Comments (2)
A set of parameters which gives quite nice looking Muller plots is:
parameters
{
spatial_structure
{
log2_deme_carrying_capacity 9
}
dispersal
{
migration_type 0
init_migration_rate 2e-03
migration_edge_only 1
migration_rate_scales_with_K 1
}
mutation_rates
{
mu_driver_birth 1e-05
mu_passenger 0.1
mu_driver_migration 0
passenger_pop_threshold -1
}
fitness_effects
{
normal_birth_rate 0.8
baseline_death_rate 0
s_driver_birth 0.1
s_passenger 0
s_driver_migration 0
max_relative_birth_rate 10
max_relative_migration_rate 10
}
non_biological_parameters
{
init_pop 1
matrix_max -1
max_pop 100000
max_time 86400
max_generations 2000
seed 10
write_grid 0
write_clones_file 0
write_demes_file 0
record_matrix 0
write_phylo 0
calculate_total_diversity 0
biopsy_size_per_sample 100
}
}
Should run in a couple minutes. The Muller plot function is plot_all_images("path_to_output_folder")
, and there's also plot_all_charts("path_to_output_folder")
which outputs evolutionary parameter graphs. I really like the idea of having a more user-friendly way to converse with demon btw!
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Actually, I need some feedback here as well @robjohnnoble:
I need a set of demon parameters which would result in a nice, presentable results. I would like to prepare an interactive example so it also need to have a reasonable runtime (a few minutes is OK). It may be a toy example population, just so that we may show and let others trigger the workflow and inspect the results themselves.
Also: I understand that the repository of yours (above) works out-of-the-box to generate Muller plots? That would be very desirable.
I plan to set up an interactive Jupyter notebook which would clone this repo, install its dependencies, install your package too and start an interactive notebook where users could trigger the workflow and then generate some simple plots out of the results.
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Related Issues (20)
- feat: SLURM cluster execution HOT 1
- double-check final output of demon / linking HOT 3
- docs: README HOT 2
- refactor: clean test directories HOT 1
- JOSS checklist HOT 1
- feat: consider full macOS support
- Minor comments
- docs: agree on a proper name
- feat: Gitpod integration
- chore: adjust binder simulation parameters
- feat: allow to clone a specific commit from demon HOT 1
- refactor: include various cool repo mechanisms
- docs: CONTRIBUTING
- mybinder does not start HOT 3
- add `md5` sum comparison for output files in the ci
- `docker.service` fails to start HOT 6
- ci: test the workflow HOT 3
- chore: cores params
- chore: check compilation issues HOT 2
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