Man pages for fossilsim/fossilsim
Simulation and Plots for Fossil and Taxonomy Data

beast.fbd.formatTransforms a tree and fossils into a sampled tree in...
count.fossilsCount the total number of fossils
count.fossils.binnedCount the total number of fossils per interval
fbdrangeCreates an fbdrange object from provided tree and data
fossilsFossils object
FossilSimFossilSim: A package for simulating and plotting fossil and...
fossils.to.BEAST.constraintsCreate a set of BEAST2 constraints to construct a DPPDIV...
fossils.to.BEAST.start.treeCreate a suitable starting tree for a DPPDIV style FBD...
fossils.to.paleotree.recordTransforms a fossils dataframe and either taxonomy or tree...
fossils.to.pyrateGenerate output in the format used by the program PyRate
get_fbdrange_from_fileImport fbdrange object from file
get.tip.descsObtain the tips that define each node in a tree
paleotree.record.to.fossilsTransforms a fossilRecordSimulation object from package...
place.fossilsPlace fossil samples from one tree in another tree, or find...
plot.fbdrangePlot oriented tree with stratigraphic ranges
plot.fossilsPlot simulated fossils
plot.taxonomyPlot simulated taxonomy
prune.fossilsRemoves all intermediate fossils from a combined tree and...
prune.fossil.tipsRemove fossil lineages from a tree
rangeplot.asymmetricMake an asymmetric stratigraphic range plot from a tree...
reconcile.fossils.taxonomyReconcile existing fossil and taxonomy objects
reconstructed.tree.fossils.objectsReturns tree and fossil objects that you can use to plot the...
remove.stem.fossilsRemove fossil samples that occur in the stem
remove.stem.lineagesRemove stem lineages from a tree.
sampled.tree.from.combinedRemoves all unsampled lineages from a combined tree. Extinct...
SAtreeTree with sampled ancestors represented as zero-length edges
SAtree.from.fossilsTransforms a tree and fossils dataframe to a combined SA...
sim.anagenetic.speciesSimulate anagenetic species on a taxonomy object
sim.cryptic.speciesSimulate cryptic species on a taxonomy object
sim.extant.samplesInclude extant samples in the fossil object, with optional...
sim.fbd.agesim.fbd.age: Simulating fossilized birth-death trees of a...
sim.fbd.rateshift.taxasim.fbd.rateshift.taxa: Simulating fossilized birth death...
sim.fbd.taxasim.fbd.taxa: Simulating fossilized birth-death trees on a...
sim.fossils.environmentSimulate fossils under an environment-dependent model of...
sim.fossils.intervalsSimulate fossils under a non-uniform model of preservation...
sim.fossils.poissonSimulate fossils under a Poisson sampling model
sim.gradientSimulate an environmental gradient
sim.interval.agesReassign fossil ages to user-specified stratigraphic...
sim.taxonomySimulate taxonomy
sim.tip.samplesInclude extant and extinct tip samples in the fossil object,...
sim.trait.valuesSimulate trait values with variation across lineages
species.endFind a species' end (i.e extinction) time from a taxonomy...
species.startFind a species' start (i.e speciation) time from a taxonomy...
subsample.fossils.oldestObtain a subsample of fossil occurrences containing the...
subsample.fossils.oldest.and.youngestObtain a subsample of fossil occurrences containing the...
subsample.fossils.uniformObtain a uniform random sample of fossil occurrences.
subsample.fossils.youngestObtain a subsample of fossil occurrences containing the...
summary.taxonomyDisplay taxonomy object
taxonomyTaxonomy object
tree.maxFind the maximum age in a phylo object (root age or origin...
fossilsim/fossilsim documentation built on Sept. 8, 2024, 4:32 a.m.