qpF4Ration

the five taxons: A, B, C, X, O. The O represents outgroup; the X represents multiple introgression groups; the B represents source of X; however, I am not sure what kind of groups can be represented as A and C. I have tested different groups in A and C, but the results were significantly different.
my results are as follows, the abbreviation represent wild relatives; Tibet and Ireland represent modern domestic.
A O X C : A O B C alpha std.err Z SNP
PYC SHEEP Tibet Ireland : PYC SHEEP FAL PYC 0.009713 0.001306 7.435 1648987
NUB SHEEP Tibet Ireland : NUB SHEEP FAL NUB 0.00687 0.001418 4.845 1648987
CYL SHEEP Tibet Ireland : CYL SHEEP FAL CYL 0.013515 0.001612 8.383 1648987
SIB SHEEP Tibet Ireland : SIB SHEEP FAL SIB 0.004771 0.00178 2.68 1648987
IBE SHEEP Tibet Ireland : IBE SHEEP FAL IBE 0.017853 0.002013 8.869 1648987
CAU SHEEP Tibet Ireland : CAU SHEEP FAL CAU 0.023936 0.002698 8.871 1648987

Start at the qpF4Ration entry point and compare the stated A, B, X, C, and O roles with the supplied sheep and wild-relative examples. Reproduce the reported runs if possible, then determine whether the issue needs clarified usage guidance or a code change; done means the group roles and expected interpretation are agreed.