NEWS

FossilSim 2.4.1 (2024-10-02)

added a new structure, the fbdrange object, to store the results of FBD-range inferences with budding (e.g. the output of the sRanges package for BEAST2)
added plotting for fbdrange objects, showing the oriented tree with stratigraphic ranges

improved checks on fossils object so invalid data types are rejected instead of crashing
removed alphanumeric option from paleotree.record.to.fossils as it was incompatible with the fix to data types

plot.fossils now integrates an optional extant sampling probability (rho) when plotting the reconstructed tree

cosmetic changes to plot.fossils to make the axis more visible
colours used for the taxonomy in plot.fossils and plot.taxonomy are no longer random and can be customized

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.

package 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 bounds

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

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

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

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.

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.

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

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.

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.

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.

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.