Description: Simulation models using metapopulation modeling framework to investigate relationship between species-traits (colonisation, extinction, dipsersal) and time lags (extinction debt and colonisation lag) in response to landscape degradation and restoration.
Manuscript in preparation:
Dagtekin, D., Moor, H., & Sutherland, C. (2025).
Extinction debts and colonisation lags in the response of spatially structured populations to degradation and restoration.
To be submitted to: Ecology Letters. [Open Science Framework (OSF) Project Link: https://osf.io/b3ky8/ ]
This repository contains all code and supporting files for simulating extinction debts and colonisation lags in metapopulations exposed to habitat degradation and restoration.
We use a spatially explicit, stochastic patch-occupancy model to explore how species traits (dispersal, extinction, colonisation) and landscape change dynamics interact to produce time-delayed responses in biodiversity.
landscape_simulation_functions_290724.R: Simulating landscapes with random patch distribution with log-normal distributed patch areas, adapted from Walker & Gilbert, 2023, Ecology, doi: 10.1002/ecy.3840
PStarFunction_290724.R: Initial occupancy probability calculator for initial, stable state in simulations, adapted from Walker & Gilbert, 2023, Ecology, doi: 10.1002/ecy.3840
sim_obsDat_landdeg_function_faster_100425.R: Simulation function for metapopulation under landscape degradation, adapted from Sutherland et al., 2014, Ecology, doi: 10.1890/14-0384.1 & Bertasello et al., 2021, Royal Soc. Open Sci. doi: 10.1098/rsos.201309
sim_obsDat_landrest_function_faster_100425.R: Simulation function for metapopulation under landscape degradation and restoration, adapted from Sutherland et al., 2014, Ecology, doi: 10.1890/14-0384.1 & Bertasello et al., 2021, Royal Soc. Open Sci. doi: 10.1098/rsos.201309
The scripts here are examples for only intermediate dispersal (alpha = 1/500) and degradation percentage = 80. All of them are used to simulate combinations with different species traits and degradation percentages. This includes low-, mid-, high-values of these parameters:
alpha = {1/200, 1/500, 1/1000}
e = {0.2, 0.5, 0.8}
c = {0.4, 1, 1.6}
degradation percentage = {20, 50, 80}
These scripts include 10 landscape repetitions and 50 metapopulation repetitions in each landscape. For the whole study in total 20 landscape repetitions and 50 metapopulation repetitions in each landscape were simulated.
sim_landdeg_a500_80p.R: Simulation script for landscape degradation only scenario. Example script for only intermediate dispersal (alpha = 1/500) and degradation percentage = 80.
sim_landrest_a500_80p.R: Simulation script for landscape degradation and restoration scenario. Example script for only intermediate dispersal (alpha = 1/500) and degradation percentage = 80.
1_sim_out_results_merge_repetitions_process.R: Script for checking simulation output and merging landscape repetitions (2 scripts, each with 10 reps) for each scenario (degradation only & degradation + restoration)
2_sim_out_results_inspect: Script for calculating values for results and visualization for each scenario (degradation only & degradation + restoration), e.g., proportion of occupied sites, number of occupied sites, number of patches in each year
All plots were done fore each species and scenarios. Each species meaning: all combinations or e, c, and alpha.
3_propocc_time_series.R: Script for plotting proportion of occupied sites over time.
4_percentage_of_extinct_metapops.R: Script for metapopulation extinction percentage over time.
5_hysteresis.R: Script for hysteresis plots - proportion of occupied sites over number of available patches.