EZR version 1.26 now available! (September 29, 2014)

New function available to create summary table of sample characterstics.

For Windows XP - 8.1, Mac OS X Snow Leopard - Marvericks, Ubuntu 11.10 - 13.04

Please cite the following paper as a reference for scientific papers in which EZR is used as a statistical software.
Bone Marrow Transplantation 2013: 48, 452–458

Free statistical software: EZR on R commander   R is a free software environment for statistical computing and graphics. R supports many functions for statistical analyses, but it does not incorporate statistical graphical user interface (GUI). The R commander provides a easy-to-use basic-statistics GUI to R based on Tcl/Tk language. However, the statistical function of the R commander is limited, especially in the field of biostatistics. Therfore, we added statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. We named it "EZR" (Easy R) and we are distributing it on this page. EZR can import Excel files, CSV files, Stata files, and so on. EZR is now available on CRAN (The Comprehensive R Archive Network) as "RcmdrPlugin.EZR" package. Contact address: Yoshinobu Kanda, M.D., saitama-hem@jichi.ac.jp.

Statistical functions of EZR

A complete manual of EZR is available only in Japanese (Chugai Igakusha, ISBN-10: 4498109007), but a report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. It can be freely downloaded from the journal website (Kanda Y. Investigation of the freely available easy-to-use software ‘EZR’ for medical statistics. Bone Marrow Transplantation 2013:48,452-458 advance online publication 3 December 2012; doi: 10.1038/bmt.2012.244).



Please cite this report as a reference for scientific papers in which EZR is used as a statistical software.

 In addition, Professor Minato Nakazawa (Kobe Univ. Grad. School Heallth Sci.) is providing an excellent manual for the use of R and EZR in medical statics on his homepage. It can be downloaded from the link below. (He told me that there may be some typos and mistakes, which will be fixed in the future.)

Medical Statistics for Gunma Univ. Graduate School of Medicine

List of published scientific papers of clinical studies using EZR.

Sample data set that includes 93 fictional patients who received allogeneic stem cell transplantation for acute leukemia.
sample.csv

Matched-pair analysis in EZR requires optmatch package and its license restricts to academic use. See http://cran.r-project.org/web/packages/optmatch/LICENSE for details

How to install EZR on Windows
There are two methods to install EZR on Windows. The first one is easier, but the version of R and R commander is fixed. The second one is a little bit complicated but it enables installation of EZR on the latest version of R and R commander. However, I recommend the easier method, because EZR may casue an unexpected error according to an update of a package that EZR depends on.

1. Easier method.
Download the following file (EZRsetupENG.exe). EZR is installed along with R and R commander just by running this installer on Windows XP, VISTA, 7 or 8 (both 32- and 64-bit versions). This method installs EZR on R 3.1.2 and R commander 2.1-2. Previous version of EZR should be uninstalled using the uninstall program of EZR before installing the current version of EZR.

Click here to download EZRsetupENG.exe for Windows. (Ver. 1.26 2014/09/29)。

2. Alternative method
1) Download R installer from the The Comprehensive R Archive Network homepage (Download R for Windows, subdirectory: base). Install R.Right-click on the shortcut of R on desktop and select "Property". Add "--sdi" to the command in "Target:" column on the "Shortcut" tab. Double-click this shortcut to run R.

2) Type

install.packages("RcmdrPlugin.EZR", dependencies=TRUE)

after ">" in the R console and push the Enter key.

3) To run R commander, type "library(Rcmdr)", after ">" in the R console and push the Enter key. Answer "Yes" to the question whether the user wants to install packagees that are required by Rcmdr. If this procedure does not work properly, Type
install.packages("Rcmdr", dependencies=TRUE)
after ">" in the R console and push the Enter key to install packages required by R commander, and then, repeat 3). EZR can be loaded by selecting RcmdrPlugin.EZR from the "Tools" > "Load Rcmdr plug-in(s)" menu in the R commander window. Answer "Yes" to "Restart now?".

4) EZR plugin package will be loaded when R commander is started, if the following sentence is added to the Rprofile.site file in etc folder in the R folder (C:\\Program Files\\R\\R-X.XX.X\\etc).

options(Rcmdr=list(plugins="RcmdrPlugin.EZR"))

In addition, if the following phrase is added to the command in "Target:" column on the "Shortcut" tab of the "Property" of "R" shorcut on the desktop (which can be opened by right-clicking on the shortcut), R commander will start at the same time with launching R.

R_DEFAULT_PACKAGES="Rcmdr"

Therefore, if these two options are added, EZR can be started just by double-clicking on the "R" shortcut on the desktop

5) The default data folder can be changed by right-clicking on this "R" shortcut on the desktop, selecting "Properties", and replacing the folder name in the "Start in:" column on the "Shortcut" tab.

How to install EZR on MacOS X
1) Download R installer from the The Comprehensive R Archive Network homepage (Download R for MacOS X). Install R and run R. Install it on the main hard drive.

2) EZR requires X11 windows system, but it may not be installed in OS X Mountain Lion or later versions. X11 windows system can be installed from a WEB site, http://xquartz.macosforge.org.

3) Open R.app and type

install.packages("RcmdrPlugin.EZR", dependencies=TRUE)

after ">" in the R console and push the Enter key.

4) To run R commander, type

library(Rcmdr)

after ">" in the R console and push the Enter key. Answer "Yes" to the question (if shown) whether the user wants to install packagees that are required by Rcmdr. If this procedure does not work properly, Type
install.packages("Rcmdr", dependencies=TRUE)
after ">" in the R console and push the Enter key to install packages required by R commander, and then, repeat 3). EZR can be loaded by selecting RcmdrPlugin.EZR from the "Tools" > "Load Rcmdr plug-in(s)" menu in the R commander window. Answer "Yes" to "Restart now?".

5) EZR will start at the same time with launching R, if following 6 lined are added to the "~/.Rprofile" file.

options(Rcmdr=list(plugins='RcmdrPlugin.EZR'))
library(Rcmdr)
local({
old <- getOption('defaultPackages')
options(defaultPackages = c(old, 'Rcmdr'))
})

These can be done by opening the Terminal.app located in the Utilities folder, followed by copying and pasting the following command.

## Starts here
echo "options(Rcmdr=list(plugins='RcmdrPlugin.EZR'))" >> ~/.Rprofile
echo "library(Rcmdr)" >> ~/.Rprofile
echo "local({" >> ~/.Rprofile
echo "old <- getOption('defaultPackages')" >> ~/.Rprofile
echo "options(defaultPackages = c(old, 'Rcmdr'))" >> ~/.Rprofile
echo "})" >> ~/.Rprofile
## Ends here

To manually edit the file, open Terminal.app, and then then copy and paste the following command. TextEdit.app is started to edit the file.

## Starts here
open -a TextEdit.app ~/.Rprofile
## Ends here

Click to view large images.


EZR menu

Summary of analysis

Survival analysis

Kaplan-Meier plot

ROC analysis

Metaanalyis