Repository navigation
How to estimate population parameters for best log models? #97
Description
Dear Ekaterina, I am currently running GADMA2 for demographic models for two population genetics projects, I would like to add a table like the one you have on your 2023 "GADMA2: more efficient and flexible demographic inference from genetic data" paper where you include the demographic parameters (Table 4), in the parameter file I added the mutation rate and sequence length and I expected to get the parameters in the log file with physical units but I'm definitely getting them in genetic units for some reason, is there another option to specify how I want the units? The only correct unit I'm getting is years due to adding the time for generation. Or how do I convert from one to another? Is there any way to get a table with the best log models and their parameters?
Activity
noscode commentedon Sep 24, 2024
Hello @lmarieslava,
Yes, sure! The setting "Relative parameters" is responsible for parameters' units. Usually, GADMA prints output in physical units if mutation rate and sequence length are set. Time is in generations unless the option "Time for generation" is set. Please check the params file in the output directory and that:
I suspect that "Relative parameters" will be True. In that case, change it to False in your original params file for GADMA.
Best regards,
Ekaterina