-
Notifications
You must be signed in to change notification settings - Fork 4
/
README.Rmd
143 lines (77 loc) · 5.01 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
---
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/",
out.width = "100%")
```
ethical-citations <img src="https://raw.githubusercontent.com/FRBCesab/templates/main/logos/compendium-sticker.png" align="right" style="float:right; height:120px;"/>
=========================================================
<!-- badges: start -->
[](https://choosealicense.com/licenses/gpl-2.0/)
<!-- badges: end -->
<p align="left">
• <a href="#overview">Overview</a><br>
• <a href="#data-sources">Data sources</a><br>
• <a href="#content">Content</a><br>
• <a href="#installation">Installation</a><br>
• <a href="#usage">Usage</a><br>
• <a href="#citation">Citation</a><br>
• <a href="#contributing">Contributing</a><br>
• <a href="#acknowledgments">Acknowledgments</a><br>
• <a href="#references">References</a>
</p>
## Overview
This project is dedicated to...
## Data sources
This project uses the following databases:
| Database | Usage | Reference | Link |
| :--------- | :------------------------------- | :-------------------------------- | :---------------------------------------: |
| Dafnee | Provide publisher business model | - | [link](https://dafnee.isem-evolution.fr/) |
| OpenAlex | Retrieve scientific publications | Priem J, Piwowar H & Orr R (2022) | [link](https://openalex.org/) |
A comprehensive description of all these databases is available [here](https://github.com/frbcesab/ethical-citations/blob/main/data/README.md).
## Workflow
The analysis pipeline follows these steps:
1. ...
## Content
This repository is structured as follow:
- [`DESCRIPTION`](https://github.com/frbcesab/ethical-citations/blob/main/DESCRIPTION): contains project metadata (authors, description, license, dependencies, etc.).
- [`make.R`](https://github.com/frbcesab/ethical-citations/blob/main/make.R): main R script to set up and run the entire project. Open this file to follow the workflow step by step.
- [`R/`](https://github.com/frbcesab/ethical-citations/blob/main/R): contains R functions developed especially for this project.
- [`data/`](https://github.com/frbcesab/ethical-citations/blob/main/data): contains raw data used in this project. See the [`README`](https://github.com/frbcesab/ethical-citations/blob/main/data/README.md) for further information.
- [`figures/`](https://github.com/frbcesab/ethical-citations/blob/main/figures): contains the figures of the project. See the [`README`](https://github.com/frbcesab/ethical-citations/blob/main/figures/README.md) for a complete description of the files.
- [`outputs/`](https://github.com/frbcesab/ethical-citations/blob/main/outputs): contains the outputs of the project. See the [`README`](https://github.com/frbcesab/ethical-citations/blob/main/outputs/README.md) for a complete description of the files.
## Installation
To install this compendium:
- [Fork](https://docs.github.com/en/get-started/quickstart/contributing-to-projects)
this repository using the GitHub interface.
- [Clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
your fork using `git clone fork-url` (replace `fork-url` by the URL of your fork).
Alternatively, open [RStudio IDE](https://posit.co/products/open-source/rstudio/)
and create a New Project from Version Control.
## Usage
Launch the [`make.R`](https://github.com/frbcesab/ethical-citations/tree/main/make.R)
file with:
```{r eval=FALSE}
source("make.R")
```
**Notes**
- All required packages listed in the [`DESCRIPTION`](https://github.com/frbcesab/ethical-citations/blob/main/DESCRIPTION) file will be installed (if necessary)
- All required packages and R functions will be loaded
- Some steps listed in the [`make.R`](https://github.com/frbcesab/ethical-citations/blob/main/make.R) might take time (several hours)
## Citation
Please use the following citation:
> ...
## Contributing
All types of contributions are encouraged and valued. For more information,
check out our [Contributor Guidelines](https://github.com/frbcesab/ethical-citations/blob/main/CONTRIBUTING.md).
Please note that this project is released with a
[Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.
## Acknowledgments
This project is a collaborative work among [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) postdocs.
## References
Priem J, Piwowar H & Orr R (2022) OpenAlex: A fully-open index of scholarly works, authors, venues, institutions, and concepts. **ArXiv**. <https://arxiv.org/abs/2205.01833>.