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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%",
echo = FALSE
)
```
# The Open Science Manual: Make Your Scientific Research Accessible and Reproducible
<img src="assets/images/banner.png" height="70px" width="100%">
<!-- badges: start -->
[](https://github.com/arca-dpss/manual-open-science/actions/workflows/deploy_bookdown.yml)
[](https://doi.org/10.5281/zenodo.6521850)
<!-- badges: end -->
The present book aims to describe programming good practices and introduce common tools used in software development to guarantee the reproducibility of the analysis results. We want to make scientific research an open-source knowledge development.
The book is available online at https://arca-dpss.github.io/manual-open-science/.
A PDF copy is available at https://arca-dpss.github.io/manual-open-science/manual-open-science.pdf.
## Book Content
In the book, we will learn to:
- Share our materials using the **Open Science Framework**
- Organize project files and data in a well structured and documented **Repository**
- Write readable and maintainable code using a **Functional Style** approach
- Use **Git** and **GitHub** for tracking changes and managing collaboration during the development
- Use dedicated tools for managing the **Analysis Workflow** pipeline
- Use dedicated tools for creating **Dynamic Documents**
- Manage project requirements and dependencies using **Docker**
As most researchers have no formal training in programming and software development, we provide a very gentle introduction to many programming concepts and tools without assuming any previous knowledge.
Examples and specific applications are based on the R programming language. However, this book provides recommendations and guidelines useful for any programming language.
## About the Authors {-}
During our careers, we both moved into the field of Data Science after a Ph.D. in Psychological Sciences. This book is our attempt to bring back into scientific research what we have learned outside of academia.
- [Claudio Zandonella Callegher](https://claudiozandonella.netlify.app/) ([email protected]). During my Ph.D., I fell in love with data science. Understanding the complex phenomena that affect our lives by exploring data, formulating hypotheses, building models, and validating them. I find this whole process extremely challenging and motivating. Moreover, I am excited about new tools and solutions to enhance the replicability and transparency of scientific results.
- [Davide Massidda](https://www.linkedin.com/in/davidemassidda/) ([email protected]). I am a data scientist specialized in psychometrics, trained at the University of Padua with a Ph.D. in experimental psychology. After my academic career and several years as a freelancer, I currently work in the private field. I deal with descriptive and predictive models using statistics and machine learning, developing web-based systems for human interaction with data, and automating statistical processing.
## ARCA
<img style = "margin-left: 20px;" align="right" width="150" height="150" src="assets/images/arca-logo.png">
ARCA courses are advanced and highly applicable courses on modern tools for research in Psychology. They are organised by the Department of Developmental and Social Psychology at the University of Padua.
## Contribute {-}
If you think something is missing, something should be described better, or something is wrong, please, feel free to contribute to this book. Anyone is welcome to contribute to this book.
This is the hearth of open-source: contribution. We will understand the real value of this book not by the number of people that will read it but by the number of people who will invest their own time trying to improve it.
For typos (the probability of typos per page is always above 1) just send a pull request with all the corrections. Instead, if you like to add new chapters or paragraphs to include new arguments or discuss more in detail some aspects, open an issue so we can find together the best way to organize the structure of the book.
View book source at GitHub repository https://github.com/arca-dpss/manual-open-science.
### Build Book Locally
To build the book locally, follow these steps:
1. Clone the repository
```bash
$ git clone [email protected]:arca-dpss/manual-open-science.git
```
1. Open the RStudio Project `manual-open-science.Rproj`
1. Install required R-packages by running
```{r, echo = TRUE, eval= FALSE}
renv::restore()
```
1. Run targets analysis using the command
```{r, echo = TRUE, eval= FALSE}
targets::tar_make(script = "analysis/targets-workflow.R",
store = "analysis/_targets")
```
1. Render the book by clicking the *“Build Book”* button from the *“Build”* panel, or by running
```{r, echo = TRUE, eval= FALSE}
rmarkdown::render_site(encoding = "UTF-8")
```
## Cite {-}
For attribution, please cite this work as:
> Zandonella Callegher, C., & Massidda, D. (2022). The Open Science Manual: Make Your Scientific Research Accessible and Reproducible. Available at https://arca-dpss.github.io/manual-open-science/. https://doi.org/10.5281/zenodo.6521850
BibTeX citation:
```bash
@book{zandonellaMassiddaOpenScience2022,
title = {The Open Science Manual: Make Your Scientific Research Accessible and Reproducible},
author = {Zandonella Callegher, Claudio and Massidda, Davide},
date = {2022},
url = {https://arca-dpss.github.io/manual-open-science/},
doi = {10.5281/zenodo.6521850}
}
```
## License {-}
```{r, fig.align="left", out.width="20%"}
knitr::include_graphics("images/cc-nc-sa.png")
```
This book is released under the [CC BY-NC-SA 4.0 License](https://creativecommons.org/licenses/by-nc-sa/4.0/).
This book is based on the [ARCA Bookown Template](https://github.com/arca-dpss/template-bookdown) released under [CC BY-SA 4.0 License](https://creativecommons.org/licenses/by-sa/4.0/).
The icons used belong to [rstudio4edu-book](https://rstudio4edu.github.io/rstudio4edu-book/) and are licensed under under [CC BY-NC 2.0 License](https://creativecommons.org/licenses/by-nc/2.0/).