如何在windows中编写R程序包
工具软件Rtools的安装和备选软件的安装。(2) r脚本的准备,也就是用来生成程序包的函数脚本。
(3) 利用R中自带的package.skeleton()函数,生成制作包所需要的Description 文件和帮助文件帮助文件.rd。
(4) 编辑该函数生成的Description 文件和帮助文件.rd
(5) 在windows cmd的命令行中输入相应的命令,生成zip文件或者.tar.gz
下面我们来一起建立只有一个函数的R程序包,来详细说明:
一 工具软件安装和配置
制作r包的工具软件包括Rtools,HTML编译器,MikTeX 或Cte等(备选软件不一定要安装):
1 工具软件安装
(1)Rtools(制作R包的主要工具)
Rtools是在windows下制作R包的一系列工具,其中包括
1) CYGWIN 在Windows下模拟UNIX环境
2) MinGW编译器,可用来编译C和Fortran语言。
3) Perl
下载地址:
http://s.pc.qq.com/discuz/image/transparent.gif
http://www.murdoch-sutherland.com/Rtools/
(2) 微软HTML编译器(备选):
用来从源文件生成HTML格式的帮助文件
下载地址:
http://go.microsoft.com/fwlink/?LinkId=14188
(3) MikTeX 或CteX(备选)
用来生成PDF格式的帮助文件
下载地址:
http://www.miktex.org/
www.ctex.org/
分别按照要求安装好。
2 设置文件启动路径:
我的电脑属性高级环境变量系统变量 PATH一项,点击“编辑”,检查是否具有以下路径,如果没有,需要手工添加:
c:\uRtools\bin;c:\uRtools\uperl\bin;c:\uRtools\uMinGW\bin; C:\uCTEX\uMiKTeX\umiktex\bin;C:\uCTEX\uCTeX\uctex\bin;C:\uCTEX\uCTeX\cct\bin;C:\uCTEX\uCTeX\ty\bin;C:\uCTEX\uGhostscript\gs8.64\bin;C:\uCTEX\uGSview\ugsview;C:\uCTEX\uWinEdt;C:\uProgram Files\R\R-2.9.0\bin\;
设置启动路径的目的是在cmd命令行可以直接调用相应的exe文件。
如果只是简单制作一个个人使用的包,只需将c:\uRtools\bin;c:\uRtools\uperl\bin;c:\uRtools\uMinGW\bin; 添加到系统路径即可
二 R脚本的准备
假如现在我们已经有了一个编好的R函数,用来给出回归的精确结果,存成了r脚本的格式,文件名为linmod.r
其内容如下所示,那么该如何制作R程序包呢?
linmod- function(x, y)
{
## compute QR-decomposition of x
qx - qr(x)
## compute (x'x)^(-1) x'y
coef - solve.qr(qx, y)
## degrees of freedom and standard deviation of residuals
df - nrow(x)-ncol(x)
sigma2 - sum((y - x%*%coef)^2)/df
## compute sigma^2 * (x'x)^-1
vcov - sigma2 * chol2inv(qx$qr)
colnames(vcov) - rownames(vcov) - colnames(x)
list(coefficients = coef,
vcov = vcov,
sigma = sqrt(sigma2),
df = df)
}
三 R包框架的准备
1 生成准备文件
登陆R :开始所有程序RR.2.9.0
(1)清除内存中的对象:
rm(list=ls())
(2)设定工作目录,这里设定为 c:/pa
setwd(c:/pa)
(3)将制作包的源文件 linmod.r拷贝到c:/pa/文件夹下,
之后输入:
package.skeleton(name=linmod,code_files=c:/pa/linmod.r)
此时,R控制台中显示
Creating directories ...
Creating DESCRIPTION ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './linmod/Read-and-delete-me'.
可以看到c:/pa文件夹下新出现了一个linmod文件夹
该文件夹下的内容就是R包的框架,包括data文件夹,man文件夹,只要按要求将其填写完整,再进行相应的编译即可。
首先查看Read-and-delete-me文件
文件内容如下:
* Edit the help file skeletons in 'man', possibly combining help
files for multiple functions.
* Put any C/C++/Fortran code in 'src'.
* If you have compiled code, add a .First.lib() function in 'R' to
load the shared library.
* Run R CMD build to build the package tarball.
* Run R CMD check to check the package tarball.
Read Writing R Extensions for more information.
