Lecture

Reproducible Research: Principles and Tools

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Description

This lecture introduces the principles and tools for reproducible research in biostatistics, emphasizing the importance of documenting the complete software environment and instructions used to generate figures. It covers steps leading to a report, problems with traditional approaches, literate programming, and good and bad practices in research practice. The instructor discusses barriers to reproducible research, tools in R for reproducible research, and the use of text editors for compiling source documents.

Instructor

Darlene Goldstein

Official source

Related concepts (32)

Literate programming

Literate programming is a programming paradigm introduced in 1984 by Donald Knuth in which a computer program is given as an explanation of how it works in a natural language, such as English, interspersed (embedded) with snippets of macros and traditional source code, from which compilable source code can be generated. The approach is used in scientific computing and in data science routinely for reproducible research and open access purposes. Literate programming tools are used by millions of programmers today.

Integrated development environment

An integrated development environment (IDE) is a software application that provides comprehensive facilities for software development. An IDE normally consists of at least a source-code editor, build automation tools, and a debugger. Some IDEs, such as NetBeans and Eclipse, contain the necessary compiler, interpreter, or both; others, such as SharpDevelop and Lazarus, do not. The boundary between an IDE and other parts of the broader software development environment is not well-defined; sometimes a version control system or various tools to simplify the construction of a graphical user interface (GUI) are integrated.

Text editor

A text editor is a type of computer program that edits plain text. Such programs are sometimes known as "notepad" software (e.g. Windows Notepad). Text editors are provided with operating systems and software development packages, and can be used to change files such as s, documentation files and programming language source code. Plain text and Rich text There are important differences between plain text (created and edited by text editors) and rich text (such as that created by word processors or desktop publishing software).

Software repository

A software repository, or repo for short, is a storage location for software packages. Often a table of contents is also stored, along with metadata. A software repository is typically managed by source or version control, or repository managers. Package managers allow automatically installing and updating repositories, sometimes called "packages". Many software publishers and other organizations maintain servers on the Internet for this purpose, either free of charge or for a subscription fee.

Programming paradigm

Programming paradigms are a way to classify programming languages based on their features. Languages can be classified into multiple paradigms. Some paradigms are concerned mainly with implications for the execution model of the language, such as allowing side effects, or whether the sequence of operations is defined by the execution model. Other paradigms are concerned mainly with the way that code is organized, such as grouping a code into units along with the state that is modified by the code.

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