NEWS.md

In FossilSim: Simulation of Fossil and Taxonomy Data

Version 2.3.2

New functionality

• sim.tip.samples and sim.extant.samples can now use tip-specific sampling probabilities by setting argument rho to a vector of values instead of a single value.

Technical changes

• package TreeSim was moved from dependencies to suggested packages. A separate installation of TreeSim is now required to run functions sim.fbd.*

Version 2.3.1

New functionality

• sim.fossils.environment now takes an argument use.exact.times which determines if fossil sampling times are recorded exactly or based on interval bounds

Bug fixes

• Fixed a bug in plot.fossils and plot.taxonomy which would not restore plotting parameters properly in some cases.

Documentation changes

• Updated the documentation of FBD simulation functions (sim.fbd.taxa, sim.fbd.age) to clarify the sampling process when complete = FALSE

Version 2.3.0

New functionality

• Added Lewis Mk, BM (Brownian motion) and OU (Ornstein-Uhlenbeck) models as options to simulate traits in function sim.trait.values.

Function changes

• SAtree.from.fossils now returns a list of tree (the resulting SA tree) and fossils (the original fossils data.frame updated to include the tip label of each fossil in the SA tree). NB: this change breaks compatibility with previous versions of the function.

Version 2.2.0

New functionality

• Added option to plot the reconstructed tree for a set of fossils and tree objects. This can be done by passing reconstructed = TRUE to plot.fossils or the objects can be generated separately using the function reconstructed.tree.fossils.objects.

Functions associated with the occurrence birth-death model

• Added fossils as a function argument to the fossil simulation functions so that existing fossil objects can be appended.
• Added ignore.taxonomy as a function argument to the fossil simulation functions. If true function will not return species or edge info.
• Added show.unknown to plotting function. If species or edge info is unknown these fossils will appear next to the tree.

Bug fixes

• Fixed bug in plot.fossils which led to proxy data being plotted the wrong way round on the x-axis.

Version 2.1.1

• Fixed a bug in sim.fbd.rateshift.taxa which led to trees being simulated with the wrong rates. NB: Any dataset simulated with this function before the fix is invalid and needs to be rerun.

Version 2.1.0

New functionality

• The new function fossils.to.pyrate can be used to convert objects generated by this package into PyRate format.
• The new functions fossils.to.BEAST.constraints and fossils.to.BEAST.start.tree.Rd can be used to convert objects generated by this package into BEAST2 format.
• The new functions subsample.fossils.oldest, subsample.fossils.oldest.and.youngest, subsample.fossils.uniform and subsample.fossils.youngest can be used to subsample fossil occurrences.

Function changes

• The innovative rates model has been integrated into the independent model in the function sim.trait.values. Parameters are unchanged.
• The asymmetric plot function has been renamed rangeplot.asymmetric and separated from the SAtree objects.

Bugfixes

• Fixed several bugs in rangeplot.asymmetric that could lead to crashes or plots with missing edges.
• Fixed a bug in SAtree.from.fossils where SAtree objects were not created properly when using an empty fossils object.

FossilSim documentation built on Oct. 5, 2023, 5:08 p.m.