TY - JOUR
T1 - NetworkExtinction
T2 - An R package to simulate extinction propagation and rewiring potential in ecological networks
AU - Ávila-Thieme, M. Isidora
AU - Kusch, Erik
AU - Corcoran, Derek
AU - Castillo, Simón P.
AU - Valdovinos, Fernanda S.
AU - Navarrete, Sergio A.
AU - Marquet, Pablo A.
PY - 2023/8
Y1 - 2023/8
N2 - Earth's biosphere is undergoing drastic reorganization due to the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, leading to secondary extinctions and exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for directly simulating and quantifying extinction cascades and creating novel interactions (i.e. rewiring) remains absent. Here, we present NetworkExtinction—a novel R package which we have developed to explore the propagation of species extinction sequences through ecological networks and quantify the effects of rewiring potential in response to primary species extinctions. With NetworkExtinction, we integrate ecological theory and computational simulations to develop functionality with which users may analyse and visualize the structure and robustness of ecological networks. The core functions introduced with NetworkExtinction focus on simulations of sequential primary extinctions and associated secondary extinctions, allowing user-specified secondary extinction thresholds and realization of rewiring potential. With the package NetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In-built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can estimate the network's degree distribution by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analysing a Chilean coastal marine food web. NetworkExtinction is a compact and easy-to-use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds and rewiring potential. Therefore, this package is particularly useful for evaluating ecosystem responses to anthropogenic and environmental perturbations that produce nonrandom and sometimes targeted, species extinctions.
AB - Earth's biosphere is undergoing drastic reorganization due to the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, leading to secondary extinctions and exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for directly simulating and quantifying extinction cascades and creating novel interactions (i.e. rewiring) remains absent. Here, we present NetworkExtinction—a novel R package which we have developed to explore the propagation of species extinction sequences through ecological networks and quantify the effects of rewiring potential in response to primary species extinctions. With NetworkExtinction, we integrate ecological theory and computational simulations to develop functionality with which users may analyse and visualize the structure and robustness of ecological networks. The core functions introduced with NetworkExtinction focus on simulations of sequential primary extinctions and associated secondary extinctions, allowing user-specified secondary extinction thresholds and realization of rewiring potential. With the package NetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In-built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can estimate the network's degree distribution by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analysing a Chilean coastal marine food web. NetworkExtinction is a compact and easy-to-use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds and rewiring potential. Therefore, this package is particularly useful for evaluating ecosystem responses to anthropogenic and environmental perturbations that produce nonrandom and sometimes targeted, species extinctions.
KW - disturbance
KW - extinction thresholds
KW - food webs
KW - mutualistic networks
KW - network science
KW - network topology
KW - robustness
UR - http://www.scopus.com/inward/record.url?scp=85160790536&partnerID=8YFLogxK
U2 - 10.1111/2041-210X.14126
DO - 10.1111/2041-210X.14126
M3 - Journal article
AN - SCOPUS:85160790536
SN - 2041-210X
VL - 14
SP - 1952
EP - 1966
JO - Methods in Ecology and Evolution
JF - Methods in Ecology and Evolution
IS - 8
ER -