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install R on Centos 6

following this thread: http://blogs.helsinki.fi/bioinformatics-viikki/documentation/getting-started-with-r-programming/installingrlatest/#CentOS

Installing the latest R on CentOS:

Add the latest EPEL repository which you can find from here. Don’t forget to add the 64 bit f you are using a 64 bit OS. I have a CentOS release 5.8, 64 bit (Check the Ubuntu installation section of this document if you don’t know your Linux distribution or whether it is 64 or 32 bit ) and I used the following script to add the proper repository:

$ sudo rpm -Uvh http://www.nic.funet.fi/pub/mirrors/fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm

then I got the error

CentOS 6.3 Instance Giving "Cannot retrieve metalink for repository: epel" Error

follow this page: https://community.hpcloud.com/article/centos-63-instance-giving-cannot-retrieve-metalink-repository-epel-error

Walkthrough Steps

Running this command will update the repo to use HTTP rather than HTTPS:

sudo sed -i "s/mirrorlist=https/mirrorlist=http/" /etc/yum.repos.d/epel.repo

You should then be able to update with this command:

yum -y update

then I am able to install R...

$ sudo yum install R

Installed:
  R.x86_64 0:3.1.2-1.el6                                                        

Dependency Installed:
  R-core.x86_64 0:3.1.2-1.el6                                                   
  R-core-devel.x86_64 0:3.1.2-1.el6                                             
  R-devel.x86_64 0:3.1.2-1.el6                                                  
  R-java.x86_64 0:3.1.2-1.el6                                                   
  R-java-devel.x86_64 0:3.1.2-1.el6                                             
  blas.x86_64 0:3.2.1-4.el6                                                     
  blas-devel.x86_64 0:3.2.1-4.el6                                               
  bzip2-devel.x86_64 0:1.0.5-7.el6_0                                            
  cups.x86_64 1:1.4.2-67.el6                                                    
  desktop-file-utils.x86_64 0:0.15-9.el6                                        
  fontconfig-devel.x86_64 0:2.8.0-5.el6                                         
  freetype-devel.x86_64 0:2.3.11-14.el6_3.1                                     
  gcc-gfortran.x86_64 0:4.4.7-11.el6                                            
  ghostscript.x86_64 0:8.70-19.el6                                              
  ghostscript-fonts.noarch 0:5.50-23.2.el6                                      
  java-1.6.0-openjdk.x86_64 1:1.6.0.0-11.1.13.4.el6                             
  java-1.6.0-openjdk-devel.x86_64 1:1.6.0.0-11.1.13.4.el6                       
  jline.noarch 0:0.9.94-0.8.el6                                                 
  kpathsea.x86_64 0:2007-57.el6_2                                               
  lapack.x86_64 0:3.2.1-4.el6                                                   
  lapack-devel.x86_64 0:3.2.1-4.el6                                             
  lcms-libs.x86_64 0:1.19-1.el6                                                 
  libRmath.x86_64 0:3.1.2-1.el6                                                 
  libRmath-devel.x86_64 0:3.1.2-1.el6                                           
  libX11-devel.x86_64 0:1.6.0-2.2.el6                                           
  libXau-devel.x86_64 0:1.0.6-4.el6                                             
  libXft-devel.x86_64 0:2.3.1-2.el6                                             
  libXmu.x86_64 0:1.1.1-2.el6                                                   
  libXrender-devel.x86_64 0:0.9.8-2.1.el6                                       
  libXt.x86_64 0:1.1.4-6.1.el6                                                  
  libgfortran.x86_64 0:4.4.7-11.el6                                             
  libicu.x86_64 0:4.2.1-9.1.el6_2                                               
  libicu-devel.x86_64 0:4.2.1-9.1.el6_2                                         
  libxcb-devel.x86_64 0:1.9.1-2.el6                                             
  netpbm.x86_64 0:10.47.05-11.el6                                               
  netpbm-progs.x86_64 0:10.47.05-11.el6                                         
  openjpeg-libs.x86_64 0:1.3-10.el6_5                                           
  pcre-devel.x86_64 0:7.8-6.el6                                                 
  poppler.x86_64 0:0.12.4-3.el6_0.1                                             
  poppler-data.noarch 0:0.4.0-1.el6                                             
  poppler-utils.x86_64 0:0.12.4-3.el6_0.1                                       
  portreserve.x86_64 0:0.0.4-9.el6                                              
  psutils.x86_64 0:1.17-34.el6                                                  
  rhino.noarch 0:1.7-0.7.r2.2.el6                                               
  tcl.x86_64 1:8.5.7-6.el6                                                      
  tcl-devel.x86_64 1:8.5.7-6.el6                                                
  tex-preview.noarch 0:11.85-10.el6                                             
  texinfo.x86_64 0:4.13a-8.el6                                                  
  texinfo-tex.x86_64 0:4.13a-8.el6                                              
  texlive.x86_64 0:2007-57.el6_2                                                
  texlive-dvips.x86_64 0:2007-57.el6_2                                          
  texlive-latex.x86_64 0:2007-57.el6_2                                          
  texlive-texmf.noarch 0:2007-38.el6                                            
  texlive-texmf-dvips.noarch 0:2007-38.el6                                      
  texlive-texmf-errata.noarch 0:2007-7.1.el6                                    
  texlive-texmf-errata-dvips.noarch 0:2007-7.1.el6                              
  texlive-texmf-errata-fonts.noarch 0:2007-7.1.el6                              
  texlive-texmf-errata-latex.noarch 0:2007-7.1.el6                              
  texlive-texmf-fonts.noarch 0:2007-38.el6                                      
  texlive-texmf-latex.noarch 0:2007-38.el6                                      
  texlive-utils.x86_64 0:2007-57.el6_2                                          
  tk.x86_64 1:8.5.7-5.el6                                                       
  tk-devel.x86_64 1:8.5.7-5.el6                                                 
  tmpwatch.x86_64 0:2.9.16-4.el6                                                
  unzip.x86_64 0:6.0-1.el6                                                      
  urw-fonts.noarch 0:2.4-10.el6                                                 
  xdg-utils.noarch 0:1.0.2-17.20091016cvs.el6                                   
  xorg-x11-proto-devel.noarch 0:7.7-9.el6                                       
  xz-devel.x86_64 0:4.999.9-0.5.beta.20091007git.el6                            

