Comments (3)
Hi @AngryMaciek, sorry for the late response!!
An init_config_file.dat I've been using a lot lately is
parameters
{
spatial_structure
{
log2_deme_carrying_capacity 7
}
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 0.001
mu_driver_migration 0.01
passenger_pop_threshold -1
}
fitness_effects
{
normal_birth_rate 0.9
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 1000000
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
}
}
It takes a few seconds to run as is. I mostly vary mu_passenger
, s_driver_migration
, and s_driver_birth
, which can make the execution time get out of hand pretty quickly, so I'd say decent ranges for testing are:
mu_passenger
between 0.001 and 0.01;
s_driver_migration
between 0 and 0.05;
s_driver_birth
between 0.1 and 0.2.
If all of these are at the largest values (particularly s_driver_birth
), it takes a couple minutes to execute for max_pop
set to 100000 (if it's 1000000 as above, we're talking a while longer), but otherwise shouldn't take more than a few seconds.
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@robjohnnoble : I would like to add more tests to the pipeline - varying different parameters; I don't really know how each of them affects the simulations and what ranges are reasonable. Could you please post here some variants of the conifguration which you especially often try out? I would include them in the CI as additional tests. Preferably on not-so-large population, so that the runtime is reasonable.
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@vesmanojlovic : Could you please help us out here? :)
I would like to refactor the repo to a cleaner state.
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