| ConstructRateFromParams(parameters, mapping, ...) | Construct a rate matrix from a flat array of parameters. |
| ConvertTIntoK(T0) | Convert a transition matrix into a rate matrix. |
| FixEntry(mapping, parameters, populations, ...) | Constrain an entry in a rate matrix. |
| GetFormat() | Construct a generator to enumerate colors for plotting. |
| LogLikelihood(C, T) | Calculate the likelihood of a transition matrix given counts C. |
| MaximizeRateLikelihood(parameters, mapping, ...) | Maximize the likelihood of a rate matrix given assignment data. |
| PlotRates(KList, LagTimeList, counts_list[, Tau]) | Plot the intermediate SCRE output to evaluate convergence. |