Man pages for thoree/mut2
Reversible mutation matrices and pairwise likelihood ratios
| adjustReversible | Adjusts reversible mutation matrix |
| boundsGamma | Upper limit for overall mutation rate |
| compareLRR | Ratio of LRs are compared for different transformations |
| exactLRR | Ratio of LRs and likelihoods calculated exactly for one... |
| expectedMutationRate | Expected mutation rate of a mutation matrix |
| ibd1.parental | Estimates for a pair of non-inbred individuals the... |
| isRegular | Checks if mutation model is well behaved |
| lik2 | Pairwise likelihood with mutation |
| LRmut | Pairwise LR with mutation |
| LRmutBounds | Pairwise LR bounds for proportional mutation models |
| makeReversible | Find reversible mutation matrix |
| makeWellBehaved | Make mutation model well behaved |
| mut2 | mut2: Balancing mutation matrix |
| reasonableMutationMatrix | Checks if pj < mij |
| simLR | Simulate LRRR |
| simLRR | Simulate LRRR |
| stepwiseReversible | Reversible stepwise mutation model |
