R语言中帮助和R包

#####获得帮助#####
#关于函数的帮助
help(glm)
?glm
#关于操作符的帮助
?`+`
#查看帮助文档中例子
example(glm)
#搜索主题
help.search("regression")
??regression
#library函数的帮助选项
library(help="grDevices")
#通过vignette查看指南文档,通过实际操作没反应
vignette("utils")
#已加载包的指南文件
vignette(all=FALSE)
#已安装包的指南文件
vignette(all=TRUE)

######R包#####
#类似于java中类
#列举本地库中R包
getOption("defaultPackags")
#已加载R包清单
(.packages())
#已安装的R包清单
(.packages(all.available=TRUE))
library()
#加载R包
library(rpart)
#搜索R包资源库：CRAN和Bioconductor
#可以通过界面也可以通过命令,建议通过界面的菜单来操作
#R控制台来安装R包
install.packages(c("tree","maptree"))
#移除R包
remove.packages(c("tree","maptree"))

输出

> #####获得帮助#####
> help(glm)
starting httpd help server ... done
> ?glm
> ?`+`
> example(glm)

glm> ## Dobson (1990) Page 93: Randomized Controlled Trial :
glm> counts <- c(18,17,15,20,10,20,25,13,12)

glm> outcome <- gl(3,1,9)

glm> treatment <- gl(3,3)

glm> print(d.AD <- data.frame(treatment, outcome, counts))
  treatment outcome counts
1         1       1     18
2         1       2     17
3         1       3     15
4         2       1     20
5         2       2     10
6         2       3     20
7         3       1     25
8         3       2     13
9         3       3     12

glm> glm.D93 <- glm(counts ~ outcome + treatment, family = poisson())

glm> anova(glm.D93)
Analysis of Deviance Table

Model: poisson, link: log

Response: counts

Terms added sequentially (first to last)


          Df Deviance Resid. Df Resid. Dev
NULL                          8    10.5814
outcome    2   5.4523         6     5.1291
treatment  2   0.0000         4     5.1291

glm> ## No test: 
glm> summary(glm.D93)

Call:
glm(formula = counts ~ outcome + treatment, family = poisson())

Deviance Residuals: 
       1         2         3         4         5         6         7  
-0.67125   0.96272  -0.16965  -0.21999  -0.95552   1.04939   0.84715  
       8         9  
-0.09167  -0.96656  

Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
(Intercept)  3.045e+00  1.709e-01  17.815   <2e-16 ***
outcome2    -4.543e-01  2.022e-01  -2.247   0.0246 *  
outcome3    -2.930e-01  1.927e-01  -1.520   0.1285    
treatment2   8.717e-16  2.000e-01   0.000   1.0000    
treatment3   4.557e-16  2.000e-01   0.000   1.0000    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for poisson family taken to be 1)

    Null deviance: 10.5814  on 8  degrees of freedom
Residual deviance:  5.1291  on 4  degrees of freedom
AIC: 56.761

Number of Fisher Scoring iterations: 4


glm> ## End(No test)
glm> 
glm> ## No test: 
glm> ## an example with offsets from Venables & Ripley (2002, p.189)
glm> utils::data(anorexia, package = "MASS")

glm> anorex.1 <- glm(Postwt ~ Prewt + Treat + offset(Prewt),
glm+                 family = gaussian, data = anorexia)

glm> summary(anorex.1)

Call:
glm(formula = Postwt ~ Prewt + Treat + offset(Prewt), family = gaussian, 
    data = anorexia)

Deviance Residuals: 
     Min        1Q    Median        3Q       Max  
-14.1083   -4.2773   -0.5484    5.4838   15.2922  

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  49.7711    13.3910   3.717 0.000410 ***
Prewt        -0.5655     0.1612  -3.509 0.000803 ***
TreatCont    -4.0971     1.8935  -2.164 0.033999 *  
TreatFT       4.5631     2.1333   2.139 0.036035 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for gaussian family taken to be 48.69504)

    Null deviance: 4525.4  on 71  degrees of freedom
Residual deviance: 3311.3  on 68  degrees of freedom
AIC: 489.97

Number of Fisher Scoring iterations: 2


glm> ## End(No test)
glm> 
glm> # A Gamma example, from McCullagh & Nelder (1989, pp. 300-2)
glm> clotting <- data.frame(
glm+     u = c(5,10,15,20,30,40,60,80,100),
glm+     lot1 = c(118,58,42,35,27,25,21,19,18),
glm+     lot2 = c(69,35,26,21,18,16,13,12,12))

glm> summary(glm(lot1 ~ log(u), data = clotting, family = Gamma))

Call:
glm(formula = lot1 ~ log(u), family = Gamma, data = clotting)

Deviance Residuals: 
     Min        1Q    Median        3Q       Max  
-0.04008  -0.03756  -0.02637   0.02905   0.08641  

