OpenPaleo.Rmd

---
title: "Open Paleo"
---

**Aim**: To perform a range of meta-analyses into the published Palaeontology literature.

Open Paleo is an open project that anyone can contribute to on [GitHub](https://github.com/Meta-Paleo/OpenPaleo/). All data sources, methods, code, and results are openly shared for collaboration and inspection as the project evolves.

We strongly encourage others to participate in the project, propose their own ideas, and to contribute or re-use any of the data or other information available here.

## Project concept

This project will include looking at factors such as:

* Quantitative analysis of the 'openness' of Palaeontology research.
* Citation frequencies for different journals, compared to their impact factors.
* Whether an 'Open Access citation advantage' exists for Palaeontology.

Ultimately, this information might prove useful in developing standards, protocols, and best practices for palaeontological research and publishing.

Two research papers have already come out of this project:

1. [An overview of Open Access publishing in palaeontology](https://palaeo-electronica.org/content/2019/2548-open-access-in-palaeontology), Tennant and Lomax (2019)

2. [Open Science in Dinosaur Paleontology](https://paleorxiv.org/wzfpb), Tennant and Farke (2019)

## Key links

* [Data](https://github.com/Meta-Paleo/OpenPaleo/tree/master/data)
* [Analysis scripts](https://github.com/Meta-Paleo/OpenPaleo/tree/master/scripts)
* [Results](https://github.com/Meta-Paleo/OpenPaleo/tree/master/results) including:
  1. [Proportion of Open Access papers](https://github.com/Meta-Paleo/OpenPaleo/tree/master/results/OA_analysis).
  1. [Citation frequencies](https://github.com/Meta-Paleo/OpenPaleo/tree/master/results/citation_analysis).
  1. [Citations versus OA state](https://github.com/Meta-Paleo/OpenPaleo/tree/master/results/citation_distribution_oa_status).

<p align="center">
  <img width="1500" height="750" src="paleo_journals_citation_distribution_oa_status.png">
</p>

## Data sources

### Google Scholar - COMPLETED

Journal selection was for the top-20 cited Paleontology journals according to [Google Scholar](https://scholar.google.com/citations?view_op=top_venues&hl=en&vq=soc_paleontology) in 2018.

### Scopus - COMPLETED

Metadata were extracted from Scopus journal-by-journal (as csv files), with the only filter being on the dates, constrained to published articles between 2015-2016. This includes information such as:

- Authors, titles, and year of publication.
- Number of citations (according to Scopus).
- Article Digital Object Identifier (DOI).

### Clean data - COMPLETED

Using [Visdat](https://github.com/ropensci/visdat) R package to visually inspect the data, we were able to spot the [misaligned rows](./data/journal_data/05-Review_of_Palaeobotany_and_Palynology/) and [block shifted columns](./data/journal_data/17-Bulletin_of_Geosciences/). These formatting errors were then fixed in MS-Excel and saved again in CSV format with UTF-8 encoding. Following this, the headers were formatted for user friendliness during analysis and the empty rows and columns were scrubbed off the data using [Janitor](https://github.com/sfirke/janitor) R package.

### PLOS ONE - COMPLETED

Data for PLOS ONE were obtained using the Rplos package in R. The code, resulting data, and Unpaywall query results can all be found [here](https://github.com/Meta-Paleo/OpenPaleo/tree/master/Journal%20data/PLOS%20ONE). Note that some of the data here are different to that obtained to Scopus queries.

### Unpaywall - COMPLETED

The next phase is to use the [Unpaywall DOI checker](https://unpaywall.org/check-dois) on the DOI list for each journal. This provides information such as:

- The Open Access state (true or false)
- Publication date
- Source of evidence for Open Access status

All of the results of these steps are available within this [repository](https://github.com/Meta-Paleo/OpenPaleo/tree/master/Journal%20data).

### Google Scholar - IN PREP

While Unpaywall checks to see if legitimate versions of articles have been made OA (i.e., via green self-archiving routes), researchers often also often tend to share their articles in non-copyright compliant ways. This includes on platforms such as ResearchGate or Academia.edu.

Therefore, data will be cross-checked with Google Scholar, which has this information at an article-level, to see:

- Whether articles are freely available;
- Which versions are available;
- Which services or platforms are most used.


### Wikidata / WikiCite - IN PREP

[WikiCite](https://meta.wikimedia.org/wiki/WikiCite) provides a lot of integrated data around scholarly literature,
linking research papers with authors, topics, species, and much, much more. All data is CCZero and integrates many
online resources. [Scholia](https://arxiv.org/abs/1703.04222) gives an idea what it can [do for paleontology](https://tools.wmflabs.org/scholia/topic/Q7205).


## Contributors
- Jon Tennant
- Prof. Dasapta Erwin Irawan
- Manojkumar Selvaraju
- Dean Lomax
- Andy Farke