briandconnelly / hankshaweffect

Model, Data, and Analysis Scripts for "The Evolution of Cooperation by the Hankshaw Effect"

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 = 0 B: wellmixed.cfg, Population:genome_length = 8 (default) C: base.cfg, Population:genome_length = 0 D: 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 = 0 B: wellmixed.cfg, Population:mutation_rate_social = 0 C: base.cfg, Population:genome_length = 0, Population:mutation_rate_social = 0 D: 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 = 0 C: Population:stress_survival_rate = 1.0 D: 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 = 16 128-Regular: regulartopology.cfg, RegularTopology:degree = 128 Complete: base.cfg, Metapopulation:Topology = complete Well-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.