API for FossilSim
Simulation and Plots for Fossil and Taxonomy Data
| Global functions | |
|---|---|
| FossilSim | Man page |
| FossilSim-package | Man page |
| SAtree | Man page Source code |
| SAtree.from.fossils | Man page Source code |
| add.depth.profile | Source code |
| ancestor | Source code |
| as.fbdrange.treedata | Source code |
| as.fossils | Man page Source code |
| as.fossils.default | Source code |
| as.taxonomy | Man page Source code |
| as.taxonomy.default | Source code |
| assign.interval | Source code |
| asymmetric.identities | Source code |
| beast.fbd.format | Man page Source code |
| bind.to.tip | Source code |
| count.fossils | Man page Source code |
| count.fossils.binned | Man page Source code |
| drop.unsampled | Source code |
| edge.end | Source code |
| edge.start | Source code |
| fbdrange | Man page Source code |
| fetch.descendants | Source code |
| find.edges.inbetween | Source code |
| find.species.in.taxonomy | Source code |
| fossils | Man page Source code |
| fossils.to.BEAST.constraints | Man page Source code |
| fossils.to.BEAST.start.tree | Man page Source code |
| fossils.to.paleotree.record | Man page Source code |
| fossils.to.pyrate | Man page Source code |
| get.dec.nodes | Source code |
| get.tip.descs | Man page Source code |
| get_fbdrange_from_file | Man page Source code |
| is.extant | Source code |
| is.fossils | Man page Source code |
| is.root | Source code |
| is.taxonomy | Man page Source code |
| is.tip | Source code |
| map_nodes | Source code |
| n.ages | Source code |
| paleotree.record.to.fossils | Man page Source code |
| place.fossils | Man page Source code |
| plot.fbdrange | Man page Source code |
| plot.fossils | Man page Source code |
| plot.taxonomy | Man page Source code |
| print.fossils | Source code |
| print.taxonomy | Source code |
| prune.fossil.tips | Man page Source code |
| prune.fossils | Man page Source code |
| rangeplot.asymmetric | Man page Source code |
| reconcile.fossils.taxonomy | Man page Source code |
| reconstructed.tree.fossils.objects | Man page Source code |
| remove.stem.fossils | Man page Source code |
| remove.stem.lineages | Man page Source code |
| remove_last_substring | Source code |
| root | Source code |
| rtnorm | Source code |
| sampled.tree.from.combined | Man page Source code |
| sim.anagenetic.species | Man page Source code |
| sim.cryptic.species | Man page Source code |
| sim.extant.samples | Man page Source code |
| sim.fbd.age | Man page Source code |
| sim.fbd.rateshift.taxa | Man page Source code |
| sim.fbd.taxa | Man page Source code |
| sim.fossils.environment | Man page Source code |
| sim.fossils.exponential | Source code |
| sim.fossils.intervals | Man page Source code |
| sim.fossils.poisson | Man page Source code |
| sim.gradient | Man page Source code |
| sim.interval.ages | Man page Source code |
| sim.taxonomy | Man page Source code |
| sim.tip.samples | Man page Source code |
| sim.trait.values | Man page Source code |
| sim.uncertain.ages | Source code |
| species.end | Man page Source code |
| species.record.from.taxonomy | Source code |
| species.start | Man page Source code |
| subsample.fossils.oldest | Man page Source code |
| subsample.fossils.oldest.and.youngest | Man page Source code |
| subsample.fossils.uniform | Man page Source code |
| subsample.fossils.youngest | Man page Source code |
| summary.fossils | Source code |
| summary.taxonomy | Man page Source code |
| taxonomy | Man page Source code |
| tree.max | Man page Source code |
| untangle | Source code |
