Simulation of Fossil and Taxonomy Data

[Up] [Top]

Documentation for package ‘FossilSim’ version 2.3.3

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
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
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.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)