link] vector of colours for regression planes, used in the order specified by fit.
[Link], [Link]
colours for lines representing negative and positive residuals.
[Link] colour to use to plot squared residuals.
[Link] colour of points.
[Link] colour of axis labels.
[Link] colour of grid lines on the regression surface(s).
fogtype type of fog effect; one of "exp2", "linear", "exp", "none".
residuals plot residuals if TRUE; if residuals="squares", then the squared residu-
als are shown as squares (using code adapted from Richard Heiberger). Residu-
als are available only when there is one surface plotted.
surface plot surface(s) (TRUE or FALSE).
fill fill the plotted surface(s) with colour (TRUE or FALSE).
grid plot grid lines on the regression surface(s) (TRUE or FALSE).
[Link] number of lines (default, 26) forming the grid, in each of the x and y directions.
[Link] degrees of freedom for the two-dimensional smooth regression surface; if NULL
(the default), the gam function will select the degrees of freedom for a smooth-
ing spline by generalized cross-validation; if a positive number, a fixed regres-
sion spline will be fit with the specified degrees of freedom.
[Link] degrees of freedom for each explanatory variable in an additive regression; if
NULL (the default), the gam function will select degrees of freedom for the
smoothing splines by generalized cross-validation; if a positive number or a vec-
tor of two positive numbers, fixed regression splines will be fit with the specified
degrees of freedom for each term.
[Link] relative sizes of spheres representing points; the actual size is dependent on the
number of observations.
threshold if the actual size of the spheres is less than the threshold, points are plotted
instead.
speed relative speed of revolution of the plot.
fov field of view (in degrees); controls degree of perspective.
fit one or more of "linear", "quadratic", "smooth", "additive"; to
display fitted surface(s); partial matching is supported – e.g., c("lin", "quad").
groups if NULL (the default), no groups are defined; if a factor, a different surface or
set of surfaces is plotted for each level of the factor; in this event, the colours
in [Link] are used successively for the points, surfaces, and residuals
corresponding to each level of the factor.
parallel when plotting surfaces by groups, should the surfaces be constrained to be
parallel? A logical value, with default TRUE.
ellipsoid plot concentration ellipsoid(s) (TRUE or FALSE).
scatter3d 39

level expected proportion of bivariate-normal observations included in the concentra-

tion ellipsoid(s); default is 0.5.
[Link]
print summary or summaries of the model(s) fit (TRUE or FALSE). scatter3d
rescales the three variables internally to fit in the unit cube; this rescaling will
affect regression coefficients.
labels text labels for the points, one for each point; defaults to the observation indices.
col colours for the point labels, given by group. There must be at least as many
colours as groups; if there are no groups, the first colour is used. Normally, the
colours would correspond to the [Link] argument to scatter3d.
offset vertical displacement for point labels (to avoid overplotting by points).

Value
scatter3d not return a useful value; it is used for its side-effect of creating a 3D scatterplot.
indentify3d returns the labels of the identified points.

Note
You have to install the rgl and mgcv packages to produce 3D plots.

Author(s)
John Fox hjfox@[Link]

See Also
[Link], gam

Examples
## Not run:
State.x77 <- [Link](state.x77)
with(State.x77, scatter3d(Income, Murder, Illiteracy))
with(State.x77, identify3d(Income, Murder, Illiteracy, labels=[Link](State.x77)))
with(State.x77, scatter3d(Income, Murder, Illiteracy, fit=c("linear", "quadratic")))

## End(Not run)
Index

∗Topic hplot 24
Hist, 15 activeDataSetP ([Link]),
plotMeans, 34 18
scatter3d, 37 activeDataSetView
Scatter3DDialog, 27 ([Link]-specific),
∗Topic htest 24
Confint, 14 ActiveModel ([Link]), 18
∗Topic manip activeModel ([Link]), 18
[Link], 29 activeModelP ([Link]), 18
Compute, 13 Arithmetic, 13
Recode, 26 assignCluster, 28
∗Topic misc
assignCluster, 28 [Link], 29
colPercents, 30 buttonRcmdr ([Link]), 18
Commander, 8
Commander-es, 2 checkActiveDataSet
hierarchicalCluster, 31 ([Link]), 18
KMeans, 16 checkActiveModel
numSummary, 33 ([Link]), 18
[Link], 34 checkBoxes ([Link]), 18
Plugins, 17 checkClass ([Link]), 18
[Link]-specific, 24 checkFactors ([Link]), 18
[Link], 18 checkMethod ([Link]), 18
RcmdrPager, 25 checkNumeric ([Link]), 18
reliability, 36 checkReplace ([Link]), 18
∗Topic models checkTwoLevelFactors
Confint, 14 ([Link]), 18
generalizedLinearModel, 30 checkVariables ([Link]),
linearModel, 32 18
∗Topic package closeCommander ([Link]),
Rcmdr-package, 17 18
closeDialog ([Link]), 18
activateMenus ([Link]), colPercents, 30
18 Commander, 8, 17
ActiveDataSet ([Link]), Commander-es, 2
18 commanderPosition
activeDataSet ([Link]), ([Link]), 18
18 CommanderWindow
activeDataSetEdit ([Link]), 18
([Link]-specific), Comparison, 31, 32

