Elevating The Status of Code in Ecology

[emmajhudgins]

Title: Elevating The Status of Code in Ecology

Study Link: https://www.sciencedirect.com/science/article/pii/S0169534715002906
Citation: @doi:10.1016/j.tree.2015.11.006

Suggested keywords that help identify the relevance of this paper to Ecology and Evolution:

• Journal practices
• Barriers
• Data provider comparison

Which areas of expertise are particularly relevant to the paper?

• ecology and/or evolution;
• biostatistics;
• informatics and computational research;
• open science and reproducibility;

Summary

This paper summarizes the current (lack of) standards for code across Ecology journals, and provides support for the role of code in ecological research, and tips to promote code sharing. Importantly, they found that (in 2016), 75% of (96) ecology journals didn't have specific code sharing requirements. Many citations for different barriers to sharing code are provided. American Naturalist is provided as an example of a journal that makes code access very clear from the first page of an article. The citing of code is encouraged. In a comparison table of different places to store code, GitHub ranks poorly in long-term stability, but has lower cost, and more flexible licensing. Zenodo+GitHub is their gold standard.

Suggested questions to answer about each paper:

• What is the general main finding or takeaway of the paper?
• What did they analyze and how did they do it?
• What does this paper suggest to improve the issue with reproducibility in science?
• Do you have any concerns about methodology or the interpretation of these results beyond this analysis?

Any comments or notes?