Reproducible research is an important topic in today's IT 可重现性研究是当今IT的一个重要主题 research and it also has a big significance for our society and the 研究它对我们的社会也有很大的意义 ethics of conducting research. It is important to keep the 进行研究的伦理。保持健康是很重要的 underlying data, algorithms, and argumentation, so that others can 基本的数据，算法，和论证，以便其他人可以 follow the analysis of the data and understand the 对数据进行分析并理解 conclusions. Today's interest in SW containers like Docker is apart 结论。今天人们对Docker这样的SW容器的兴趣是不同的 from being a great deployment mechanism also powered by this desire 从一个伟大的部署机制，也由这一愿望 to allow the conservation of computational environments in an 允许计算环境的守恒 easily sharable form. 轻松分享形式。

The concept of Reproducible research is closely related to the 可重复研究的概念与 idea of literate programing that Donald Knuth launched with [[http://www.literateprogramming.com/knuthweb.pdf][his 这是Donald Knuth在http://www.literateprogramming.com/knuthweb.pdf[他的][http://www.literateprogramming.com/knuthweb.pdf]发起的*文字编程*的想法 seminal article]] in 1984. Literate programming environments allow 在1984年。文字编程环境允许 the free mixing of code parts with extensive documentation 代码部分与大量文档的自由混合 parts. The source of a literate programming document contains all 部分。一个有文字的编程文档的来源包含所有 necessary data as well as the code for manipulating the data to 必要的数据以及操作数据的代码 produce results and plots. It also contains all the text and 产生结果和情节。它还包含所有的文本和 argumentation. Out of this source document one then can generate a 论证。从这个源文档中可以生成一个 nice publication, but also other derived information (e.g. a 不错的出版物，但也有其他衍生信息(如a standalone software program and a data set, or an excel sheet to 独立的软件程序和数据集，或excel表格 give to management). 给管理)。

Org mode for Emacs is one such environment, but there are also Org mode for Emacs就是这样一个环境，但是也有这样的环境 others (e.g. look at this list of links maintained by 其他(如查看此链接列表由 reproducibleresearch.net). Another open source environment in rapid reproducibleresearch.net)。另一个快速的开源环境 development is given by Jupyter notebooks. They are very popular 开发是由Jupyter笔记本提供的。它们很受欢迎 among scientists. These frameworks are not only great for 科学家之一。这些框架不仅适用于 publishing research in a reproducible manner, but also are becoming 以一种可复制的方式发表研究，但也正在变得 one of the best teaching aids, since students can easily experiment 最好的教学辅助之一，因为学生可以很容易地进行实验 with self-contained documents. 与独立的文件。

Changes of source code should be tracked by *revision control 源代码的更改应该通过*版本控制进行跟踪 systems* (RCS) like git. An optimal tracking is possible, if the 系统* (RCS)像[[https://git-scm.com/] [git]]。最优跟踪是可能的，如果 differences from one version of a document to the next can be 文档的不同版本之间可能存在差异 easily visualized. This usually requires that the document format 轻松可视化。这通常需要文档格式 is in a text based format and not some closed binary format. 是基于文本的格式，而不是一些封闭的二进制格式。 The RCS help us to track changes through time, and we also can RCS帮助我们跟踪时间的变化，我们也可以 add metadata in the form of comments to explain the motivations for the 以注释的形式添加元数据来解释 changes. 的变化。

Humans will make errors, and each time one does something non-trivial, especially *人会犯错误*，特别是每次做一些不平凡的事情 when it is of a repetitive nature, errors easily creep in. Also, doing changes 当它具有重复性时，错误很容易出现。同时,做改变 in one part of a complex thing may cause other parts of our wonderful ivory tower 在一件复杂的事情的一部分可能导致我们美妙的象牙塔的其他部分 computation to collapse. So, in SW engineering the ideas of unit and intergration tests 计算崩溃。因此，在软件工程中，需要考虑单元测试和集成测试 has become an accepted paradigm. 已成为公认的范例。

Versioning. Documents should be versioned in a clearly defined way similar as *版本控制。*文档的版本应该像 to what we do with widely accepted standards like semantic versioning. 到我们使用广泛接受的标准语义版本控制所做的事情。

