Extra parameter file
GADMA take an extra parameter file as input. However one probably do not need them. Nevertheless, if one is interested, extra_params_template
with all options and their descriptions can be found in gadma/cli/
folder.
Related options
Options of parameter bounds:
Min N
- minimum value (in genetic units) of population size (0.01).Max N
- maximum value (in genetic units) of population size (100).Min T
- minimum value (in genetic units) of epoch time (0).Max T
- maximum value (in genetic units) of epoch time (5).Min M
- minimum value (in genetic units) of migration rate (0).Max M
- maximum value (in genetic units) of migration rate (10).
Options of genetic algorithm:
Size of generation
- number of demographic models on one iteration (generation) of the genetic algorithm (10).Fractions
- fractions of best, mutated and crossed models that are taken to the new generation (None).N elitism
- number of best models that are taken to the new generation (2).P mutation
- fraction of models that are mutants in new generation (0.56).P crossover
- fraction of models that are children in new generation (0.19).P random
- fraction of models that were randomly generated for new generation (0.13).Mean mutation strength
- initial value of mean number of parameters that are mutated in the chosen model during mutation (0.63).Const for mutation strength
- constant for ‘one-fifth’ rule to change mutation strength (1.02).Mean mutation rate
- initial value of mean rate of parameter change during mutation (0.45).Const for mutation rate
- constant for ‘one-fifth’ rule to change mutation rate (1.07).Stuck generation number
- genetic algorithm stops when there is no improvement during this number of iterations.Eps
- change of log-likelihood that is considered significant.Random N_A
- enables random generation of ancestral size value and scales other parameters to this value during random generation of model parameters (True).
Options of bayesian optimization:
Kernel
- name of kernel for Gaussian process (Matern52).Acquisition function
- name of acquisition function (EI).
Options of global optimizations:
X_init
- points for initial design.Y_init
- value of log-likelihood on this points.