Evolutionary rescue

Simulation and analysis code for the paper "How density dependence, genetic erosion and the extinction vortex impact evolutionary rescue" by Nordstrom et al.

Requirements:

• R (version used: 4.1.2)
• dplyr (1.0.7)
• tidyr (1.1.13)
• rstanarm (2.21.1)

For figures:

• ggplot2 (3.3.4)
• cowplot (1.1.1)

The robustness checks also use the parallel package (4.1.2).

Repository structure

sim_functions.R: Source script for simulation functions and other handy wrappers sim_bh_functions.R: Source script for simulations with Beverton-Holt density dependence (for robustness analysis)

Directory simulations:

• simulations/run_final_scripts/ scripts for running simulations used in analysis

  • simulations/run_final_scripts/sim_alldata_n{20/100}_a{000/035}_{hi/low}var.R: script for running 15-generation simulations with size 20/100, alpha 0/0.0035, high/low genetic diversity

  • simulations/run_final_scripts/longsims_n{20/100}_a{000/035}_{hi/low}var.R: script for running 50-generation simulations with size 20/100, alpha 0/0.0035, high/low genetic diversity

  • simulations/combine_alldata.R: short script for concatenating 15-generation simulation output files into one output file

• simulations/run_robust_checks scripts for running robust checks (one per parameter for each of nloci (number of loci - m in manuscript), sig2e (environmental contribution to phenotypic variance, sig^2_e in manuscript), wfitn (width of selection surface), w_max (maximum intrinsic fitness), theta (degree of environmental change), and bholt (with Beverton-Holt density dependence))

• simulations/outputs/ subdir for holding CSV outputs from simulations (used in analysis)

  • simulations/outputs/alldata_n{20/100}_a{000/035}_{hi/low}var.csv: 15-generation simulation output (size 20/100, alpha 0/0.0035, high/low genetic diversity)

  • simulations/outputs/longsims_n{20/100}_a{000/035}_{hi/low}var.R: 50-generation simulation output (size 20/100, alpha 0/0.0035, high/low genetic diversity)

  • subdirectory robust_checks_out with one output csv for each robustness check

Directory analysis_results:

• Contains individual scripts labelled to reflect contents (including tables, figures, and supplemental information)

• Contains subdirectory robustness_checks with code for making robustness check figures

Contact information

Scott Nordstrom (scottwatsonnordstrom&gmail)

Changelog

Readme finalized October 24, 2022.

Additional analysis for new submission finalized and merged in June 2, 2023.

Revisions for Figure 5 (legend addition) and source code for Beverton-Holt simulations added September 22, 2023.

Code for robustness checks (simulations and figure production) added October 13, 2023.

Readme updated October 14, 2023.

Correct and up-to-date Fig. 2 script (including analytical solutions) added to repo after being mistakenly left out, October 20, 2023.

Tidy up comments, update filenames for figures (and in some cases, Rscripts) to reflect proper names in ESM, add a Readme to the analysis_results subdirectory. All added November 13 2023.