Dependency Updated:
  cpp.x86_64 0:4.4.7-11.el6                                                     
  cups-libs.x86_64 1:1.4.2-67.el6                                               
  gcc.x86_64 0:4.4.7-11.el6                                                     
  gcc-c++.x86_64 0:4.4.7-11.el6                                                 
  libgcc.x86_64 0:4.4.7-11.el6                                                  
  libgomp.x86_64 0:4.4.7-11.el6                                                 
  libstdc++.x86_64 0:4.4.7-11.el6                                               
  libstdc++-devel.x86_64 0:4.4.7-11.el6                                         
  xz-libs.x86_64 0:4.999.9-0.5.beta.20091007git.el6                             

Complete!

Tags centos, epel, R

日常应用

据说是R 2014年最重要的发明...

今儿听Hadley大人做training，才第一次好好去看pipe这个东西...以前有点印象，主要是R会上有人讲过，当时只是记住了一个名词。今儿才有机会好好的去看看去想一想。（吐槽：R有的时候是不是太灵活了...）

pipe的广告语： the pipe operator is one (if not THE) most important innovation introduced, this year, to the R ecosystem. 听起来挺神奇的，好像是从F#那里搬过来的....R果然是耐揉。

短短的历史就是，随着Hadley大人搞定了dplyr，MAGRITTR 这个包开始浮出水面，各种热门...

然后果然COS上有人介绍过，Ren Kun童鞋早已经进一步弄好了一个pipeR包可以玩：http://cos.name/2014/04/use-pipeline-operators-in-r/

然后再去看今年5月份北京R会议的slides...原来这么赞（可是当时我明明在北京呀，当时干嘛去了...总是这么后知后觉）。

然后COS论坛上果然早早就有讨论了，这群geek...

