FossilSim               FossilSim: A package for simulating and
                        plotting fossil and taxonomy data
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.
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
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
get.tip.descs           Obtain the tips that define each node in a tree
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.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
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.
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)
