Create your first

package (in windows)

Gaston Sanchez
www.gastonsanchez.com
Creating an
R package?
What many of
us go through
f(T) = g(T, T)
g(T, W) = tr(T' A(w) T)
g(T, W) < h(T, W)
Maximize tr(T' A(w) T)
T' T = 1
revolutionary breakthrough,
statistical method
# core function
fun_xy <- function(x, y)
{
n = nrow(x)
p = ncol(x)
q = ncol(y)
mx = rowMeans(x)
my = rowMeans(y)
z = t(x) %*% y
...
lots of functions and scripts
Very Fancy Method for Analyzing
and Visualizing Multivariate Data
Your Name
a,b
, Graduate Student
b
, Intern Student
b
a
Renowned Statistical Research Center
b
Department of Stuffmetrics and Computational Methods,
Famous School (Pretty City)
Abstract
This paper depicts a new methodology devoted to
analyze complex data generated from extremely
expensive experiments in the field of Stuffmetrics. The
ultimate goal is to bla, bla, bla
One or more publications
Dear colleague,
Thank you for your deep interest in the super cool
method that I've been working on for so many years.
Unfortunately, I haven't had the time to implement any
software.
I'll let you know when I launch it.
white lie
Re: software request
To: your.colleague@email.com
People ask you for software, BUT...
Dear colleague,
Thank you for your deep interest in the super cool
method that I've been working on for so many years.
Unfortunately, I haven't had the time to implement any
software.
I'll let you know when I launch it.
white lie
Re: software request
To: your.colleague@email.com
L
e
t
'
s

m
a
k
e

i
t

h
a
p
p
e
n
People ask you for software, BUT...
Dear colleague,
I finally found some time to implement an R package for
my super cool method.
You can now find "myawesomepkg" on CRAN:
http://cran.r-project.org/web/packages/myawesomepkg/index.html
white lie
Subject: launching myawesomepkg
Hopefully after finishing this workshop
(and many working hours later) ...
To: your.colleague@email.com
useRs &
creatoRs
u
s
e
R
c
r
e
a
t
o
R
useRs
creatoRs
package?
So you want
to create an
You should
know upfront
(Getty Images / Robert Gray)
... for the first
time?
(Getty Images / Robert Gray)
in Windows?
(Getty Images / Robert Gray)
Let's do it!
x
x
x
x
x
x
G
a
m
e