大致意思如下:
可以man文件夹下编辑帮助文件
C/C++/Fortran 的源代码应该放入src文件夹下
需要在登录时载入包
可以运行R CMD建立和检查相应的包
查看更多信息,应该阅读Writing R Extensions
2 编辑Description文件和rd文件
(1) Description文件的编辑
按照提示,填好各项
Package: linmod
Type: Package
Title: test for linear regression
Version: 1.0
Date: 2009-07-20
Author: helixcn
Maintainer: helixcn zhangjl@ibcas.ac.cn
Description: To give the exactly results of linear regression.
License: GNU 2 or later
LazyLoad: yes
(2)man文件夹中.rd文件编辑
man文件夹中包含两个文件 linmod.Rd和linmod-package.Rd,分别是对linmod()函数和linmod包的介绍,下面逐项填写:
1) linmod.Rd
ame{linmod}
\uRdversion{1.1}
\ualias{linmod}
%- Also NEED an '\ualias' for EACH other topic documented here.
\utitle{
linear regression
}
\udescription{
to give the more exactly results of linear regression
}
%usage{
linmod(x, y)
}
%- maybe also 'usage' for other objects documented here.
\uarguments{
\uitem{x}{
a numeric design matrix for the model
}
\uitem{y}{
a numeric vector of responses
}
}
\udetails{
%% ~~ If necessary, more details than the description above ~~
}
\uvalue{
%% ~Describe the value returned
%% If it is a LIST, use
%% \uitem{comp1 }{Description of 'comp1'}
%% \uitem{comp2 }{Description of 'comp2'}
%% ...
}
\ureferences{
Friedrich Leisch,2008 Creating R Packages: A Tutorial
}
\uauthor{
helixcn
}
ote{
Please read Friedrich Leisch,2008
}
%% ~Make other sections like Warning with \usection{Warning }{....} ~
\useealso{
%% ~~objects to See Also as \ucode{\ulink{help}}, ~~~
}
\uexamples{
##---- Should be DIRECTLY executable !! ----
##-- == Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (x, y)
{
qx - qr(x)
coef - solve.qr(qx, y)
df - nrow(x) - ncol(x)
sigma2 - sum((y - x \%*\% coef)^2)/df
vcov - sigma2 * chol2inv(qx$qr)
colnames(vcov) - rownames(vcov) - colnames(x)
list(coefficients = coef, vcov = vcov, sigma = sqrt(sigma2),
df = df)
}
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\ukeyword{ ~kwd1 }
\ukeyword{ ~kwd2 }% __ONLY ONE__ keyword per line
2)linmod-package.Rd
ame{linmod-package}
\uRdversion{1.1}
\ualias{linmod-package}
\ualias{linmod}
\udocType{package}
\utitle{Linear Regression Modification}
\udescription{to Give the more exactly output of linear regression rather than R default}
\udetails{
\utabular{ll}{
Package: \tab linmod\cr
Type: \tab Package\cr
Version: \tab 1.0\cr
Date: \tab 2009-07-20\cr
License: \tab GNU 2.0 or later\cr
LazyLoad: \tab yes\cr
}
~~The aim of the package was to give the more exactly output of linear regression~~ linmod~~
}
\uauthor{helixcn
Maintainer: helixcn helixcn@163.com}
\ureferences{
Friedrich Leisch,2008,Creating R Packages: A Tutorial
}
\useealso{lm}
\uexamples{
data(cats, package=MASS)
mod1 - linmod(Hwt~Bwt*Sex, data=cats)
mod1
summary(mod1)
}
四 通过cmd创建R包
开始运行cmd
键入 cd c:\pa\ 将工作目录转移到c:/pa下
键入 Rcmd build --binary linmod 制作window zip包
键入 Rcmd build linmod 制作linux平台下可运行的tar.gz包
命令运行完之后可以发现,在c:/pa/文件夹下分别生成了linmod.zip和linmod.tar.gz压缩包。
注意R CMD 系列命令是在windows控制台下运行,而非R控制台
参考网址
http://www.robjhyndman.com/researchtips/building-r-packages-for-windows/
http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
http://faculty.chicagobooth.edu/peter.rossi/research/bayes%20book/bayesm/Making%20R%20Packages%20Under%20Windows.pdf
http://www.biostat.uni-hannover.de/teaching/fallstudien/schaarschmidt2.pdf
页:
[1]