Ecological Toolbox: A short guide for research projects in ecology

Author

Gustavo Paterno

Published

April 9, 2024

Before defining study aims & hypothesis

  • Betts MG , Hadley AS , Frey DW , et al. When are hypotheses useful in ecology and evolution?. Ecol Evol. 2021; 11: 5762–5776. | link

  • Popovic, et al. 2024. Four principles for improved statistical ecology. Methods in Ecology and Evolution, 00, 1–16. | link

  • Book chapter by Gonçalves-Souza, T., Provete, D.B., Garey, M.V., da Silva, F.R., Albuquerque, U.P. (2019). Going Back to Basics: How to Master the Art of Making Scientifically Sound Questions. | link

Before collecting data

Must read
  • Marshall, D. J. (2024). Principles of experimental design for ecology and evolution. Ecology Letters, 27(4), e14400. | link
  • Kimmel, K., Dee, L. E., Avolio, M. L., & Ferraro, P. J. (2021). Causal assumptions and causal inference in ecological experiments. Trends in Ecology & Evolution, 36(12), 1141–1152. | link

Also, think about experimental design, causal links and confounding factors:

  • Zeleny D. (2022). Blog Post: Sampling design of ecological experiments. | link

  • Zeleny D. (2022). Blog Post: Pseudoreplication & autocorrelation. | link.

  • Byrnes, J. E. K., & Dee, L. E. (2024). Causal inference with observational data and unobserved confounding variables. | link

Improve your management skills

  • BES Guide: “Data Management (2019) | link

Going deeper:

  • Take a look at this great book: The Turing Way handbook to reproducible, ethical and collaborative data science | Link

Before writing code

  • BES Guide: “Reproducible Code (2019) | link
  • How to choose the right license for code & data? | link

Before analyzing data

Learn R ;)

  • Online book: McKinley et al. Introduction to Data Analysis with R. | link
  • Online book: Da Silva et al. 2022. Ecological analysis in R (in portuguese) | link

Define the purpose of your analysis

  • Tredennick, A. T., G. Hooker, S. P. Ellner, and P. B. Adler. 2021. A practical guide to selecting models for exploration, inference, and prediction in ecology. Ecology 102(6):e03336. | link

Key papers for avoiding statistical problems

  • Zuur, A.F., Ieno, E.N. and Elphick, C.S. (2010), A protocol for data exploration to avoid common statistical problems. Methods in Ecology and Evolution, 1: 3-14. | link

  • Zuur, A.F. and Ieno, E.N. (2016), A protocol for conducting and presenting results of regression-type analyses. Methods Ecol Evol, 7: 636-645. | link

  • Harrison, X. A., Donaldson, L., Correa-Cano, M. E., Evans, J., Fisher, D. N., Goodwin, C. E. D., Robinson, B. S., Hodgson, D. J., & Inger, R. (2018). A brief introduction to mixed effects modelling and multi-model inference in ecology. PeerJ, 2018(5), 1–32 | link

How to interpret significance / pvalues?

  • Dushoff J, Kain MP, Bolker BM. I can see clearly now: Reinterpreting statistical significance. Methods Ecol Evol. 2019; 10: 756–759. | link

  • Blog post by Daniel Lakens: Why p-values should be interpreted as p-values and not as measures of evidence | link

Going further

  • Data Science for Ecologists - Courses and tutorials from Coding Club | link

  • Zeleny 2023. Blog: Analysis of community ecology data in R. | link

Before model selection

  • C. Sutherland, D. Hare, P. J. Johnson, D. W. Linden, R. A. Montgomery, and E. Droge (2023). Practical advice on variable selection and reporting using Akaike information criterion. Proceedings of the Royal Society B: Biological Sciences, vol. 290, no. 2007, Sep. 2023. | link

Before making figures

Must read

  • Weissgerber, T. L., Milic, N. M., Winham, S. J., & Garovic, V. D. (2015). Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLOS Biology, 13(4), e1002128 | link

  • Rougier, N. P., Droettboom, M., & Bourne, P. E. (2014). Ten Simple Rules for Better Figures. PLoS Computational Biology, 10(9), e1003833 | link

  • Alla Katsnelson (2021). Colour me better: fixing figures for colour blindness. Nature 598, 224-225 (2021) | link

Types of data visualizations:

Going deeper

  • Wilke Claus 2019. Book: Fundamentals of Data Visualization | link

Choosing the right colors

  • Explore and choose the right color scheme ar R-color brewer | link

  • Use Scico in R: color-blind friendly pallets to represent data fairly | link

  • Check if you figure is colorblind safe using this online simulator: link.

Before writing your manuscript

Agree on authorship as soon as possible

  • Idiv - Molecular Interaction Ecology Co-authorship Charte | link

Scientific writing tips / guidelines

  • Turbek, S.P., Chock, T.M., Donahue, K., Havrilla, C.A., Oliverio, A.M., Polutchko, S.K., Shoemaker, L.G. and Vimercati, L. (2016), Scientific Writing Made Easy: A Step-by-Step Guide to Undergraduate Writing in the Biological Sciences. Bull Ecol Soc Am, 97: 417-426. | link

  • The British Ecological Society Short Guide to Scientific Writing | link

  • McGill (2016). BlogPost: The 5 pivotal paragraphs in a paper. | link

  • Davis, Amy J., and Shannon Kay. 2023. Writing Statistical Methods for Ecologists. Ecosphere 14(5): e4539 | link

  • Suggestions by a Nature science editor to make your paper fly through the review process | link

Writing a author contributions

  • CRediT (Contributor Roles Taxonomy) | link

Before publishing your manuscript

  • BES Guide: A Guide to Getting Published in Ecology and Evolution. (2015) | link

Contribute

Feel free to improve this repository by suggesting corrections or new content. You can directly edit the content here or submit a Pull Request on our GitHub repository.

Header image: by vladhilitanu