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Input Data in R using the top 3 R GUI

PC-DOS was an early OS for personal computers ...

Image via Wikipedia

One area where clearly GUI methods are preferable to command line methods in R, is data input. There is no need of learning read.csv or read.table when these options are only two clicks away in any R GUI. For academics/students there is a definite need to easily access

datasets from attached packages just as it is a need for business analysts to access databases with a few clicks than learn or read pages of pdf on RODBC. However some GUI (like Rattle) need data only in data frames, rather than list or arrays-this limits R’s flexibility. These are my views but you can see and compare views of data input in R Commander, Rattle and Deducer.



The Latest GUI for R- BioR

Once more a spanking new shiny software -

Bio7 is a integrated development environment for ecological modelling based on the Rich-Client-Platformconcept of the Java IDE Eclipse. The Bio7 platform contains several perspectives which arrange several views for a special purpose useful for the development and analysis of ecological models. One special perspective bundles a feature rich GUI (Graphical User Interface) for the statistical software R.
For the bidirectional communication between Java and R the Rserve application is used (as a backend to evaluate R code and transfer data from and to Java).
The Bio7 R perspective (see figure below) is divided into a R-Shell view on the left side (conceptual the R side) and a Table view on the right side (conceptual the Java side).
Data can be imported to a spreadsheet, edited and then transferred to the R workspace. Vice versa data from R can be transferred to a sheet of the Table view and then exported e.g. to an Excel or OpenOffice file.

and

General:

Built upon Eclipse 3.6.1.

Now works with the latest Java version! (Windows version bundled with the latest JRE release).

Removed the Soil perspective (now soils can be modeled with ImageJ (float precision). Active images can be displayed in the 3D discrete view (new example available).

Removed the database perspective and the plant layer. You can now built any discrete models without any plant layer.

Removed several controls in the Control view. Added the “Custom Controls” view. In addition ported the Swing component of the Time panel to Swt.

Deleted the avi to swf converter in the ImageJ menu.

Now patterns can be saved with opened Java editor source. If this file is reopened and dragged on Bio7 the pattern is loaded, the source is compiled and the setup method (if available) is executed. In this way model files can be used for presentations ->drag, setup and run. The save actions are located in the Speadsheet view toolbar.

More options available to disable panel painting and recording of values (if not needed for speed!).

New Setup button in the toolbar of Bio7 to trigger a compiled setup method if available.

Removed the load and save pattern buttons from the toolbar of Bio7. Discrete patterns can now be stored with the available action in the spreadsheet view menu.

New P2 Update Manager available in Bio7.

Updated the Janino Compiler.

New HTML perspective added with a view which embeds the TinyMC editor.

New options to disable painting operations for the discrete panels.

New option to explicitly enable scripts at startup (for a faster startup).

Quadgrid (Hexgrid)

Only states are now available which can be created in the “Spreadsheet” view menu easily. Patterns can be stored and restored as usual but are now stored in an *.exml file.

New method to transfer the quadgrid pattern as a matrix to R.

New method to transfer the population data of all quadgrid states to R.

ImageJ:

Update to the latest version (with additional fixes).

Fixed a bug to rename the image.

Thumbnail browser can now open images recursevely(limited to 1000 pics), the magnifiyng glass can be disabled, too.

Plugins can be installed dynamically with a drag and drop operation on the ImageJ view or toolbar (as known from ImageJ).

Installed plugins now extend the plugin menu as submenus or subsubmenus (not finished yet!).

Plugins can now be created with the Java editor. New Bio7 Wizard available to create a plugin template.

Compiled Java files can be added to a *.jar file with a new available action in the Navigator view (if you rightclick on the files in the Navigator). In this way ImageJ plugins can be packaged in a *.jar.

Floweditor:

Fixed a repaint bug in the debug mode of a flow (now draws correctly the active shape in the flow).

Resize with Strg+Scrollwheel works again.

Comments with more than one line works again.

New Test action to verify connections in a flow.

Debug mode now shows all executed Shapes.

Integrated more default tests (for the verification of a regular flow).

A mouse-click now deletes colored shapes in a flow (e.g. in debug mode).

Points panel:

Integrated (dynamic) Voronoi, Delauney visualization (with area and clip to rectangle action).

Points coordinates can now be set in double precision.

Transfer of point coordinates to R now in double precision.

Bio7 Table:

New import and export of Excel 2007 OOXML.

Row headers can now be resized with the mouse device.

R:

Updated R (2.12.1) and Rserve (0.6.3) to the latest version.

New help action in the R-Shell view.

New action to display help for R specific commands in the embedded Bio7 browser (which opens automatically).

New Key actions to copy the selected variable names to the expression dialog (c=cocatenate (+), a=add (,)).

New action to transfer character or numeric vectors horizontally or vertically in an opened spread (Table view) at selection coordinates.

Empty spaces in the filepath are now allowed under Windows if Rserve is started with a system shell or the RGUI (for the tempfile select a location in the Preferences dialog which is writeable) is started.This works also for the RGUI action.

Improved the search for the “Install packages” action (option “Case Sensitive” added).

API:

New API methods available!

And:

Many fixes since the last version!

