New RCommander with ggplot #rstats

 

My favorite GUI (or one of them) R Commander has a relatively new plugin called KMGGplot2. Until now Deducer was the only GUI with ggplot features , but the much lighter and more popular R Commander has been a long champion in people wanting to pick up R quickly.

 

http://cran.r-project.org/web/packages/RcmdrPlugin.KMggplot2/

RcmdrPlugin.KMggplot2: Rcmdr Plug-In for Kaplan-Meier Plot and Other Plots by Using the ggplot2 Package

 

As you can see by the screenshot- it makes ggplot even easier for people (like R  newbies and experienced folks alike)

 

This package is an R Commander plug-in for Kaplan-Meier plot and other plots by using the ggplot2 package.

Version: 0.1-0
Depends: R (≥ 2.15.0), stats, methods, grid, Rcmdr (≥ 1.8-4), ggplot2 (≥ 0.9.1)
Imports: tcltk2 (≥ 1.2-3), RColorBrewer (≥ 1.0-5), scales (≥ 0.2.1), survival (≥ 2.36-14)
Published: 2012-05-18
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou. <triadsou at gmail.com>
License: GPL-2
CRAN checks: RcmdrPlugin.KMggplot2 results

 

----------------------------------------------------------------
NEWS file for the RcmdrPlugin.KMggplot2 package
----------------------------------------------------------------

----------------------------------------------------------------

Changes in version 0.1-0 (2012-05-18)

 o Restructuring implementation approach for efficient
   maintenance.
 o Added options() for storing package specific options (e.g.,
   font size, font family, ...).
 o Added a theme: theme_simple().
 o Added a theme element: theme_rect2().
 o Added a list box for facet_xx() functions in some menus
   (Thanks to Professor Murtaza Haider).
 o Kaplan-Meier plot: added confidence intervals.
 o Box plot: added violin plots.
 o Bar chart for discrete variables: deleted dynamite plots.
 o Bar chart for discrete variables: added stacked bar charts.
 o Scatter plot matrix: added univariate plots at diagonal
   positions (ggplot2::plotmatrix).
 o Deleted the dummy data for histograms, which is large in
   size.

----------------------------------------------------------------

Changes in version 0.0-4 (2011-07-28)

 o Fixed "scale_y_continuous(formatter = "percent")" to
   "scale_y_continuous(labels = percent)" for ggplot2
   (>= 0.9.0).
 o Fixed "legend = FALSE" to "show_guide = FALSE" for
   ggplot2 (>= 0.9.0).
 o Fixed the DESCRIPTION file for ggplot2 (>= 0.9.0) dependency.

----------------------------------------------------------------

Changes in version 0.0-3 (2011-07-28; FIRST RELEASE VERSION)

 o Kaplan-Meier plot: Show no. at risk table on outside.
 o Histogram: Color coding.
 o Histogram: Density estimation.
 o Q-Q plot: Create plots based on a maximum likelihood estimate
   for the parameters of the selected theoretical distribution.
 o Q-Q plot: Create plots based on a user-specified theoretical
   distribution.
 o Box plot / Errorbar plot: Box plot.
 o Box plot / Errorbar plot: Mean plus/minus S.D.
 o Box plot / Errorbar plot: Mean plus/minus S.D. (Bar plot).
 o Box plot / Errorbar plot: 95 percent Confidence interval
   (t distribution).
 o Box plot / Errorbar plot: 95 percent Confidence interval
   (bootstrap).
 o Scatter plot: Fitting a linear regression.
 o Scatter plot: Smoothing with LOESS for small datasets or GAM
   with a cubic regression basis for large data.
 o Scatter plot matrix: Fitting a linear regression.
 o Scatter plot matrix: Smoothing with LOESS for small datasets
   or GAM with a cubic regression basis for large data.
 o Line chart: Normal line chart.
 o Line chart: Line char with a step function.
 o Line chart: Area plot.
 o Pie chart: Pie chart.
 o Bar chart for discrete variables: Bar chart for discrete
   variables.
 o Contour plot: Color coding.
 o Contour plot: Heat map.
 o Distribution plot: Normal distribution.
 o Distribution plot: t distribution.
 o Distribution plot: Chi-square distribution.
 o Distribution plot: F distribution.
 o Distribution plot: Exponential distribution.
 o Distribution plot: Uniform distribution.
 o Distribution plot: Beta distribution.
 o Distribution plot: Cauchy distribution.
 o Distribution plot: Logistic distribution.
 o Distribution plot: Log-normal distribution.
 o Distribution plot: Gamma distribution.
 o Distribution plot: Weibull distribution.
 o Distribution plot: Binomial distribution.
 o Distribution plot: Poisson distribution.
 o Distribution plot: Geometric distribution.
 o Distribution plot: Hypergeometric distribution.
 o Distribution plot: Negative binomial distribution.

R Commander Plugins-20 and growing!