P
l
a
n
x
1 Setting up your PC
2 Anatomy of an R package
3 Standard -painful- Development
4 Building and Checking
5 Develop smarter, not harder
Caveat
learning R
programming in R
debugging your code
writing more efficient code
These slides are NOT about:
There is more than one way to
create an R package
There's a learning curve to create
R packages
Windows is badly equipped for
creating R packages
1 Setting up your PC
2 Anatomy of an R package
3 Standard -painful- Development
4 Building and Checking
5 Develop smarter, not harder
Installing
some stuff
R
http://www.r-project.org/
Rtools
http://cran.r-project.org/bin/windows/Rtools/
Latex compiler (eg MiKTeX)
http://miktex.org/download or http://www.tug.org/protext/
FTP Client (eg FileZilla)
https://filezilla-project.org/
RStudio (strongly recommended)
http://www.rstudio.com/ide/download/
Stuff you need to install
Windows 7 Professional (2009)
R-3.0.1 for Windows
Rtools30.exe (R >2.15.1 to R 3.0.x)
MiKTeX 2.9
RStudio 0.97.551 - Windows Xp/Vista/7
For this workshop I'm using:
Modify your
system's PATH
After downloading and
installing all the necessary
software, you need to
modify the PATH of your
PC's system
Meet the Windows command prompt
(aka MS-DOS prompt)
How to open the
command prompt?
Start
Programs
Accessories
Command Prompt
Comment lancer l'invite
de commandes?
Dmarrer
Tous les programmes
Accessoires
Invite de commandes
Type PATH in your
command prompt
This is the PATH
(yours will be different)
1
2
One way to get your PATH
3
4
6
7
8
Here's the PATH
(copy-and-paste it in a text editor)
5
c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;c:\Program Files
(x86)\Intel\iCLS Client\;c:\Program Files\Intel\iCLS
Client\;C:\Windows\system32;C:\Windows;C:
\Windows\System32\Wbem;C:
\Windows\System32\WindowsPowerShell\v1.0\;C:\Program
Files\Intel\Intel(R) Management Engine Components\DAL;C:
\Program Files\Intel\Intel(R) Management Engine
Components\IPT;C:\Program Files (x86)\Intel\Intel(R)
Management Engine Components\DAL;C:\Program Files (x86)
\Intel\Intel(R) Management Engine Components\IPT;c:
\Program Files (x86)\Hewlett-Packard\HP ProtectTools
Security Manager\Bin\
Checking the PATH
PATH example
(one single text line!)
C:\Rtools\bin;
C:\Rtools\gcc-4.6.3;
C:\Program Files\R\R-3.0.1\bin;
C:\Program Files\MiKTeX 2.9\miktex\bin\x64\;
You MUST add these in your PATH:
My PATH
(one single text line!)
Modifying the PATH
c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;C:\Program
Files\R\R-3.0.1\bin;C:\Program Files\MiKTeX 2.9
\miktex\bin\x64\;c:\Program Files (x86)\Intel\iCLS
Client\;c:\Program Files\Intel\iCLS Client\;C:
\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:
\Windows\System32\WindowsPowerShell\v1.0\;C:\Program
Files\Intel\Intel(R) Management Engine Components\DAL;C:
\Program Files\Intel\Intel(R) Management Engine
Components\IPT;C:\Program Files (x86)\Intel\Intel(R)
Management Engine Components\DAL;C:\Program Files (x86)
\Intel\Intel(R) Management Engine Components\IPT;c:
\Program Files (x86)\Hewlett-Packard\HP ProtectTools
Security Manager\Bin\;
Test the PATH
gcc --help
TeX --help
R CMD --help
Type the following commands in the command prompt:
If you get error messages, check your PATH again
If you don't get errors... you're all set to go!
Check that all works
Anatomy of an
R package
Before jumping into the
creation process, you
need to learn how an R
package is structured
Download and open the
tar file to check the
package structure
"plyr" CRAN
page (repository)
A set of text files
(with no extension)
A set of
subdirectories
You can also check the guts of
plyr in its github repository.
Recommendation: A good way
to learn about the structure of R
packages is to check those that
are available in github
There are some
additional -not
relevant- files
These are the important files
and subdirectories that form
the structure of "plyr"
What's in an R
package?
DESCRIPTION
NAMESPACE
NEWS
README
LICENSE
INDEX
R
man
data
inst
tests
src
demo
subdirectories
(ie folders)
text files
(no extension)
DESCRIPTION
NAMESPACE
NEWS
README
LICENSE
INDEX
R
man
data
inst
tests
src
demo
subdirectories
(ie folders)
text files
(no extension)
required
optional
DESCRIPTION
NAMESPACE
NEWS
README
LICENSE
INDEX
R
man
data
inst
tests
src
demo
subdirectories
(ie folders)
text files
(no extension)
W
h
a
t
'
s
t
h
e
m
e
a
n
in
g
&

p
u
r
p
o
s
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f
a
ll t
h
e
s
e
f
ile
s

