Specifying an engine

GADMA uses either dadi or moments to simulate expected AFS from the demographic model. moments is used by default. To use dadi it is recommended to check the value of the Pts option in the params_file. Pts is sequence of three numbers, each of which is equal to the number of points in grid size. The greater the numbers are, the more accurate dadi numerical solution of partial differential equation is. However, finding such a solution take more time. By default, GADMA takes Pts : n, n + 10, n + 20, where n — is the largest sample size among populations of interest.

moments library does not need Pts to be specified. To change moments to dadi engine, specify option in the parameters file:

# param file
...
Engine : moments
...

or to use dadi:

# param file
...
Engine : dadi
Pts: [40, 50, 60]
...

Note

Using moments engine uses Pts settings for generation of dadi’s code. So if one want to use dadi’s code then maybe Pts argument must be set too.