First graphical user interface in 1973.
Image via Wikipedia
R Commander Extensions: Enhancing a Statistical Graphical User Interface by extending menus to statistical packages

R Commander ( see paper by Prof J Fox at http://www.jstatsoft.org/v14/i09/paper ) is a well known and established graphical user interface to the R analytical environment.
While the original GUI was created for a basic statistics course, the enabling of extensions (or plug-ins  http://www.r-project.org/doc/Rnews/Rnews_2007-3.pdf ) has greatly enhanced the possible use and scope of this software. Here we give a list of all known R Commander Plugins and their uses along with brief comments.

  1. DoE – http://cran.r-project.org/web/packages/RcmdrPlugin.DoE/RcmdrPlugin.DoE.pdf
  2. doex
  3. EHESampling
  4. epack- http://cran.r-project.org/web/packages/RcmdrPlugin.epack/RcmdrPlugin.epack.pdf
  5. Export- http://cran.r-project.org/web/packages/RcmdrPlugin.Export/RcmdrPlugin.Export.pdf
  6. FactoMineR
  7. HH
  8. IPSUR
  9. MAc- http://cran.r-project.org/web/packages/RcmdrPlugin.MAc/RcmdrPlugin.MAc.pdf
  10. MAd
  11. orloca
  12. PT
  13. qcc- http://cran.r-project.org/web/packages/RcmdrPlugin.qcc/RcmdrPlugin.qcc.pdf and http://cran.r-project.org/web/packages/qcc/qcc.pdf
  14. qual
  15. SensoMineR
  16. SLC
  17. sos
  18. survival-http://cran.r-project.org/web/packages/RcmdrPlugin.survival/RcmdrPlugin.survival.pdf
  19. SurvivalT
  20. Teaching Demos

Note the naming convention for above e plugins is always with a Prefix of “RCmdrPlugin.” followed by the names above
Also on loading a Plugin, it must be already installed locally to be visible in R Commander’s list of load-plugin, and R Commander loads the e-plugin after restarting.Hence it is advisable to load all R Commander plugins in the beginning of the analysis session.

However the notable E Plugins are
1) DoE for Design of Experiments-
Full factorial designs, orthogonal main effects designs, regular and non-regular 2-level fractional
factorial designs, central composite and Box-Behnken designs, latin hypercube samples, and simple D-optimal designs can currently be generated from the GUI. Extensions to cover further latin hypercube designs as well as more advanced D-optimal designs (with blocking) are planned for the future.
2) Survival- This package provides an R Commander plug-in for the survival package, with dialogs for Cox models, parametric survival regression models, estimation of survival curves, and testing for differences in survival curves, along with data-management facilities and a variety of tests, diagnostics and graphs.
3) qcc -GUI for  Shewhart quality control charts for continuous, attribute and count data. Cusum and EWMA charts. Operating characteristic curves. Process capability analysis. Pareto chart and cause-and-effect chart. Multivariate control charts
4) epack- an Rcmdr “plug-in” based on the time series functions. Depends also on packages like , tseries, abind,MASS,xts,forecast. It covers Log-Exceptions garch
and following Models -Arima, garch, HoltWinters
5)Export- The package helps users to graphically export Rcmdr output to LaTeX or HTML code,
via xtable() or Hmisc::latex(). The plug-in was originally intended to facilitate exporting Rcmdr
output to formats other than ASCII text and to provide R novices with an easy-to-use,
easy-to-access reference on exporting R objects to formats suited for printed output. The
package documentation contains several pointers on creating reports, either by using
conventional word processors or LaTeX/LyX.
6) MAc- This is an R-Commander plug-in for the MAc package (Meta-Analysis with
Correlations). This package enables the user to conduct a meta-analysis in a menu-driven,
graphical user interface environment (e.g., SPSS), while having the full statistical capabilities of
R and the MAc package. The MAc package itself contains a variety of useful functions for
conducting a research synthesis with correlational data. One of the unique features of the MAc
package is in its integration of user-friendly functions to complete the majority of statistical steps
involved in a meta-analysis with correlations. It uses recommended procedures as described in
The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).

A query to help for ??Rcmdrplugins reveals the following information which can be quite overwhelming given that almost 20 plugins are now available-

