NetworkExtinction: an R package to simulate extinction’s propagation and rewiring potential in ecological networks

Abstract

Biodiversity loss is one of the current drivers of global change with an acute impact on community structure. Different measures and tools (e.g., simulations of extinction events) have been developed to analyze the structure of ecological systems and their stability under biodiversity loss, especially in complex settings with multiple interacting species, such as food webs. However, there remains the need for tools that enable a quick assessment of the ensuing impacts on food webs structure due to species extinction. Here, we develop an R package to explore the propagation of species extinctions through food webs, measured as secondary extinctions, according to user-defined node removal sequences. In the NetworkExtinction package, we seek the integration between theory and computational simulations by developing six functions to analyze and visualize the structure and robustness of food webs represented as binary adjacency matrices. Three functions simulate the sequential extinction of species; a fourth function compares food web metrics between random and non-random extinction sequences; a fifth function visualizes the change in a given network metric along with the steps of sequential species extinction; a sixth function allows the user to fit and visualize the degree distribution of the network, fitting linear and non-linear regressions. We illustrate the package's use and its outputs by analysing a Chilean coastal marine food web. By using the NetworkExtinction package, the user can estimate the food web robustness after performing species' extinction routines based on several algorithms. Moreover, the user can compare the number of simulated secondary extinctions against a null model of random extinctions. The visualizations allow graphing topological indexes that the deletion sequences functions calculate after each removal step. Finally, the user can fit the degree distribution of the food web. The NetworkExtinction R package is a compact and easy-to-use package to visualize and assess the food web structure (degree distribution) and robustness to different sequences of species loss. Therefore, this package is particularly useful to evaluate the ecosystem response to anthropogenic and environmental perturbations that produce non-random species extinctions. In that way, it also allows us to assess the contribution of central nodes to food webs stability.