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plot.fossils now integrates an optional extant sampling probability (rho) when plotting the reconstructed treeplot.fossils to make the axis more visibleplot.fossils and plot.taxonomy are no longer random and can be customizedsim.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.TreeSim was moved from dependencies to suggested packages. A separate installation of TreeSim is now required to run functions sim.fbd.*sim.fossils.environment now takes an argument use.exact.times which determines if fossil sampling times are recorded exactly or based on interval boundsplot.fossils and plot.taxonomy which would not restore plotting parameters properly in some cases.sim.fbd.taxa, sim.fbd.age) to clarify the sampling process when complete = FALSEsim.trait.values.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.reconstructed = TRUE to plot.fossils or the objects can be generated separately using the function reconstructed.tree.fossils.objects.fossils as a function argument to the fossil simulation functions so that existing fossil objects can be appended.ignore.taxonomy as a function argument to the fossil simulation functions. If true function will not return species or edge info.show.unknown to plotting function. If species or edge info is unknown these fossils will appear next to the tree.plot.fossils which led to proxy data being plotted the wrong way round on the x-axis.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.fossils.to.pyrate can be used to convert objects generated by this package into PyRate format.fossils.to.BEAST.constraints and fossils.to.BEAST.start.tree.Rd can be used to convert objects generated by this package into BEAST2 format.subsample.fossils.oldest, subsample.fossils.oldest.and.youngest, subsample.fossils.uniform and subsample.fossils.youngest can be used to subsample fossil occurrences.sim.trait.values. Parameters are unchanged.rangeplot.asymmetric and separated from the SAtree objects.rangeplot.asymmetric that could lead to crashes or plots with missing edges.SAtree.from.fossils where SAtree objects were not created properly when using an empty fossils object.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.