Templating and Repetition Repetitive parts in a document, e.g. if *模板和重复*文档中重复的部分，例如if for a budget of many services a certain basic text/table/graphics 对于许多服务的预算，一定的基本文本/表格/图形 structure needs to be repeated multiple times, we would like to 结构需要重复多次，我们愿意 generate it by a single code block that we call with different 生成它的一个单一的代码块，我们调用不同的 arguments - and not by copy/paste and manual editing. Senseless 参数-而不是通过复制/粘贴和手动编辑。毫无意义的 repetition or copy/paste is useless human toil and leads to 重复或复制/粘贴是徒劳无功的 errors. later changes to the basic structure should not involve us 错误。以后对基本结构的修改不应该涉及到我们 in making changes in a hundered places. 在混乱的地方做出改变。

There exists a plethora of programming languages and libraries to 存在大量的编程语言和库 deal with data in all of its forms. In particular, Python is a 处理所有形式的数据。特别地，*Python*是一个 language which has found increasing adoption by the scientific 这种语言已被越来越多的科学工作者采用 community over the last decade. It is expressive and provides a 在过去的十年里。它是表达性的，并提供了一个 wealth of libraries and also frameworks for interactive data 丰富的库和交互式数据框架 analysis. Naturally there are other solutions as well, e.g. [[https://www.r-project.org/][the R 分析。当然，也有其他的解决方案，例如https://www.r-project.org/ project]]. 项目]]。

Since I am a Python person, I will recommend the following libraries for tackling 由于我是一个Python人员，所以我将推荐以下库进行处理 the kind of management related problems we are talking about 我们正在讨论的与管理相关的问题

• Pandas: easy-to-use data structures and data analysis tools
• panda:易于使用的数据结构和数据分析工具
• numpy: fundamental package for scientific computing. Used by Pandas
• numpy:科学计算的基本包。使用的熊猫
• matplotlib and seaborn for visualization
• matplotlib和seaborn进行可视化

Outliners are ideal for jotting down thoughts and ideas. Some 外行是记录思想和想法的理想场所。一些 people may prefer mind-maps, but in the end the underlying data 人们可能更喜欢思维导图，但最终还是基础数据 structures are mostly identical. The outliner lists are certainly 结构基本相同。当然，例外的名单 more efficient for a proficient typist and are easily mixed with 更有效率的一个熟练的打字员，很容易混合 other parts of a text. 文本的其他部分。

I have used outlines for years for the initial planning of most tasks. 多年来，我一直使用提纲来初步规划大多数任务。 Actually the approach is now so engrained with me that I use lists as 实际上，这种方法现在对我来说已经根深蒂固了，我使用列表作为 the starting point for almost all documents I write. Their inherent 我写的几乎所有文档的起点。其固有的 simple structure allows to express the main ideas as top level items, and then 简单的结构允许表达的主要思想作为顶层项目，然后 use Sub-items to further refine them or add newer information in a way that 使用子项进一步细化它们或以以下方式添加更新的信息 is transparent. 是透明的。

I also have used this approach for drawing up project and service 我也用这种方法来制定项目和服务 budgets for our scientific computing section over the last years, 过去几年我们科学计算部门的预算， But only now I implemented a better way to automatically derive a 但直到现在我实现了一个更好的方法来自动推出a useful data structure from such a list in a new Emacs package 新Emacs包中此类列表的有用数据结构 org-listcruncher (you can get the package from MELPA). org-listcruncher(您可以从MELPA获取package from MELPA)。

Here is an example of a planning list for a budget of two (non-IT) services. 以下是两个(非it)服务预算的规划列表示例。

My rules for writing such a planning list are 我写这样一个计划清单的规则是

1. Each line contains a tag defining wheter the line will become a table row. For this
2. 每行包含一个标记，定义该行是否将成为表行。对于这个

example I defined this as the string "item:". Rows without such a tag just serve as 例如，我将其定义为字符串“item:”。没有这样标记的行仅作为 metadata. 元数据。

1. A string following the output tag "item:" is taken as the description of the table row.
2. 输出标记“item:”后面的字符串作为表行的描述。
3. Each line can contain any number of key/value pairs in parentheses in the form

