Changes in version 2.4.4 (2026-02-26)                  

  - some dependencies were made optional to make installation easier

                 Changes in version 2.4.3 (2025-11-06)                  

  - technical changes for compatibility with the new ggtree version.

                 Changes in version 2.4.2 (2025-10-28)                  

Bug fixes

  - fixed an issue leading to duplicated tip IDs in SAtree.from.fossils
  - fixed a bug with the prune.fossil.tips function in trees with edges
    of length 0

New functionality

  - added ordering options to SAtree.from.fossils to choose whether
    fossils are ordered from the youngest or oldest
  - added option for custom X axis label in plot.fossils

                 Changes in version 2.4.1 (2024-10-02)                  

  - fixed dependency issues due to the new ggtree version

                 Changes in version 2.4.0 (2024-09-05)                  

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

                 Changes in version 2.3.3 (2024-04-29)                  

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

                 Changes in version 2.3.2 (2023-10-05)                  

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.*

                 Changes in version 2.3.1 (2022-07-19)                  

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

                 Changes in version 2.3.0 (2022-04-19)                  

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.

                 Changes in version 2.2.0 (2021-04-05)                  

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.

                 Changes in version 2.1.1 (2019-02-21)                  

  - 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.

                 Changes in version 2.1.0 (2018-11-16)                  

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.