Man pages for FossilSim
Simulation and Plots for Fossil and Taxonomy Data
| beast.fbd.format | Transforms a tree and fossils into a sampled tree in... |
| count.fossils | Count the total number of fossils |
| count.fossils.binned | Count the total number of fossils per interval |
| fbdrange | Creates an fbdrange object from provided tree and data |
| fossils | Fossils object |
| FossilSim | FossilSim: A package for simulating and plotting fossil and... |
| fossils.to.BEAST.constraints | Create a set of BEAST2 constraints to construct a DPPDIV... |
| fossils.to.BEAST.start.tree | Create a suitable starting tree for a DPPDIV style FBD... |
| fossils.to.paleotree.record | Transforms a fossils dataframe and either taxonomy or tree... |
| fossils.to.pyrate | Generate output in the format used by the program PyRate |
| get_fbdrange_from_file | Import fbdrange object from file |
| get.tip.descs | Obtain the tips that define each node in a tree |
| paleotree.record.to.fossils | Transforms a fossilRecordSimulation object from package... |
| place.fossils | Place fossil samples from one tree in another tree, or find... |
| plot.fbdrange | Plot oriented tree with stratigraphic ranges |
| plot.fossils | Plot simulated fossils |
| plot.taxonomy | Plot simulated taxonomy |
| prune.fossils | Removes all intermediate fossils from a combined tree and... |
| prune.fossil.tips | Remove fossil lineages from a tree |
| rangeplot.asymmetric | Make an asymmetric stratigraphic range plot from a tree... |
| reconcile.fossils.taxonomy | Reconcile existing fossil and taxonomy objects |
| reconstructed.tree.fossils.objects | Returns tree and fossil objects that you can use to plot the... |
| remove.stem.fossils | Remove fossil samples that occur in the stem |
| remove.stem.lineages | Remove stem lineages from a tree. |
| sampled.tree.from.combined | Removes all unsampled lineages from a combined tree. Extinct... |
| SAtree | Tree with sampled ancestors represented as zero-length edges |
| SAtree.from.fossils | Transforms a tree and fossils dataframe to a combined SA... |
| sim.anagenetic.species | Simulate anagenetic species on a taxonomy object |
| sim.cryptic.species | Simulate cryptic species on a taxonomy object |
| sim.extant.samples | Include extant samples in the fossil object, with optional... |
| sim.fbd.age | sim.fbd.age: Simulating fossilized birth-death trees of a... |
| sim.fbd.rateshift.taxa | sim.fbd.rateshift.taxa: Simulating fossilized birth death... |
| sim.fbd.taxa | sim.fbd.taxa: Simulating fossilized birth-death trees on a... |
| sim.fossils.environment | Simulate fossils under an environment-dependent model of... |
| sim.fossils.intervals | Simulate fossils under a non-uniform model of preservation... |
| sim.fossils.poisson | Simulate fossils under a Poisson sampling model |
| sim.gradient | Simulate an environmental gradient |
| sim.interval.ages | Reassign fossil ages to user-specified stratigraphic... |
| sim.taxonomy | Simulate taxonomy |
| sim.tip.samples | Include extant and extinct tip samples in the fossil object,... |
| sim.trait.values | Simulate trait values with variation across lineages |
| species.end | Find a species' end (i.e extinction) time from a taxonomy... |
| species.start | Find a species' start (i.e speciation) time from a taxonomy... |
| subsample.fossils.oldest | Obtain a subsample of fossil occurrences containing the... |
| subsample.fossils.oldest.and.youngest | Obtain a subsample of fossil occurrences containing the... |
| subsample.fossils.uniform | Obtain a uniform random sample of fossil occurrences. |
| subsample.fossils.youngest | Obtain a subsample of fossil occurrences containing the... |
| summary.taxonomy | Display taxonomy object |
| taxonomy | Taxonomy object |
| tree.max | Find the maximum age in a phylo object (root age or origin... |
