Man pages for ndukler/phyloGLM
Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles
| alleleData | alleleData |
| alleleData-class | Class alleleData |
| bic | Compute BIC for rate models |
| copy | Copy rateModel |
| disCharToProb | Discrete characters to probabailites |
| fit | Fits rate model |
| forceParameterZero | Remove parameter from model |
| getAlleleData | Returns alleleData |
| getEdgeTable | Get edge table |
| getParams | Plot coefficents |
| getRateBounds | Get rate bounds |
| getSiblings | Get siblings |
| getSiteInfo-methods | Extract site information table |
| getTree | Gets tree |
| ll | Compute log-likelihood |
| logSumExp | Vector logSumExp |
| lrt | Compute LRT for rate models |
| marginal | Node marginals |
| marginalTransitions | Expected transitions per site |
| matrixToStlXptr | matrixToStlPointer |
| pack | Pack rateModel |
| packedModel-class | Class packedModel |
| phyloGLM | phyloGLM |
| phyloGrad | Compute parameter gradients |
| phyloHess | Compute hessian |
| pi | Compute site-wise stationary distribution |
| plotElementTransitions | Plot turnover events on the tree |
| plotParams | Plot parameter values |
| plotTree | Tree visualization |
| predict | Predict phylogenetic parameter values |
| rateModel | rateModel |
| rateModel-class | Class rateModel |
| rates | Compute rates |
| readPAF | Read in *.paf file |
| scaledLL | Compute scaled negative log-likelihood |
| se | Compute standard errors for parameters |
| setFixed | Set fixed |
| setParams | Set params |
| setRateBounds | Set rate bounds |
| show | Replace default print format |
| simulateSites | Simulate data |
| siteLL | Compute sitewise log-likelihoods |
| stlMatrix | stlMatrix |
| stlMatrix-class | Class stlMatrix |
| unpack | Unpack rateModel |
| updateFixed | updateFixed |
| updateFormula | Update formula |