 

Installation

Important information:

A certain firewall software can corrupt the Bio7 *.zip file (as well as other files).
Please ensure that you have downloaded a functioning Bio7 1.5 version. In addition it is also reported that a certain antivirus software detects the bundled R software (on Windows) as malware. Often the R specific “open.exe” is detected as malware. Please use a different scanner to make sure that the software is not infected if you have any doubts. For more details see:

http://r.789695.n4.nabble.com/trojan-at-current-development-version-td3244348.html

 

R Graphs Resources

Relevant GUI-

GrapheR and Deducer

https://rforanalytics.wordpress.com/graphical-user-interfaces-for-r/

Websites-


Graphics by Examples

. UCLA: Academic Technology Services,  Statistical Consulting Group. from https://www.ats.ucla.edu/stat/R/gbe/default.htm (accessed Feb 10, 2011)

https://www.ats.ucla.edu/stat/R/gbe/default.htm

Quick-R

http://www.statmethods.net/graphs/

Graph Gallery

http://addictedtor.free.fr/graphiques/allgraph.php

Frank McCown

https://www.harding.edu/fmccown/r/

Detailed Tutorial

https://math.illinoisstate.edu/dhkim/rstuff/rtutor.html

Advanced Data Visualization

Hadley Wickham

Courses- http://had.co.nz/stat645/

and Package-  http://had.co.nz/ggplot2/

example-

http://had.co.nz/ggplot2/geom_density.html

Using R from other Software

Bridge to R for WPS

http://www.minequest.com/Bridge2R.html

SAS/IML Interface to R

http://www.sas.com/technologies/analytics/statistics/iml/index.html

Official Screenshot-

RapidMiner Extension to R

https://rapid-i.com/content/view/202/206/lang,en/#r

(UN)Official Screenshot-

IBM SPSS plugin for R

https://www.spss.com/software/statistics/developer/

and

https://www.spss.com/devcentral/index.cfm?pg=rresources

Tutorial-

https://sites.google.com/site/r4statistics/running-r-from-spss

http://rwiki.sciviews.org/doku.php?id=tips:callingr:spss

(UN)official Screenshot

Knime

http://www.knime.org/downloads/extensions

Official Screenshot-

Oracle Data Miner

http://www.oracle.com/technetwork/database/options/odm/odm-r-integration-089013.html

Official Screenshot-

JMP

http://jmp.com/software/jmp9/keyfeatures.shtml

and

http://www.jmp.com/applications/analytical_apps/

Tutorial

http://blogs.sas.com/jmp/index.php?/archives/298-JMP-Into-R!.html

Screenshot-

Interviews with R Community

This chart represents several constituent comp...

Image via Wikipedia

Authors

Interview Luis Torgo Author Data Mining with R

http://decisionstats.com/2011/01/12/interview-luis-torgo-author-data-mining-with-r/

John Fox, R Commander

http://decisionstats.com/2009/09/14/interview-professor-john-fox-creator-r-commander/

Interview Dr Graham Williams RATTLE GUI

http://decisionstats.com/2009/01/13/interview-dr-graham-williams/

Hadley Wickham

http://decisionstats.com/2010/01/12/interview-hadley-wickham-r-project-data-visualization-guru/

R for SAS and SPSS Users

http://decisionstats.com/2009/01/21/r-for-sas-and-spss-users-2/

R for Stata Users

http://decisionstats.com/2010/06/29/interview-r-for-stata-users/

R Consulting

Interview David Katz ,Dataspora /David Katz Consulting

http://decisionstats.com/2011/02/11/interview-david-katz-dataspora-david-katz-consulting/

Case Study

(http://www.predictiveanalyticsworld.com/sanfrancisco/2011/agenda.php#day2-16a)

Room: Salon 5 & 6
4:45pm – 5:05pm

Track 2: Social Data and Telecom 
Case Study: Major North American Telecom
Social Networking Data for Churn Analysis

A North American Telecom found that it had a window into social contacts – who has been calling whom on its network. This data proved to be predictive of churn. Using SQL, and GAM in R, we explored how to use this data to improve the identification of likely churners. We will present many dimensions of the lessons learned on this engagement.

Speaker: David Katz, Senior Analyst, Dataspora, and President, David Katz Consulting

Q&A with David Smith, Revolution Analytics

http://decisionstats.com/2010/08/03/q-a-with-david-smith-revolution-analytics/

Inference for R

http://decisionstats.com/2009/06/04/inference-for-r/

David Smith Revolution Computing

http://decisionstats.com/2009/05/29/interview-david-smith-revolution-computing/

Richard Schultz Revolution Computing

http://decisionstats.com/2009/01/31/interviewrichard-schultz-ceo-revolution-computing/

Karime Chine, Elastic R

http://decisionstats.com/2009/06/21/interview-karim-chine-biocep-cloud-computing-with-r/

R for Analytics is now live

Okay, through the weekend I created a website for a few of my favourite things.

It’s on at https://rforanalytics.wordpress.com/

Graphical User Interfaces for R

 

Jerry Rubin said: “Don’t trust anyone over thirty

I dont trust anyone not using atleast one R GUI. Here’s a list of the top 10.

 

Code Enhancers for R

Here is a list of top 5 code enhancers,editors in R

R Commercial Software

A list of companies and software making (and) selling R software (and) services. Hint- it is almost 5 (unless I missed someone)

R Graphs Resources

R’s famous graphing capabilities and equally famous learning curve can be made a bit more humane- using some of these resources.

Internet Browsing

Because that’s what I do (all I do as per my cat) , and I am pretty good at it.

Using R from other Software

R can be used successfully from a lot of analytical software including some surprising ones praising the great 3000 packages library.

(to be continued- as I find more stuff I will keep it there, some ideas- database access from R, prominent R consultants, prominent R packages, famous R interviewees ;) )

ps- The quote from Jerry Rubin seems funny for a while. I turn 34 this year.

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

 

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