EX Virtual species

Exercise

Plot the habitat suitability response curves for different transformation functions and observe how they change as you adjust the values. Each course participant should choose one transformation function (e.g., linear, logistic, or beta) and read the corresponding help page to understand how it works. Experiment with plotting the response curve for your chosen function and explain how the parameters (e.g., p1, p2, alpha, gamma in the beta function) influence the shape and results of the curve. Explain the behavior of the functions to your peers.

Note: It may in general be helpful to first plot the response functions of the environmental variables before creating virtual species. This approach will give you an idea of how the different responses interact with the environmental variables and how they affect the habitat suitability for the species. Here is some basic code to help you get started with plotting the response function:

Further reading

Grimmett, L., Whitsed, R., & Horta, A. (2021). Creating virtual species to test species distribution models: The importance of landscape structure, dispersal and population processes. Ecography, 44(5), 753–765. https://doi.org/10.1111/ecog.05555

Leroy, B., Meynard, C. N., Bellard, C., & Courchamp, F. (2016). Virtualspecies, an R package to generate virtual species distributions. Ecography, 39(6), 599–607. https://doi.org/10.1111/ecog.01388

Malinowska, K., Markowska, K., & Kuczyński, L. (2023). Making virtual species less virtual by reverse engineering of spatiotemporal ecological models. Methods in Ecology and Evolution, 14(9), 2376–2389. https://doi.org/10.1111/2041-210X.14176

Meynard, C. N., Leroy, B., & Kaplan, D. M. (2019). Testing methods in species distribution modelling using virtual species: What have we learnt and what are we missing? Ecography, 42(12), 2021–2036. https://doi.org/10.1111/ecog.04385

Qiao, H., Peterson, A. T., Campbell, L. P., Soberón, J., Ji, L., & Escobar, L. E. (2016). NicheA: Creating virtual species and ecological niches in multivariate environmental scenarios. Ecography, 39(8), 805–813. https://doi.org/10.1111/ecog.01961