niemasd / coatran Goto Github PK

Perhaps restructure code to seed the RNG in main(). If the user specifies a seed, use that to seed the RNG; if not, use system time

The current implementation is broken. I redid the math here:

https://github.com/niemasd/CoaTran/wiki/Exponential-Effective-Population-Growth

I just need to update the code

Implement logistic effective population growth

Hello,

I am trying to run CoaTrans in the example files, and I do the following:
../coatran_constant big_transmissions.tsv big_times.tsv 1

But my output is only
(80296|CNG0-COM12-1399|0.821187:0.821187):0.000000;

So, I am wandering whether it is because there are more than one tree per transmission chain, the program is not outputting all the trees?
I am using a MAC OS Big Sur version 11.6.7

Thanks,
Fabricia.

"Transmission Tree" will coalesce at the latest time possible (forward in time), meaning each coalescence will happen at the time of transmission. This is equivalent to using a constant effective population size of 0.

"Infection Time" will coalesce at the earliest time possible (forward in time, meaning each coalescence will happen at the time of infection. This is equivalent to using a constant effective population size of infinity.

I've laid out the relevant details in the Makefile and .gitignore; I just need to actually implement.