3.每一行都可以在表单的括号中包含任意数量的键/值对 (key1: val1, key2: val2, ...) (key1: val1, key2: val2，…)

1. Lines of lower hierarchical order in the list inherit their default settings for key/values
2. 列表中较低层次结构的行继承键/值的默认设置

from the upper items. 从上面的项目。

1. The key value of a higher order item can be overwritten by a new new value for the same key
2. 高阶项目的键值可以被相同键的新值覆盖

in a lower order line. 在低阶直线上。

Note that org-listcruncher allows the user to supply an own parsing function, so the 注意，org-listcruncher允许用户提供自己的解析函数，因此 rules for how the key/values, the description, and the tagging for a row can get 关于如何获取键/值、描述和行的标记的规则 arbitrarily defined by the end user. The present default function is just an easy example. 由最终用户任意定义。当前的默认函数就是一个简单的例子。

One can easily imagine using the same kind of approach to derive a table of ingredients and their amounts 人们可以很容易地想象用同样的方法得出一个成分表和它们的数量 from the instructions of a cooking recipe that is given as a sequential list of steps. Just needs a bit 从一个烹饪食谱的说明，作为一个连续的步骤列表。只是需要一点 a smarter parsing function. 更智能的解析功能。

We now would like to derive from the planning list a more suitable 现在我们想从中推导出一个更合适的计划表 data format for doing computations. A table is an optimal 用于计算的数据格式。表是最优的 format. The main function of org-listcruncher provides just this 格式。https://github.com/dfeich/org-listcruncher的主函数提供了这个功能 conversion. Based on the semantics defined in the previous section. 转换。基于上一节定义的语义。

The following Org mode code block contains a single line of Emacs 下面的Org模式代码块包含一行Emacs lisp for calling org-listcruncher's main function and uses the lisp调用org-listcruncher的主要函数，并使用 above list (which I named lstShipGalante) to create a table based 上面的列表(我将其命名为=lstShipGalante=)用于创建一个基于表的表 on an "outer join" of all the keys found with the respective values 使用各自的值找到所有键的“外连接” arranged in columns. 安排在列。

The list from which we generate the table can later be further 稍后，我们可以进一步生成用于生成表的列表 edited, and all derived results will change accordingly when 编辑后，所有导出的结果将随之更改 recalculating the whole document. The audit trail is conserved in 重新计算整个文档。审计跟踪是保守的 the list itself through the comments, and naturally it will also be 名单本身通过评论，自然它也会 conserved in the commits into the revision control system. 保存提交到修订控制系统。

Now, as the data is in an easily accessible form, we can use Org mode's Babel feature to 现在，由于数据是易于访问的形式，我们可以使用Org模式的Babel特性 read in the table into a python code block and perform some Pandas data 将表读入python代码块并执行一些panda数据 manipulation magic on it. 上面有操纵魔法。

And another little code block lets us visualize cuts of the data with matplotlib and seaborn. 另一个小代码块让我们可以用matplotlib和seaborn可视化数据切割。

And we can generate the plots for our report. 我们可以为我们的报告生成图表。

file:/// www /资产/图片/ listcruncher-grouped。png

4.4版本控制、模板、测试

I will only refer cursorily how to address the other points 我将只简略地提及如何处理其他问题

• Org mode is part of Emacs which offers a number of powerful templating systems. Org itself supports
• Org模式是Emacs的一部分，它提供了许多强大的模板系统。Org本身支持

Macros which can generate text parts. 可以生成文本部分的宏。

• Versioning can easily be combined with org mode documents and integrated in the common ways with

-版本控制可以很容易地与org模式文档相结合，并以通用的方式与之集成 revision control systems like git (e.g. via tags) 像git这样的修订控制系统(例如，通过标签)

• testing: Since org offers native inclusion of code snippets in different programming languages, tests

-测试:由于org提供了不同编程语言的代码片段的本地包含，所以进行测试 can easily be formulated in the avaible test frameworks of these languages. One can also 可以很容易地在这些语言的可用测试框架中表示。一个也可以 define simple tests in form of document code blocks putting out warnings into the document. 以文档代码块的形式定义简单的测试，将警告放入文档中。