Units of parameters

GADMA shows model parameters and their units in general GADMA.log output at the end of each model, for example:

[000:01:20]
All best by log-likelihood models
Number      log-likelihood          Model   Units
Run 1       -1277.31         [Nanc = 8273]  physical, time in generations

There are two possible types of units:

Physical
Genetic

Time units (generations or years) are specified when units are physical.

Warning

Parameters specified in additional output files (e.g. in 1/GADMA_GA.log) are always in genetic units.

Physical Units

Definition of physical units for parameters
Parameter type	Symbol	Description of physical units
Population size	`N`	Number of individuals
Time	`T`	Generations or years (depending on `Time for generation` option)
Migration rate	`m`	Proportion of migrants in population per generation
Inbreeding coefficient	`F`	Probability that two alleles at any locus in an individual are identical by descent from the common ancestor(s) of the two parents
Fraction in population split	`s`	Franction of population size that goes stays at the same population

In order to get output in physical units the following options should be specified in params_file:

Mutation rate
Sequence length

If Time for generation is specified then time will be presented not in generations (default), but years.

Genetic units

Parameters are presented in genetic units means that they are scaled to the reference population size Nref that is ancestral population size.

Definition of genetic units for parameters
Parameter type	Symbol	Description of physical units
Population size	`N`	Number of individuals divided by `Nref`
Time	`T`	Generations divided by `2 * Nref`
Migration rate	`m`	Proportion of migrants in population per generation multiplied by `2 * Nref`
Inbreeding coefficient	`F`	Fraction, the same as for physical units
Fraction in population split	`s`	Franction, the same as for physical units

In order to get output in genetic units the Relative parameters option should be set to True in params_file. If Mutation rate or Sequence length are not specified, then Relative parameters option is set automatically to be True.

To translate parameters from genetic units to physical units one should first get Nref as:

theta / (4 * mu * L),

where mu is mutation rate, L corresponds to sequence length and theta is given in the output of the model. Then translate values the following way: sizes of populations — multiply by Nref; time — multiply by 2 * Nref; migration rates — divide by 2 * Nref.