Coefficients:
              Estimate Std. Error t value Pr(>|t|)    
(Intercept) -0.0165544  0.0009275  -17.85 4.28e-07 ***
log(u)       0.0153431  0.0004150   36.98 2.75e-09 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for Gamma family taken to be 0.002446059)

    Null deviance: 3.51283  on 8  degrees of freedom
Residual deviance: 0.01673  on 7  degrees of freedom
AIC: 37.99

Number of Fisher Scoring iterations: 3


glm> summary(glm(lot2 ~ log(u), data = clotting, family = Gamma))

Call:
glm(formula = lot2 ~ log(u), family = Gamma, data = clotting)

Deviance Residuals: 
     Min        1Q    Median        3Q       Max  
-0.05574  -0.02925   0.01030   0.01714   0.06371  

Coefficients:
              Estimate Std. Error t value Pr(>|t|)    
(Intercept) -0.0239085  0.0013265  -18.02 4.00e-07 ***
log(u)       0.0235992  0.0005768   40.91 1.36e-09 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for Gamma family taken to be 0.001813354)

    Null deviance: 3.118557  on 8  degrees of freedom
Residual deviance: 0.012672  on 7  degrees of freedom
AIC: 27.032

Number of Fisher Scoring iterations: 3


glm> ## Not run: 
glm> ##D ## for an example of the use of a terms object as a formula
glm> ##D demo(glm.vr)
glm> ## End(Not run)
glm> 
glm> 
> help.search("regression")
> ??regression
> library(help="grDevices")
> vignette("affy")
Warning message:
vignette ‘affy’ not found 
> local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
> vignette("base")
Warning message:
vignette ‘base’ not found 
> vignette(all=FALSE)
> vignette("utils")
Warning message:
vignette ‘utils’ not found 
> vignette(all=FALSE)
> vignette('utils')
Warning message:
vignette ‘utils’ not found 
> vignette(utils)
Error in vignette(utils) : object 'utils' not found
> vignette(all=TRUE)
> vignette(all=TRUE)
> #搜索主题
> vignette('colorspace')
Warning message:
vignette ‘colorspace’ not found 
> vignette("colorspace")
Warning message:
vignette ‘colorspace’ not found 
> getOption("defaultPackags")
NULL
> local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
> getOption("defaultPackags")
NULL
> utils:::menuInstallLocal()
Error in install.packages(choose.files("", filters = Filters[c("zip",  : 
  no packages were specified
> utils:::menuInstallPkgs()
Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) : 
  no packages were specified
> local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
> 
> 
> 
> library(utils)
> getOption("defaultPackags")
NULL
> (.packages())
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"  
[7] "base"     
> vignette("utils")
Warning message:
vignette ‘utils’ not found 
> vignette(all=FALSE)
> (.packages(all.available=TRUE))
 [1] "base"         "boot"         "class"        "cluster"     
 [5] "codetools"    "colorspace"   "compiler"     "datasets"    
 [9] "dichromat"    "digest"       "foreign"      "ggplot2"     
[13] "graphics"     "grDevices"    "grid"         "gtable"      
[17] "KernSmooth"   "labeling"     "lattice"      "MASS"        
[21] "Matrix"       "methods"      "mgcv"         "munsell"     
[25] "nlme"         "nnet"         "parallel"     "plyr"        
[29] "proto"        "RColorBrewer" "Rcpp"         "reshape2"    
[33] "Rlab"         "rpart"        "scales"       "spatial"     
[37] "splines"      "stats"        "stats4"       "stringr"     
[41] "survival"     "tcltk"        "tools"        "utils"       
> library()
> library(rpart)
> (.packages())
[1] "rpart"     "stats"     "graphics"  "grDevices" "utils"     "datasets" 
[7] "methods"   "base"     
> install.packages(c("tree","maptree"))
trying URL 'http://ftp.ctex.org/mirrors/CRAN/bin/windows/contrib/3.1/tree_1.0-35.zip'
Content type 'application/zip' length 117524 bytes (114 Kb)
opened URL
downloaded 114 Kb

trying URL 'http://ftp.ctex.org/mirrors/CRAN/bin/windows/contrib/3.1/maptree_1.4-7.zip'
Content type 'application/zip' length 115110 bytes (112 Kb)
opened URL
downloaded 112 Kb

package ‘tree’ successfully unpacked and MD5 sums checked
package ‘maptree’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\hui.qian\AppData\Local\Temp\Rtmpk3BoLc\downloaded_packages
> #移除R包
> remove.package(c("tree","maptree"))
Error: could not find function "remove.package"
> #移除R包
> remove.packages(c("tree","maptree"))
Removing packages from ‘D:/R/R-3.1.2/library’
(as ‘lib’ is unspecified)
>