可重复性研究week2

1.1  coding standards

.常用文本文件/文本编辑器，即 text files/text editor

.缩进代码

。缩进提高可读性

。修正行长（80列）能让你从容的面对嵌套和长函数

。小建议：最少缩进（4个格）；8个最理想

.限制代码的宽度（80列？可否随自己）

.限制单个函数的长度，避免又臭又长的函数

1.2 markdown相关文件

What is Markdown?

"Markdown is a text-to-HTML conversion tool for web writers. Markdown allows you to write using an easy-to-read, easy-to-write plain text format（纯文本）, then convert it to structurally valid XHTML (or HTML)."

- John Gruber, creator of Markdown

1. Markdown是一名超级简单的书写语言，你可以在1小时内学会它，详细内容点这里
   简书上的介绍

Markdown Resources

• The Offical Markdown Documentation

• Github's Markdown Guide

What is Markdown?

• Created by John Gruber and Aaron Swartz

• A simplified version of "markup" languages

• Allows one to focus on writing as opposed to formatting

• Simple/minimal intuitive formatting elements

• Easily converted to valid HTML (and other formats) using existing tools

• Complete information is available at http://daringfireball.net/projects/markdown/

• Some background information at http://daringfireball.net/2004/03/dive_into_markdown

What is R Markdown?

• R markdown is the integration of R code with markdown

• Allows one to create documents containing "live" R code

• R code is evaluated as part of the processing of the markdown

• Results from R code are inserted into markdown document

• A core tool in literate statistical programming

• 
  

What is R Markdown?

• R markdown can be converted to standard markdown using the knitr package in R

• Markdown can be converted to HTML using the markdown package in R

• Any basic text editor can be used to create a markdown document; no special editing tools needed

• The R markdown --> markdown --> HTML work flow can be easily managed using R Studio (but not required)

• These slides were written in R markdown and converted to slides using the slidify package

当然有时也可如下

library(knitr)

setwd(<working directory>)

knit2html("document. Rmd")将输出变为html格式

browseURL("document.html")将上面输出的那个打开

knitr文件的过程（在黑匣子下发生了什么？）

书写RMarkdown文件（.Rmd)

knitr产生了一个Markdown文件(.md)

knitr将Markdown文件转化为HTML（默认）

.rmd-.md-.html

如果没有完成的话，最好不好去碰（比如说edit/save)这些.md或是.html文件

some common Options

.output

-results: "asis","hide"

-echo:TRUE,FALSE

figures

-fig.height:numeric

-fig.width:numeric

asis 意味着不postprocess这结果，而是用原始结果来输出