Man pages for ndukler/epiAllele
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 |
| branchRateMatrix | Compute exponentiated rate matrix for all branches |
| branchTransitions | Compute transitions per branch |
| clone | Copy object |
| disCharToProb | Discrete characters to probabailites |
| epiAllele | epiAllele |
| epiAllele-package | A short title line describing what the package does |
| exportScaledTree | Exports scaled tree |
| fit | Fits rate model |
| getAlleleData | Returns alleleData |
| getEdgeGroupTable | Get edgeGroupTable |
| getEdgeTable | Get edge table |
| getIndexLabels | Get all site labels for an index |
| getLabelIndices | Get all site indices for a label |
| getParams | Returns alleleData |
| getParamValue | Get parameter values |
| getParmIndex | Get parameter index |
| getPiIndex | Get pi parameter index |
| getRateIndex | Get rate parameter index |
| getSiblings | Compute transitions per branch |
| getSiteInfo | Extract site information table |
| getTree | Gets tree |
| logLikelihood | Compute log-likelihood |
| logSumExp | Vector logSumExp |
| lrt | Compute LRT for rate models |
| multiProbToStick | multiProbToStick |
| multiStickToProb | multiStickToProb |
| nSites | Extract site information table |
| plotTree | Tree visualization |
| probToStick | probToStick |
| rateModel | rateModel |
| rateModel-class | Class rateModel |
| rateSE | Estimates the standard error of the rate |
| rcpp_hello_world | Simple function using Rcpp |
| readPAF | Read in *.paf file |
| scaledLL | Compute scaled negative log-likelihood |
| setParamValue | Set parameter values |
| simData | Simulate data |
| siteTransitions | Compute transitions per branch |
| stickToProb | stickToProb |
| tieRates | Tie rates across siteLabels or edgeGroups |
