knitr引擎=bash。要为每个区块分别设置工作目录吗

我需要写一些关于使用外壳的讲座。我已经做了100多份SWEED R文件。当我看到knitr拥有bash引擎（）时，我将其用于一个测试用例

这个效果不错，不是很好。区块没有正在进行的会话，每个区块评估都从文档的工作目录开始。他们之间没有意识 因此，很难以连贯的方式写出关于使用“cd”和“pwd”的文章

我希望每个区块都有一个参数“working.directory”

如果你知道其他方法，我洗耳恭听。目前，我正在探索Emacs组织模式作为替代方案。它可以为每个块设置工作目录。但它更难形成风格

这是我的knitr测试文件

---
title: "Command Line, Shell"
author:
 - name: Paul Johnson
   affiliation: Center for Research Methods and Data Analysis, University of Kansas
   email: pauljohn@ku.edu
abstract: 
    This uses knitr to interleave shell commands and output.
Note to Authors: please_dont_change_the_next 4 lines!
date: "`r format(Sys.time(), '%Y %B %d')`"
output:
  html_document:
    highlight: haddock
---

```{r setup, include=FALSE}
outdir <- paste0("tmpout")
options("prompt" = "$ ")
options("continue" = "$ ")

if (!file.exists(outdir)) dir.create(outdir, recursive = TRUE)
knitr::opts_chunk$set(engine="bash", echo=TRUE, comment="output:",
prompt = TRUE, fig.path=paste0(outdir, "/p-", root.dir="/tmp"))
options(width = 70)
```

## Getting Started in the Shell

### Start a Terminal Emulator
   * Mac (Utilities/Terminal, iTerm, many others)

   * Windows (Git for Windows provides a BASH shell). Others available (Cygwin, Ubuntu BASH for Windows)

   * Linux (many terminal programs, some more exciting than others)

### High points
   * Type commands, see textual output

   * Not much pointing and clicking (copy/paste possible on some)

### What is a Shell?
   * Computer has many settings that programs can access. A "shell"
     is a "behind the scenes" program that keeps those settings
     and passes them out to programs when needed
   * BASH: Bourne Again Shell, a widely-used shell
   * Almost all Unix/Mac systems will have many shell programs
     available, such as "sh", "bash", "dash", and so forth. We
     are mostly interested in BASH because it has the most user comfort
   * A terminal program relies on the shell to translate between user and operating system

#### **Prompt**. Where you type 
   * Prompt might be verbose 
```
pauljohn:Documents/Projects $
```
   * On some it is very lean, just the dollar sign
```
$
```
   * Dollar sign is customary prompt for non-root user (non-administrators)
   * Prompt is configurable, it is a good exercise for somebody who has used the Terminal for a week or two on a daily basis.

## Basic things to type

#### What is my working directory
```{r getwd}
pwd
```

```{r ls}
ls
```
See there, the output says it is still in my working directory
where the document is, not "/tmp" as requested.

The following efforts produce errors if you uncomment them.

I can't figure even how to change directory with system or Sys.setenv.

<!-- ```{r whoami5} -->
<!-- system("cd /tmp") -->
<!-- ls -->
<!-- ``` -->



<!-- ```{r whoami6} -->
<!-- Sys.setenv(PWD = "/tmp") -->
<!-- ls -->
<!-- ``` -->

---
标题：“命令行，Shell”
作者：
-姓名：保罗·约翰逊
勘萨斯大学研究方法与数据分析中心
电邮：pauljohn@ku.edu
摘要：
这将使用knitr交错shell命令和输出。
作者注意：请不要更改接下来的4行！
日期：“`r格式（Sys.time（），'%Y%B%d'）`”
输出：
html_文件：
推荐理由：黑线鳕
---
```{r设置，include=FALSE}
outdir这是一个有效的解决方案。它没有实现持久的BASH会话，但它实现了与Emacs组织模式相同的解决方法。它允许为各种代码BASH块分别设置工作目录。这几乎和拥有一个持久的shell会话一样好

怎么做？当需要更改工作目录时，使用engine=“R”代码块中的knitr:：opts_knitr在块之间重置root.dir。下面的bash块尊重新设置

只有@Yihui可以告诉我们这是否会在缓存中造成危险等；在R块中有关于setwd的强烈警告

下面是一个有效的示例，首先从工作目录“/tmp”开始，然后是我的主目录“~”

---
标题：“命令行，Shell”
作者：
-姓名：保罗·约翰逊
勘萨斯大学研究方法与数据分析中心
电邮：pauljohn@ku.edu
摘要：
这将使用knitr交错shell命令和输出。
作者注意：请不要更改接下来的4行！
日期：“`r格式（Sys.time（），'%Y%B%d'）`”
输出：
html_文件：
推荐理由：黑线鳕
---
```{r设置，include=FALSE}
outdir knitr中的大多数非R会话都不是持久的，因此
cd
将不会执行以下bash块。请看另一种可能性。你好@Yihui。我试试runr。你在knitr页面上对它的评论不太热情。很抱歉让你分心。我找到了一个可行的答案，并把它贴在下面。能否请您告诉我们，由于在bash块之间多次运行opts_knitr来更改root.dir，是否会出现缺陷？
---
title: "Command Line, Shell"
author:
 - name: Paul Johnson
   affiliation: Center for Research Methods and Data Analysis, University of Kansas
   email: pauljohn@ku.edu
abstract: 
    This uses knitr to interleave shell commands and output.
Note to Authors: please_dont_change_the_next 4 lines!
date: "`r format(Sys.time(), '%Y %B %d')`"
output:
  html_document:
    highlight: haddock
---

```{r setup, include=FALSE}
outdir <- paste0("tmpout")
options("prompt" = "$ ")
options("continue" = "$ ")

if (!file.exists(outdir)) dir.create(outdir, recursive = TRUE)
knitr::opts_chunk$set(engine="bash", echo=TRUE, comment="output:",
prompt = TRUE, fig.path=paste0(outdir, "/p-"))
options(width = 70)
knitr::opts_knit$set(root.dir="/tmp")
```

## Basic things to type

#### What is my working directory. These are BASH chunks, not R chunks!
```{r getwd}
pwd
```

```{r ls}
ls
```

Here is how I change directory for following bash chunks.
Note engine = bash in this document, so we set R 
engine just for this one

```{r, engine = "R"}
opts_knit$set(root.dir="~")
```

```{r ls2}
ls
```