a
n
d
s
u
b
d
ir
e
c
t
o
r
ie
s
?
R technical
documentation
Technical
Documentation!
http://cran.r-project.org/manuals.pdf
An Introduction to R
R Data Import / Export
R Installation and Administration
Writing R Extensions
The R Language Definition
R Internals
Official Manuals (R Development Core Team)
http://cran.r-project.org/manuals.html
An Introduction to R
R Data Import / Export
R Installation and Administration
Writing R Extensions
The R Language Definition
R Internals
Official Manuals (R Development Core Team)
Good News =)
Everything is here
Bad News =(
Not beginner friendly
Sooner or later you
will have to read this
... and more
(text) Files
DESCRIPTION
NAMESPACE
NEWS
README
LICENSE
INDEX
R
man
data
inst
tests
src
demo
subdirectories
(ie folders)
text files
(no extension)
DESCRIPTION
Package: pkgname
Version: 1.0.0
Date: 2013-06-01
Title: Toy package
Author: Your Name <your.email@address.com>
Maintainer: Your Name <your.email@address.com>
Depends:
R (>= 2.15),
somepackage
Suggests: otherpackage
Description: This is a toy package
License: GPL-3
URL: http://www.toypackage.com
LazyData: true
This is your package's
business card
R Licenses?
The "GNU Affero General Public License" version 3
The "Artistic License" version 2.0
The "BSD 2-clause License"
The "BSD 3-clause License"
The "GNU General Public License" version 2
The "GNU General Public License" version 3
The "GNU Library General Public License" version 2
The "GNU Lesser General Public License" version 2.1
The "GNU Lesser General Public License" version 3
The "MIT License"
http://www.r-project.org/Licenses/
NAMESPACE
export(my_function1)
export(my_function2)
export(my_function3)
S3method(print, class1)
S3method(print, class2)
S3method(plot, class3)
import(package_A)
importFrom(package_B, function_b1)
useDynLib(C_code)
NAMESPACE
export(my_function1)
export(my_function2)
export(my_function3)
S3method(print, class1)
S3method(print, class2)
S3method(plot, class3)
import(package_A)
importFrom(package_B, function_b1)
useDynLib(C_code)
These are your
documented functions
NAMESPACE
export(my_function1)
export(my_function2)
export(my_function3)
S3method(print, class1)
S3method(print, class2)
S3method(plot, class3)
import(package_A)
importFrom(package_B, function_b1)
useDynLib(C_code)
S3 methods for your
S3 classes
NAMESPACE
export(my_function1)
export(my_function2)
export(my_function3)
S3method(print, class1)
S3method(print, class2)
S3method(plot, class3)
import(package_A)
importFrom(package_B, function_b1)
useDynLib(C_code)
If you are using stuff
from other packages
NAMESPACE
export(my_function1)
export(my_function2)
export(my_function3)
S3method(print, class1)
S3method(print, class2)
S3method(plot, class3)
import(package_A)
importFrom(package_B, function_b1)
useDynLib(C_code)
If you have code in other
languages (C, C++, Fortran)
NAMESPACE
export(my_function1)
export(my_function2)
export(my_function3)
S3method(print, class1)
S3method(print, class2)
S3method(plot, class3)
import(package_A)
importFrom(package_B, function_b1)
useDynLib(C_code)
How R searches and
finds stuff?
With NAMESPACE's
http://obeautifulcode.com/R/How-R-Searches-And-Finds-Stuff/
(by Suraj Gupta)
f
o
r m
o
re
in
f
o
:
README
Toy Package
This package is just an example of a toy package.
It offers several dummy functions

Bla, bla, bla
This workshop is so boring!
Optional README file
(ignored by R but
useful for readers)
NEWS
Version 0.2
-------------------------------------------------------------------------
NEW FEATURES
* created new functions fun1() and fun2(), which operate with vectors.
BUG FIXES
* fixed bug in bad_function(). Now can be successfully applied.
Version 0.1
-------------------------------------------------------------------------
NEW FEATURES
* added new parameter 'time' in function boring()

* added a plot method
* user can specify several input files
Optional NEWS file
(helps for keeping
track of changes)
LICENSE
This package is distributed under the XYZ license at
http://www.xyz.org/publications/policies/software.
In detail:
1. Fortran code (src/*.f):
Copyrighted and Licensed by XYZ,
2. R interface (src/init.c src/cooler.h R/*.R man/*.Rd data/*):
The R interface code has been developed as work based on the
XYZ licensed code, hence it is also XYZ licensed, copyright
is by Some Guy <some.guy@email.com>.
In order to fulfill the XYZ copyright and license noted above,
it is stated here that this work contains modified XYZ material,
and to fulfill this, the modified work including the R interface
is available free to secondary users, and no charge is associated
with such copies.
Optional LICENSE file
with additional terms
when a package license
restricts a base license
Subdirectories
DESCRIPTION
NAMESPACE
NEWS
README
LICENSE
INDEX
R
man
data
inst
tests
src
demo
subdirectories
(ie folders)
text files
(no extension)
Let's go back to the package
plyr example
Package
Subdirectories
Most important
subdirectory
This is where all the
R functions live
For example, let's
check the function
a_ply
Another example
with function
r_ply
use this if you
have data files
files you wish an
end user to see
manual (help)
documentation
for the package
functions
folder for files
with code in C,
C++, Fortran
folder for files
testing your
code
Writing R
documentation
(Getty Images / Gary Robert)
Writing .Rd files?
Probably the worst part
about creating a package
manual (help)
documentation
for the package
functions
manual (help)
documentation
for the package
functions
a_ply.Rd
Rd file for
function a_ply
a_ply.Rd
Rd file for
function a_ply (cont)
Remember the Official M
anual
"W
riting R Extensions"