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Style changes to episode 1 callout "Why should I care"
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@@ -34,21 +34,20 @@ That is, enabling others to run our code and obtain the same results we did.
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## Why should I care about reproducibility?
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Scientific transparency and rigor are key factors in research.
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Scientific methodology and results need to be published openly and replicated and confirmed by several independent parties.
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However, research papers often lack the full details required for independent reproduction or replication.
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Many attempts at reproducing or replicating the results of scientific studies have failed in a variety of disciplines ranging from psychology ([The Open Science Collaboration (2015)][replication-crisis-osc]) to cancer sciences ([Errington et al (2021)][replication-crisis-errington]).
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These are called [**the reproducibility and replicability crises**][reproducibility-crisis] - ongoing methodological crises in which the results of many scientific studies are difficult or impossible to repeat.
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Scientific methodology and results need to be published openly, replicated and confirmed by several independent parties.
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However, research papers often lack the full details required for independent reproduction (reaching the same results with the same data) or replication (reaching the same results with new data).
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Across many disciplines, the failure of attempts to reproduce or replicate scientific conclusions have resulted in [**reproducibility and replicability crises**][reproducibility-crisis], leading to reduced confidence in the scientific conclusions of fields as diverse as psychology ([The Open Science Collaboration (2015)][replication-crisis-osc]) and cancer sciences ([Errington et al (2021)][replication-crisis-errington]).
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Reproducible research is a practice that ensures that researchers can repeat the same analysis multiple times with the same results.
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It offers many benefits to those who practice it:
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* Reproducible research helps researchers remember how and why they performed specific tasks and analyses; this enables easier explanation of work to collaborators and reviewers.
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* Reproducible research enables researchers to quickly modify analyses and figures - this is often required at all stages of research and automating this process saves loads of time.
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* Reproducible research enables reusability of previously conducted tasks so that new projects that require the same or similar tasks become much easier and efficient by reusing or reconfiguring previous work.
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* Reproducible research supports researchers' career development by facilitating the reuse and citation of all research outputs - including both code and data.
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* Reproducible research helps researchers remember how and why they performed specific tasks and analyses; this makes work easier to explain to collaborators and reviewers.
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* Reproducible research enables researchers to quickly modify analyses and figures, saving time and effort when datasets or methods change.
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* Reproducible research is reusable; tasks can be recycled or reconfigured in future work.
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* Reproducible research supports researchers' career development by facilitating the citation of all research outputs, including both code and data.
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* Reproducible research is a strong indicator of rigor, trustworthiness, and transparency in scientific research.
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This can increase the quality and speed of peer review, because reviewers can directly access the analytical process described in a manuscript.
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It increases the probability that errors are caught early on - by collaborators or during the peer-review process, helping alleviate the reproducibility crisis.
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It increases the probability that errors are caught early on, by collaborators or during the peer-review process, helping alleviate the reproducibility crisis.
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However, reproducible research often requires that researchers implement new practices and learn new tools.
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This course aims to teach some of these practices and tools pertaining to the use of software to conduct reproducible research.

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