reproducible_workflows/rr-presentation.Rpres at master · NoushinN/reproducible_workflows · GitHub

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reproducible research workshop
========================================================
author: Noushin Nabavi & Monica Granados
date:
autosize: true

learning outcomes
========================================================

- 1. explain what is reproducible research
- 2. tools that can help make research more reproducible
- 3. components of a reproducible project
- 4. use of rmarkdown for reproducible research
- 5. use of github for reproducible research

What is reproducible research
========================================================

- Reproducible research means that future you and anyone else will be able to pick up your analysis and reproduce the same results, including figures and tables.

- This implies well-documented research, well commented codes and documents and reasoning behind analyses

- Also, the communication aspect should not be an afterthought, it should be recorded with the analysis as you are going through it.

Rmarkdown is a way of literate programing that keeps code, words and sentences together. The ability to easily collaborate and share your analysis goes hand-in-hand with good record-keeping and reproducibility.

Reproducible research tools
========================================================

- Software tool: R / RStudio
- Communication tools: Markdown / Rmarkdown
- Version control tools: Git / Github


Markdown reproducible research
========================================================

Markdown or Rmardown (when built in R environment) is a way of literate programing that keeps code, words and sentences together.

The ability to easily collaborate and share your analysis goes hand-in-hand with good record-keeping and reproducibility.


Github reproducible research
========================================================

- We can repurpose the git version control tool and leverage the GitHub remote hosting provider for managing and sharing our work.

- Git + GitHub will provide a very powerful resource for global collaboration and exposure of your work.
- In this workshop, we are going to use version control our work and push it to github, which can then be accessed by your collaborators and supervisors.

- Git + GitHub should become an integral part of your workflow.

Making table summaries reproducible
========================================================

```{r}
summary(cars)
```

Making plots reproducible
========================================================

```{r, echo=FALSE}
plot(cars)
```