Simulation and Plots for Fossil and Taxonomy Data
Transforms a tree and fossils into a sampled tree in beast-usable form...
Count the total number of fossils per interval
Count the total number of fossils
Creates an fbdrange object from provided tree and data
Fossils object
Create a set of BEAST2 constraints to construct a DPPDIV style fixed e...
Create a suitable starting tree for a DPPDIV style FBD analysis in BEA...
Transforms a fossils dataframe and either taxonomy or tree into a foss...
Generate output in the format used by the program PyRate
FossilSim: A package for simulating and plotting fossil and taxonomy d...
Import fbdrange object from file
Obtain the tips that define each node in a tree
Transforms a fossilRecordSimulation object from package paleotree to a...
Place fossil samples from one tree in another tree, or find the ancest...
Plot oriented tree with stratigraphic ranges
Plot simulated fossils
Plot simulated taxonomy
Remove fossil lineages from a tree
Removes all intermediate fossils from a combined tree and labels the f...
Make an asymmetric stratigraphic range plot from a tree object of clas...
Reconcile existing fossil and taxonomy objects
Returns tree and fossil objects that you can use to plot the reconstru...
Remove fossil samples that occur in the stem
Remove stem lineages from a tree.
Removes all unsampled lineages from a combined tree. Extinct tips are ...
Transforms a tree and fossils dataframe to a combined SA tree. Sampled...
Tree with sampled ancestors represented as zero-length edges
Simulate anagenetic species on a taxonomy object
Simulate cryptic species on a taxonomy object
Include extant samples in the fossil object, with optional rho samplin...
sim.fbd.age: Simulating fossilized birth-death trees of a fixed age.
sim.fbd.rateshift.taxa: Simulating fossilized birth death trees incorp...
sim.fbd.taxa: Simulating fossilized birth-death trees on a fixed numbe...
Simulate fossils under an environment-dependent model of preservation ...
Simulate fossils under a non-uniform model of preservation for a given...
Simulate fossils under a Poisson sampling model
Simulate an environmental gradient
Reassign fossil ages to user-specified stratigraphic intervals
Simulate taxonomy
Include extant and extinct tip samples in the fossil object, with opti...
Simulate trait values with variation across lineages
Find a species' end (i.e extinction) time from a taxonomy object
Find a species' start (i.e speciation) time from a taxonomy object
Obtain a subsample of fossil occurrences containing the oldest and you...
Obtain a subsample of fossil occurrences containing the oldest fossil ...
Obtain a uniform random sample of fossil occurrences.
Obtain a subsample of fossil occurrences containing the youngest fossi...
Display taxonomy object
Taxonomy object
Find the maximum age in a phylo object (root age or origin time)
Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.