Contents | Preface | Dependencies | R | Dependencies for building a Shiny server from source | R packages we need | Installing Shiny Server | Putting the app on the server | Firewall tweaks | Starting Shiny Server | Further Reading

Contents | Launching the app | Phylogenetic Tree | Generating a tree | Importing a tree from Newick format | Generating Taxonomy | Simulating Fossils | Saving your tree as a .png | Last words | Additional information

Zero-edge format | Converting to SAtree | Other useful functions

Contents | Background and motivation | Installing the package | Package dependencies | Calling functions from FossilSim and other packages | Quick start | FossilSim input | FossilSim output | What next?

ML.MSBD package | Running an inference | Likelihood calculation

sim.fbd functions | Simulating trees from a time-homogeneous fossilized-birth death process | Simulating trees from an episodic fossilized-birth death process

Compatibility with paleotree

Contents | The fossils object | Constant fossil recovery | Simulating fossils for a tree object | Simulating fossils for a taxonomy object | Interval-dependent fossil recovery | Simulating fossils for a fixed number of intervals | Simulating fossils for a set of non-uniform intervals | Simulating fossils using per-interval probabilities | Incorporating stratigraphic age uncertainty | Environment-dependent fossil recovery | Lineage-dependent fossil recovery | The autocorrelated fossil recovery model | The independent fossil recovery model | Environment and lineage-dependent fossil recovery | Extant species and tip sampling | See also | References

Contents | The taxonomy object | See also | References