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06_glossary.Rmd
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06_glossary.Rmd
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# Glossary {#glossary}
## Acronym {#acronym}
An acronym is a word or name formed as an abbreviation from the initial
components of a phrase or a word.
([Wikipedia](https://en.wikipedia.org/wiki/Acronym))
## Small research institute {#small-institute}
Research institute with less than about 100 employees.
A detailed glossary covering the following topics is provided by
`r citet(manual["Rokem_2018"])` is used throughout the glossary.
## [Reproducibility](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#reproducibility)
> "... is a cornerstone of science. Definitions vary greatly across
scientific disciplines, but the meaning that we find most prevalent is the
'calculation of quantitative scientific results by independent scientists using
the original datasets and methods' (Stodden, Leisch, & Peng, 2014). The goals of
reproducibility go beyond duplicating someone else’s investigation: it also
entails having reproducibility for yourself, defeating self-deception in
scientific results (Ioannidis, 2005; Nuzzo, 2015), and extending another
researcher’s methods to build your own work. Reproducibility is a matter of
degree, not of kind. We say that research is reproducible if reproducibility
applies to the results to some extent. That is, some of the corresponding
experiments and scientific methods are deemed to be reproducible.
>
> --- `r citep(manual["Rokem_2018"])`
For more details see: `r citet(manual["Rokem_2018"])`
## [Provenance](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#provenence)
> "As the volume of digital data increases and the complexity of computational
processes that manipulate these data grows, it is becoming increasingly
important to manage their provenance. The Oxford English Dictionary defines
provenance as the source or origin of an object; its history and pedigree;
a record of the ultimate derivation and passage of an item through its various
owners. Provenance helps determine the value, accuracy, and authorship of an object."
>
> --- `r citep(manual["Rokem_2018"])`
For more details see: `r citet(manual["Rokem_2018"])`
## [Techniques](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#techniques)
- [Version control](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#version-control)
- [Literate Programming](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#literate-programming)
- [Data Publication](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#data-publication)
- [Data cleaning/munging](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#munging)
- [Software Testing](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#software-testing)
- [Continuous Integration](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#continuous-integration)
- [Workflow Management](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#workflow-management)
- [File Format Standards](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#file-format-standards)
- [Licensing](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#licensing)
- [Virtualization and Environment Isolation](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#virtualization-and-environment isolation)
For details see: `r citet(manual["Rokem_2018"])`
## [Tools](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#tools)
- [Programming Language and Related Tools](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#programming-language-and-related-tools)
- [Documentation Generators](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#documentation-generators)
- [Version Control](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#documentation-generators)
- [Data Munging and Analysis](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#data-munging-and-analysis)
- [Data Visualization](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#data-visualization)
- [Software Testing and Continuous Integration](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#software-testing-and-continuous-integration)
- [Virtualization and Environment Isolation](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#software-testing-and-continuous-integration)
- [Data Sharing and Repositories](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#data-sharing-and-repositories)
- [Document Authoring](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#document-authoring)
- [File Formats](https://www.practicereproducibleresearch.org/core-chapters/7-glossary.html#document-authoring)
For details see: `r citet(manual["Rokem_2018"])`