Man pages for rachelwarnock/fossilsim
Simulation of 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
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.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.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
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...
rachelwarnock/fossilsim documentation built on Nov. 11, 2018, 4:01 a.m.