Rev Language Reference
dnPhylodynamicBirthDeathProcess
Aliases
- dnPhylodynamicBDP
- dnPhylodynamicBDSTP
Usage
dnPhylodynamicBirthDeathProcess(RealPos rootAge/originAge, RealPos lambda, RealPos mu, RealPos phi/psi, RealPos[] timeline, RealPos[] lambdaTimeline, RealPos[] muTimeline, RealPos[] phiTimeline/psiTimeline, RealPos[] PhiTimeline/rhoTimeline, String condition, Taxon[] taxa, TimeTree initialTree, Natural ageCheckPrecision, Probability Phi/rho, Probability[] R, Probability r, RealPos[] rTimeline)
Arguments
| rootAge/originAge : | RealPos (pass by const reference) |
| The start time of the process. | |
| lambda : | RealPos (pass by const reference) |
| The birth rate(s). | |
| mu : | RealPos (pass by const reference) |
| The death rate(s). | |
| phi/psi : | RealPos (pass by const reference) |
| The serial sampling rate(s). | |
| timeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the piecewise constant process. | |
| Default : NULL | |
| lambdaTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the speciation rate. | |
| Default : NULL | |
| muTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the extinction rate. | |
| Default : NULL | |
| phiTimeline/psiTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the sampling rate. | |
| Default : NULL | |
| PhiTimeline/rhoTimeline : | RealPos[] (pass by const reference) |
| Times at which all taxa are sampled with some probability. There is always additionally a sampling event at the present. | |
| Default : NULL | |
| condition : | String (pass by value) |
| The condition of the process. | |
| Default : time | |
| Options : time|survival|sampling | |
| taxa : | Taxon[] (pass by const reference) |
| The taxa used for initialization. | |
| initialTree : | TimeTree (pass by value) |
| Instead of drawing a tree from the distribution, initialize distribution with this tree. | |
| Default : NULL | |
| ageCheckPrecision : | Natural (pass by value) |
| If an initial tree is provided, how many decimal places should be used when checking its tip ages against a taxon file? | |
| Default : 4 | |
| Phi/rho : | Probability (pass by const reference) |
| The probability of sampling taxa at sampling events (at present only if input is scalar). | |
| Default : 0 | |
| R : | Probability[] (pass by const reference) |
| The treatment probabilities for the sampling events (excluding sampling at present). | |
| Default : NULL | |
| r : | Probability (pass by const reference) |
| The probabilit(y|ies) of death upon sampling (treatment). | |
| Default : 1 | |
| rTimeline : | RealPos[] (pass by const reference) |
| The rate interval change times of the (serial) treatment probability. | |
| Default : NULL |
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