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.