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 use this report as a reference, when an article in which EZR is
used as a statistical software is published.
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. At the present moment, I recommend the easier method,
because R ver 3.0.0 with a major upgrade will be released shortly.
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 2.13.0
and R commander 1.8-4.
Click here to download EZRsetupENG.exe for Windows. (Ver. 1.11 2013/02/26)。
2. Formal 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) For R 2.8.0-2.15.3, download and install tcltk graphical environment
tool, tcltk-8.5.5-x11.dmg, which can be found in the subdirectory: tools of the page, Download R
for MacOS X). For R 3.0.0 or later version, this step is not required,
because Tck/Tk 8.6.0. is bundled with R.
3) Download and install IPA fonts.
http://ossipedia.ipa.go.jp/ipafont/IPAfont00303.php (Direct link to a zip file)
Unarchive the zip file and open and install the following font files:
ipag.ttf
ipagp.tff
ipam.ttf
ipamp.ttf
4) Open R64.app. Type
install.packages("RcmdrPlugin.EZR", dependencies=TRUE)
after ">" in the R console and push the Enter key.
5) 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?".
6) R commander will start at the same time with launching R, if "library(Rcmdr)" is added to the "~/.Rprofile" file.
In addition, EZR plugin package will be automatically loaded when R commander
is started, if the following line is added to the same file.
options(Rcmdr=list(plugins="RcmdrPlugin.EZR"))
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 "library(Rcmdr)" >> ~/.Rprofile
echo "options(Rcmdr=list(plugins='RcmdrPlugin.EZR'))" >>
~/.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 |