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NEWS.md

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Version 2.4.1

  • fixed dependency issues due to the new ggtree version

Version 2.4.0

New functionality

  • 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

Bug fixes

  • 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

Version 2.3.3

New functionality

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

Function changes

  • 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

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.