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Minor improvements
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fkohrt committed Jan 27, 2025
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2 changes: 1 addition & 1 deletion LICENSE.txt
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Expand Up @@ -2,4 +2,4 @@ Except where noted otherwise, the narrative text in this tutorial is licensed un

The files "Manuscript.qmd" and "Bibliography.bib" are made available by Josephine Zerna and Christoph Scheffel under CC0 1.0 <https://creativecommons.org/publicdomain/zero/1.0/>.

The screenshots of the RStudio IDE are Copyright (C) 2024 Posit PBC and available under the GNU Affero General Public License v3 (available below). The source code is available on GitHub: <https://github.com/rstudio/rstudio/tree/v2024.04.2%2B764>
The screenshots of the RStudio IDE are Copyright (C) 2024 Posit PBC and available under the GNU Affero General Public License v3. The source code is available on GitHub: <https://github.com/rstudio/rstudio/tree/v2024.04.2%2B764>
2 changes: 2 additions & 0 deletions code.qmd
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Expand Up @@ -183,6 +183,8 @@ We recommend adding a short paragraph to `LICENSE.txt` to describe its license.
::: {#tip-apaquarto-licensetxt .callout-tip collapse="true"}
### Addition to `LICENSE.txt` (Solution)

It is best to provide attribution even if the license does not require it.

```{.txt .code-overflow-wrap filename="LICENSE.txt"}
"apaquarto" stored in "_extensions/wjschne/apaquarto" by W. Joel Schneider available from <https://github.com/wjschne/apaquarto> is licensed under CC0 1.0: <https://creativecommons.org/publicdomain/zero/1.0/>
```
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4 changes: 2 additions & 2 deletions intro.qmd
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Expand Up @@ -6,15 +6,15 @@ In the following, we will set the stage by highlighting the importance of sharin

## The Importance of Sharing

Suppose you are reading an article about a new imaging method to turn seismological data into subsurface images. The article describes the ideas that went into developing this method and presents a few examples to illustrate its superiority over previous approaches. You got interested and would like to apply this method to your own data. However, with only the article available, it could take months to come up with a working solution, if possible at all. This situation has been put aptly by Buckheit & Donoho [-@Buckheit1995, p. 59, emphasis in original], distilling an idea by the geophysicist Jon Claerbout:
Suppose you are reading an article about a new imaging method to turn seismological data into subsurface images. The article describes the ideas that went into developing this method and presents a few examples to illustrate its superiority over previous approaches. You got interested and would like to apply this method to your own data. However, with only the article available, it could take you months to come up with a working solution, if possible at all. This situation has been put aptly by Buckheit & Donoho [-@Buckheit1995, p. 59, emphasis in original], distilling an idea by the geophysicist Jon Claerbout:

> "An article about computational science in a scientific publication is __not__ the scholarship itself, it is merely __advertising__ of the scholarship. The actual scholarship is the complete software development environment and the complete set of instructions which generated the figures."
Even when researchers merely apply existing methods (rather than report on a new method), sharing the source code and being transparent about the computational environment is imperative to making their results reproducible [@Ince2012]. By reproducibility, we mean "obtaining consistent results using the same input data; computational steps, methods, and code; and conditions of analysis" [@NASEM2019, p. 46].

## Document Materials

However, there's more to code publishing than sharing. Researchers should document (i.e., track) which data, software, images, texts, and other materials contributed to their work. In more elaborate terms, researchers should preserve the _provenance_ of shared materials, for at least three tangible reasons:
However, there's more to code publishing than sharing. Researchers should document (i.e., track) which foreign data, software, images, texts, and other materials contributed to their work. In more elaborate terms, researchers should preserve the _provenance_ of shared materials, for at least three tangible reasons:

- **Academic integrity**: Providing citations for works that are not one's own avoids plagiarism.
- **Complying with the law**: Providing attribution and license texts (among other things) may be a legal obligation when redistributing materials.
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