没了，我要好好学习去了，R永远是个学不完的东西啊啊啊啊！三观总是不时被重新颠覆一次，唉。

Tags dplyr, Hadley, MAGRITTR, pipe, piper, R

日常应用

Shiny的架构浅析

不是说学一门语言学的不仅仅是他的语法，更重要的是他背后的思想么？R本身是个大杂烩，ggplot可以单独拎出来作为一门语言学，shiny其实也可以单独拎出来学一番。

只是简单的实现一个shiny app确实不难，就像官网上一进去看到的那个例子那样。基本上如果只是做一些比较简单的可控的dashboard，shiny的代码无非就是写的细致一点，谈不上什么架构之类的。

直到某一天...你发现这东西还可以玩的更深，然后就毅然跳入了下一个大坑——shiny reactivity。官网的开场白很直接：

It’s easy to build interactive applications with Shiny, but to get the most out of it, you’ll need to understand the reactive programming model used by Shiny.

然后就介绍三剑客：reactive sources, reactive conductors, and reactive endpoints。

最简单的情况：没有conductor，直接从source到endpoint。

继续拷贝官网图：

嗯，听起来不难...其实大部分情况下shiny app处理的都是这样的情况。基本上就是一个输入（input）和输出（output）的过程。最简单的，就是我们经常在shiny app里面需要处理的input对象，会读入各种用户操作带来的值，然后后面返回一个表格或者图或者文字什么的。回到官网的例子（继续拷贝官网图）

shinyServer(function(input, output) {
  output$distPlot <- renderPlot({
    hist(rnorm(input$obs))
  })
})

大概就是这么一个简单的架构。在这种架构下，自然可以写很多if else之类的在server.R中加入各种各样输入输出的组合，然后在ui.R中排列一下输入的各种框框和输出的各种图标文字什么的。

考虑conductors的情况

shiny用的稍稍熟悉了，就开始想更多的控制这个东西。其实conductor说白了有点中间变量的感觉，就是他本身并不会最终显示出来，但是作为一个中间过程存在着。比如官网一个计算Fibonacci 序列的例子：

fib <- function(n) ifelse(n<3, 1, fib(n-1)+fib(n-2))

shinyServer(function(input, output) {
  currentFib         <- reactive({ fib(as.numeric(input$n)) })

  output$nthValue    <- renderText({ currentFib() })
  output$nthValueInv <- renderText({ 1 / currentFib() })
})

这里无非就是多了一个新的对象currentFib（跟input和output都无关），暂时的存储了一下计算过程中的变量，然后基于这个东西，又衍生了两个最终显示出来的返回值。新的架构图就多了一个conductor这样。

再复杂一点：考虑Reactive expressions

按照官网的说法，这个东西包括：

accessing a database
reading data from a file
downloading data over the network
performing an expensive computation

基本就是从其他的数据源而不是用户的input那里读数据的情况。常见的场景比如，按照用户给定的一些条件(由input传入），返回一个符合条件的数据子集。如果数据全集是会不断更新的（比如每次都应该重新load("xxx.rdata")这样），那么这个这句话就必须写在reactive里面。同理，如果直接利用input生成一句SQL然后连接数据库读取数据，那么也要写在reactive里面。

再复杂一点：自动还是手动更新

shiny默认的情况下，如果没有放submit按钮，那么就是随便一个操作就trigger整个reactive的流程。比如官网首页上，我们拖拖鼠标那个直方图就跟着变化。如果不想让他直接变化，那么简单的可以放一个submit按钮，然后只有submit之后才会变化。

如果希望更好的控制一个app界面上各个部分呢？就要动用更高级一点的actionButton。

这东西还要配合一个isolate()，就是你要告诉shiny哪些东西跟着这个button变化，哪些不属于这个button的控制范围。比如官网的例子：

shinyServer(function(input, output) {
  output$distPlot <- renderPlot({
    # Take a dependency on input$goButton
    input$goButton

    # Use isolate() to avoid dependency on input$obs
    dist <- isolate(rnorm(input$obs))
    hist(dist)
  })
})

这里只有goButton被点击的时候，才会执行下面的抽随机数并画图。actionButton是随着每次点击而不断增加计数的，从0开始一直增加过去，所以可以在server.R里面利用这个button的返回值来进行流程控制。

篇外废话：

shiny有希望成长成一个可以替代php这样实现客户端和服务器端大部分交互请求的巨人么？从这点来看，Tableau还是限制太多了。