# Simulation and Plots for Fossil and Taxonomy Data

## Documentation for package ‘FossilSim’ version 2.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

FossilSim-package | FossilSim: A package for simulating and plotting fossil and taxonomy data
as.fossils | Fossils object
as.taxonomy | Taxonomy object
beast.fbd.format | Transforms a tree and fossils into a sampled tree in beast-usable format and writes it in Newick format. Designed to work with FBD.
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
fossils.to.BEAST.constraints | Create a set of BEAST2 constraints to construct a DPPDIV style fixed extant topology FBD analysis
fossils.to.BEAST.start.tree | Create a suitable starting tree for a DPPDIV style FBD analysis in BEAST2
fossils.to.paleotree.record | Transforms a fossils dataframe and either taxonomy or tree into a fossilRecordSimulation object from package paleotree.
fossils.to.pyrate | Generate output in the format used by the program PyRate
FossilSim | FossilSim: A package for simulating and plotting fossil and taxonomy data
get.tip.descs | Obtain the tips that define each node in a tree
get_fbdrange_from_file | Import fbdrange object from file
is.fossils | Fossils object
is.taxonomy | Taxonomy object
paleotree.record.to.fossils | Transforms a fossilRecordSimulation object from package paleotree to a tree and taxonomy and fossils objects.
place.fossils | Place fossil samples from one tree in another tree, or find the ancestral node for each fossil sample in one tree.
plot.fbdrange | Plot oriented tree with stratigraphic ranges
plot.fossils | Plot simulated fossils
plot.taxonomy | Plot simulated taxonomy
prune.fossil.tips | Remove fossil lineages from a tree
prune.fossils | Removes all intermediate fossils from a combined tree and labels the first and last fossils of each lineage. Can be used with sampled or complete trees. If only one fossil is present for a particular species it is labelled as first.
rangeplot.asymmetric | Make an asymmetric stratigraphic range plot from a tree object of class phylo
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 reconstructed tree.
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 tips are only sampled if they are fossils. With default settings all extant tips are sampled.
SAtree | Tree with sampled ancestors represented as zero-length edges
SAtree.from.fossils | Transforms a tree and fossils dataframe to a combined SA tree. Sampled ancestors are represented as tips on zero-length edges to maintain compatibility with the ape format. Tip labels are set to "species id"_"index", where the most recent tip of a given species receives index 1 and indices increase towards the past.
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 rho sampling.
sim.fbd.age | sim.fbd.age: Simulating fossilized birth-death trees of a fixed age.
sim.fbd.rateshift.taxa | sim.fbd.rateshift.taxa: Simulating fossilized birth death trees incorporating rate shifts.
sim.fbd.taxa | sim.fbd.taxa: Simulating fossilized birth-death trees on a fixed number of extant taxa.
sim.fossils.environment | Simulate fossils under an environment-dependent model of preservation (Holland, 1995)
sim.fossils.intervals | Simulate fossils under a non-uniform model of preservation for a given set of consecutive time intervals
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 intervals
sim.taxonomy | Simulate taxonomy
sim.tip.samples | Include extant and extinct tip samples in the fossil object, with optional rho sampling.
sim.trait.values | Simulate trait values with variation across lineages
species.end | Find a species' end (i.e extinction) time from a taxonomy object
species.start | Find a species' start (i.e speciation) time from a taxonomy object
subsample.fossils.oldest | Obtain a subsample of fossil occurrences containing the oldest fossil sample in each node of the tree.
subsample.fossils.oldest.and.youngest | Obtain a subsample of fossil occurrences containing the oldest and youngest fossil sample found at each node of the tree.
subsample.fossils.uniform | Obtain a uniform random sample of fossil occurrences.
subsample.fossils.youngest | Obtain a subsample of fossil occurrences containing the youngest fossil sample in each node of the tree.
summary.taxonomy | Display taxonomy object
taxonomy | Taxonomy object
tree.max | Find the maximum age in a phylo object (root age or origin time)