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fbdrange object, to store
the results of FBD-range inferences with budding (e.g. the output of the
sRanges package for BEAST2)fbdrange objects, showing the
oriented tree with stratigraphic rangesfossils object so invalid data types
are rejected instead of crashingalphanumeric option from
paleotree.record.to.fossils as it was incompatible with the
fix to data typesplot.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.