Rev Language Reference
simForwardBirthDeath
Usage
simForwardBirthDeath(RealPos[] timeline, RealPos[][] lambda, RealPos[][] mu, RealPos[][] phi, Probability[][] r, Probability[][] Lambda, Probability[][] Mu, Probability[][] Phi, Probability[][] R, Simplex rootCategory, RealPos time, String condition, Natural maxNumLineages, Bool completeTree)
Arguments
| timeline : | RealPos[] (pass by const reference) |
| The endpoints of the time intervals (episodes). You should include 0 at the end. We use ages before the present. | |
| Default : [ 0.000 ] | |
| lambda : | RealPos[][] (pass by const reference) |
| The speciation rates for each interval. | |
| mu : | RealPos[][] (pass by const reference) |
| The extinction rates for each interval. | |
| Default : 0 | |
| phi : | RealPos[][] (pass by const reference) |
| The sampling rates for each interval. | |
| Default : 0 | |
| r : | Probability[][] (pass by const reference) |
| The extinction probability when rate-sampling happens for each interval. | |
| Default : 0 | |
| Lambda : | Probability[][] (pass by const reference) |
| The burst probability at the end of each interval (first value is ignored). | |
| Default : 0 | |
| Mu : | Probability[][] (pass by const reference) |
| The (mass) extinction probability at the end of each interval (first value is ignored). | |
| Default : 0 | |
| Phi : | Probability[][] (pass by const reference) |
| The sampling probability at the end of each interval. | |
| Default : 0 | |
| R : | Probability[][] (pass by const reference) |
| The extinction probability when event-sampling happens for each interval (first value is ignored). If NULL, r is used instead. | |
| Default : NULL | |
| rootCategory : | Simplex (pass by const reference) |
| The probabilities of the categories for the root. | |
| Default : [ 1.000 ] | |
| time : | RealPos (pass by const reference) |
| The time/age before the present. | |
| condition : | String (pass by value) |
| What outcome should we condition on? | |
| Default : root | |
| Options : time|root|survival | |
| maxNumLineages : | Natural (pass by const reference) |
| The maximum number of lineages allowed by the simulator. Simulations that reach this size will be aborted and re-started. | |
| Default : 100000 | |
| completeTree : | Bool (pass by const reference) |
| Should the tree include all lineages, even those that went extinct? | |
| Default : FALSE |
Edit this page