40
INDEX 41

Compute, 13 [Link]
Confint, 14 ([Link]-specific),
confint, 14 24
cor, 34 [Link] ([Link]),
cov, 36 18
cut, 29
cutree, 28 justDoIt ([Link]), 18

dataSetsP ([Link]), 18 KMeans, 16, 28

defmacro ([Link]), 18 kmeans, 16, 28, 29
dialogSuffix ([Link]), 18
dist, 31, 32 labelRcmdr ([Link]), 18
doItAndPrint ([Link]), 18 linearModel, 32
listAllModels ([Link]),
errorCondition ([Link]), 18
18 listAOVModels ([Link]),
[Link] ([Link]), 18
18 listDataSets ([Link]), 18
listFactors ([Link]), 18
Factors ([Link]), 18
listGeneralizedLinearModels
factorsP ([Link]), 18
([Link]), 18
family, 31
listLinearModels
formulaFields ([Link]),
([Link]), 18
18
listMultinomialLogitModels
gam, 27, 28, 38, 39 ([Link]), 18
generalizedLinearModel, 30 listNumeric ([Link]), 18
getFrame ([Link]), 18 listPlugins ([Link]), 18
getRcmdr ([Link]), 18 listProportionalOddsModels
getSelection ([Link]), 18 ([Link]), 18
gettext, 24 listTwoLevelFactors
gettextRcmdr ([Link]), 18 ([Link]), 18
glm, 30, 31 listVariables ([Link]),
glmP ([Link]), 18 18
GrabFocus ([Link]), 18 lm, 32
groupsBox ([Link]), 18 lmP ([Link]), 18
groupsLabel ([Link]), 18 logger ([Link]), 18
LogWindow ([Link]), 18
hclust, 28, 31, 32
hclustSolutionsP MacOSXP ([Link]), 18
([Link]), 18 mean, 33
hierarchicalCluster, 31 Message ([Link]), 18
Hist, 15 MessagesWindow ([Link]),
hist, 15 18
modelFormula ([Link]), 18
identify3d, 27, 28 modelsP ([Link]), 18
identify3d (scatter3d), 37 multinomP ([Link]), 18
initializeDialog
([Link]), 18 nobs ([Link]), 18
[Link], 35 Numeric ([Link]), 18
42 INDEX

numericP ([Link]), 18 scatter3d, 27, 28, 37

numSummary, 33 Scatter3DDialog, 27
sd, 33
OKCancelHelp ([Link]), 18 sortVarNames ([Link]), 18
optionAttachDataSet subOKCancelHelp
([Link]-specific), ([Link]), 18
24 subsetBox ([Link]), 18
optionLogCommand svCommander
([Link]-specific), ([Link]-specific),
24 24
optionSortVariables svlogger
([Link]-specific), ([Link]-specific),
24 24
OutputWindow ([Link]), 18
tclvalue ([Link]), 18
packageAvailable tkbutton, 24
([Link]), 18 tkentry, 24
[Link], 34 tkfocus
plotMeans, 34 ([Link]-specific),
Plugins, 7, 9, 11, 13, 17 24
polrP ([Link]), 18 tkframe, 24
popOutput ([Link]), 18 tklabel, 24
[Link] (numSummary), 33 tkpager, 26
[Link] (reliability), tkradiobutton, 24
36 tkscrollbar, 24
putRcmdr ([Link]), 18 totPercents (colPercents), 30
[Link] ([Link]), 18
quantile, 33
ttkbutton, 24
radioButtons ([Link]), 18 ttkentry, 24
Rcmdr (Rcmdr-package), 17 ttkentry ([Link]), 18
Rcmdr-package, 17 ttkframe, 24
[Link]-specific, 13 ttkframe ([Link]), 18
[Link]-specific, 24 ttklabel, 24
[Link], 9, 13, 18 ttkradiobutton, 24
RcmdrPager, 25 ttkradiobutton ([Link]),
RcmdrTclSet ([Link]), 18 18
RcmdrTkmessageBox ttkscrollbar, 24
([Link]), 18 ttkscrollbar ([Link]), 18
Recode, 26 TwoLevelFactors
recode, 26, 27 ([Link]), 18
refreshStatus twoLevelFactorsP
([Link]-specific), ([Link]), 18
24
reliability, 36 UpdateModelNumber
[Link], 28, 39 ([Link]), 18
rglLoaded ([Link]), 18
variableListBox
rowPercents (colPercents), 30
([Link]), 18
Scatter3D (Scatter3DDialog), 27 Variables ([Link]), 18