Model, Data, and Analysis Scripts for The Evolution of Cooperation by the Hankshaw Effect
Contents
These subdirectories may contain additional information
- configuration - Configuration files for reported simulations
- data - Result data sets
- figures - Figures
- model - Model source code
- scripts - Scripts for analyzing and plotting result data
Contents by Figure
To re-create the simulations described, see the Configuration column. For example, the data used to create Figure 1C were generated by simulations started with the command:
hankshaw --config base.cfg --param Population genome_length 0| Figure | Related Files | Configuration |
|---|---|---|
| 1 | data, analysis, figure | A: wellmixed.cfg, Population:genome_length = 0B: wellmixed.cfg, Population:genome_length = 8 (default)C: base.cfg, Population:genome_length = 0D: base.cfg |
| 2A | data, analysis, figure | envchange-regular.cfg |
| 2B | data, analysis, figure |
envchange-regular.cfg, EnvironmentalChange:frequency values 250, 500, 750, 1000, 1250, 2500 |
| 3A | data, analysis, figure |
base.cfg, Population:initial_producer_proportion = 0.0 |
| 3B | data, analysis, figure | envchange-exponential.cfg |
| 3C | data, analysis, figure |
envchange-exponential.cfg, EnvironmentalChange:frequency values 500, 1000, 5000, 10000 |
Supporting Information
| Figure | Related Files | Configuration |
|---|---|---|
| S1A | data, analysis, figure |
base.cfg, Population:genome_length = 0, 8 |
| S1B | data, analysis, figure |
base.cfg, Population:genome_length = 0..10 |
| S1C | data, analysis, figure |
base.cfg, Population:capacity_max = 800..2450 |
| S1D | data, analysis, figure |
base.cfg, Population:production_cost = 0..0.5 |
| S1E | data, analysis, figure |
base.cfg, Metapopulation:migration_rate = 5e-07, 5e-06, 5e-05, 5e-04, 5e-03, 5e-02, 5e-01 |
| S1F | data, analysis, figure |
base.cfg, Population:mutation_rate_social and Population:mutation_rate_adaptation = 1e-07, 1e-06, 1e-05, 1e-04, 1e-03, 1e-02, 1e-01 |
| S2A | data, analysis, figure |
base.cfg, Population:mutation_rate_adaptation = 1e-07, 1e-06, 1e-05, 1e-04, 1e-03, 1e-02, 1e-01 |
| S2B | data, analysis, figure |
base.cfg, Population:mutation_rate_social = 1e-07, 1e-06, 1e-05, 1e-04, 1e-03, 1e-02, 1e-01 |
| S2C | data, analysis, figure |
base.cfg, Population:mutation_rate_adaptation = 1e-01 |
| S3 | data, analysis, figure | A: wellmixed.cfg, Population:genome_length = 0, Population:mutation_rate_social = 0B: wellmixed.cfg, Population:mutation_rate_social = 0C: base.cfg, Population:genome_length = 0, Population:mutation_rate_social = 0D: base.cfg, Population:mutation_rate_social = 0 |
| S4 | data, analysis, figure |
envchange-regular.cfg, EnvironmentalChange:frequency was varied in each panel.A: Base parameter values B: Population:genome_length = 0C: Population:stress_survival_rate = 1.0D: Population:genome_length = 0, Population:stress_survival_rate = 1.0 |
| S5 | data, analysis, figure |
envchange-exponential.cfg, EnvironmentalChange:affected_loci = 1..8 |
| S6A | data, analysis, figure |
base.cfg, Population:stress_survival_rate = 1e-04 (With Thinning), 1.0 (Without thinning) |
| S6B | data, analysis, figure |
base.cfg, Population:stress_survival_rate = 1e-04 (With Thinning), 1.0 (Without thinning), Population:genome_length = 0..10 |
| S7 | data, analysis, figure | Lattice: base.cfg 16-Regular: regulartopology.cfg, RegularTopology:degree = 16128-Regular: regulartopology.cfg, RegularTopology:degree = 128Complete: base.cfg, Metapopulation:Topology = completeWell-Mixed: wellmixed.cfg |
| S8 | data, analysis, figure | Viability selection. See viability branch. |
| S9A | data, analysis, figure | - |
| S9B | data, analysis, figure |
base.cfg, Population:capacity_shape = 0.25, 0.5, 1.0, 2.0, 4.0 |
| S10A | data, analysis, figure | - |
| S10B | data, analysis, figure |
base.cfg, Population:fitness_shape = 0.3, 0.6, 0.9, 1.0, 1.5, 2.0 |
| S11 | data, analysis, figure | 5xpopulation.cfg |
| S12 | data, analysis, figure |
base.cfg, Population:initial_producer_proportion = 0.01, 0.1, 0.5, 0.9, 0.99, 1.0 |
| S13A | data, analysis, figure | spite.cfg |
| S13B | data, analysis, figure |
spite.cfg, dilution_prob_min = 0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 0.75, 1.0 |
| S13C | data, analysis, figure | spite-envchange-regular.cfg |
Additional Materials
| Figure | Related Files | Configuration |
|---|---|---|
| R1 | data, analysis, figure |
base.cfg, MetapopulationMixing:enabled = True, MetapopulationMixing:frequency = 1 |
| R2 | data, analysis, figure |
envchange-regular.cfg, EnvironmentalChange:frequency = 5, MetapopulationMixing:enabled = True, MetapopulationMixing:frequency = 1 |
| R3 | data, analysis, figure | wellmixed-histress.cfg |
| R4 | data, analysis, figure |
base.cfg, Population:mutation_rate_social = 0 |
License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
