Rev Language Reference
dnPiecewiseOccurrenceBirthDeath
Aliases
- dnOBDP
Usage
dnPiecewiseOccurrenceBirthDeath(RealPos rootAge/originAge, RealPos lambda, RealPos mu, RealPos psi, RealPos r, RealPos omega, Probability rho, RealPos[] timeline, RealPos[] lambdaTimeline, RealPos[] muTimeline, RealPos[] psiTimeline, RealPos[] omegaTimeline, RealPos[] rTimeline, String condition, Taxon[] taxa, TimeTree initialTree, Natural maxHiddenLin, Real[] occurrence_ages, Bool useMt, Bool verbose)
Arguments
| rootAge/originAge : | RealPos (pass by const reference) |
| Start time of the process. | |
| lambda : | RealPos (pass by const reference) |
| Speciation/birth rate(s). | |
| mu : | RealPos (pass by const reference) |
| Extinction/death rate(s). | |
| psi : | RealPos (pass by const reference) |
| Serial sampling rate(s). | |
| r : | RealPos (pass by const reference) |
| Probabilit(y|ies) of death upon sampling (treatment). | |
| omega : | RealPos (pass by const reference) |
| Occurrence sampling rate(s). | |
| Default : 0 | |
| rho : | Probability (pass by const reference) |
| Sampling fraction at present. | |
| Default : NULL | |
| timeline : | RealPos[] (pass by const reference) |
| Rate interval change times of the piecewise constant process. | |
| Default : [ ] | |
| lambdaTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the speciation/birth rate. | |
| Default : NULL | |
| muTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the extinction/death rate. | |
| Default : NULL | |
| psiTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the serial sampling rate. | |
| Default : NULL | |
| omegaTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the occurrence sampling rate. | |
| Default : NULL | |
| rTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the (serial) treatment probability. | |
| Default : NULL | |
| condition : | String (pass by value) |
| Condition of the process on the survival of either 1 (survival) or 2 lineages (survival2) to the present | |
| Default : none | |
| Options : survival|survival2 | |
| taxa : | Taxon[] (pass by const reference) |
| Taxa used for initialization. | |
| initialTree : | TimeTree (pass by value) |
| Instead of drawing a tree from the distribution, initialize distribution with this tree. | |
| Default : NULL | |
| maxHiddenLin : | Natural (pass by const reference) |
| Maximum number of hidden lineages. | |
| Default : 30 | |
| occurrence_ages : | Real[] (pass by value) |
| Fixed occurrence ages | |
| Default : NULL | |
| useMt : | Bool (pass by const reference) |
| If true computes densities with the Mt forward traversal algorithm otherwise uses Lt backward one. | |
| Default : TRUE | |
| verbose : | Bool (pass by const reference) |
| If true displays warnings and information messages. | |
| Default : FALSE |
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