RcmdrPlugin.DoE::DoEGlossary
Glossary for DoE terminology as used in
RcmdrPlugin.DoE
RcmdrPlugin.DoE::Menu.linearModelDesign
RcmdrPlugin.DoE Linear Model Dialog for
experimental data
RcmdrPlugin.DoE::Menu.rsm
RcmdrPlugin.DoE response surface model Dialog
for experimental data
RcmdrPlugin.DoE::RcmdrPlugin.DoE-package
R-Commander plugin package that implements
design of experiments facilities from packages
DoE.base, FrF2 and DoE.wrapper into the
R-Commander
RcmdrPlugin.DoE::RcmdrPlugin.DoEUndocumentedFunctions
Functions used in menus
RcmdrPlugin.doex::ranblockAnova
Internal RcmdrPlugin.doex objects
RcmdrPlugin.doex::RcmdrPlugin.doex-package
Install the DOEX Rcmdr Plug-In
RcmdrPlugin.EHESsampling::OpenSampling1
Internal functions for menu system of
RcmdrPlugin.EHESsampling
RcmdrPlugin.EHESsampling::RcmdrPlugin.EHESsampling-package
Help with EHES sampling
RcmdrPlugin.Export::RcmdrPlugin.Export-package
Graphically export objects to LaTeX or HTML
RcmdrPlugin.FactoMineR::defmacro
Internal RcmdrPlugin.FactoMineR objects
RcmdrPlugin.FactoMineR::RcmdrPlugin.FactoMineR
Graphical User Interface for FactoMineR
RcmdrPlugin.IPSUR::IPSUR-package
An IPSUR Plugin for the R Commander
RcmdrPlugin.MAc::RcmdrPlugin.MAc-package
Meta-Analysis with Correlations (MAc) Rcmdr
Plug-in
RcmdrPlugin.MAd::RcmdrPlugin.MAd-package
Meta-Analysis with Mean Differences (MAd) Rcmdr
Plug-in
RcmdrPlugin.orloca::activeDataSetLocaP
RcmdrPlugin.orloca: A GUI for orloca-package
(internal functions)
RcmdrPlugin.orloca::RcmdrPlugin.orloca-package
RcmdrPlugin.orloca: A GUI for orloca-package
RcmdrPlugin.orloca::RcmdrPlugin.orloca.es
RcmdrPlugin.orloca.es: Una interfaz grafica
para el paquete orloca
RcmdrPlugin.qcc::RcmdrPlugin.qcc-package
Install the Demos Rcmdr Plug-In
RcmdrPlugin.qual::xbara
Internal RcmdrPlugin.qual objects
RcmdrPlugin.qual::RcmdrPlugin.qual-package
Install the quality Rcmdr Plug-In
RcmdrPlugin.SensoMineR::defmacro
Internal RcmdrPlugin.SensoMineR objects
RcmdrPlugin.SensoMineR::RcmdrPlugin.SensoMineR
Graphical User Interface for SensoMineR
RcmdrPlugin.SLC::Rcmdr.help.RcmdrPlugin.SLC
RcmdrPlugin.SLC: A GUI for slc-package
(internal functions)
RcmdrPlugin.SLC::RcmdrPlugin.SLC-package
RcmdrPlugin.SLC: A GUI for SLC R package
RcmdrPlugin.sos::RcmdrPlugin.sos-package
Efficiently search R Help pages
RcmdrPlugin.steepness::Rcmdr.help.RcmdrPlugin.steepness
RcmdrPlugin.steepness: A GUI for
steepness-package (internal functions)
RcmdrPlugin.steepness::RcmdrPlugin.steepness
RcmdrPlugin.steepness: A GUI for steepness R
package
RcmdrPlugin.survival::allVarsClusters
Internal RcmdrPlugin.survival Objects
RcmdrPlugin.survival::RcmdrPlugin.survival-package
Rcmdr Plug-In Package for the survival Package
RcmdrPlugin.TeachingDemos::RcmdrPlugin.TeachingDemos-package
Install the Demos Rcmdr Plug-In

 

Top ten RRReasons R is bad for you ?

This is the original symbol of the Perl progra...
Image via Wikipedia

R stands for programming language based out of www.r-project.org

R is bad for you because –

1) It is slower with bigger datasets than SPSS language and SAS language .If you use bigger datasets, then you should either consider more hardware , or try and wait for some of the ODBC connect packages.

2) It needs more time to learn than SAS language .Much more time to learn how to do much more.

3) R programmers are lesser paid than SAS programmers.They prefer it that way.It equates the satisfaction of creating a package in development with a world wide community with the satisfaction of using a package and earning much more money per hour.

4) It forces you to learn the exact details of what you are doing due to its object oriented structure. Thus you either get no answer or get an exact answer. Your customer pays you by the hour not by the correct answers.

5) You can not push a couple of buttons or refer to a list of top ten most commonly used commands to finish the project.

6) It is free. And open for all. It is socialism expressed in code. Some of the packages are built by university professors. It is free.Free is bad. Who pays for the mortgage of the software programmers if all softwares were free ? Who pays for the Friday picnics. Who pays for the Good Night cruises?

7) It is free. Your organization will not commend you for saving them money- they will question why you did not recommend this before. And why did you approve all those packages that expire in 2011.R is fReeeeee. Customers feel good while spending money.The more software budgets you approve the more your salary is. R thReatens all that.

8) It is impossible to install a package you do not need or want. There is no one calling you on the phone to consider one more package or solution. R can make you lonely.

9) R uses mostly Command line. Command line is from the Seventies. Or the Eighties. The GUI’s RCmdr and Rattle are there but still…..

10) R forces you to learn new stuff by the month. You prefer to only earn by the month. Till the day your job got offshored…

Written by a R user in English language

( which fortunately was not copyrighted otherwise we would be paying Britain for each word)

Ajay- The above post was reprinted by personal request. It was written on Jan 2009- and may not be truly valid now. It is meant to be taken in good humor-not so seriously.