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v4.2.0

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@Neves-P Neves-P released this 30 May 16:36
· 279 commits to master since this release
57d347a

DAISIE 4.2.0

  • Important bugfixes on estimation when data contains a lineage or a clade for
    which (see stac_key vignette for details on each case):
    • The divergence time is unknown but known to have occurred after a
      specific point in time in the island's existence.
    • The divergence time is unknown but known to have occurred before a
      specific point in time in the island's existence (usually known when dated
      population level phylogenetic data is available).
  • Improve and finalise the continental island estimation scenario, when there
    are initially species present on the island on inception.
  • Improve tests related to the two points above.
  • Remove DAISIE time dependent estimation code for now to ease work on the remaining
    code. Development will proceed separately.
  • Rate computations in simulation are first calculated per lineage, to then be
    calculated per island. This will be needed for time dependent estimation later on.
  • Improve zenodo metadata.
  • Add methode = "odeint::adams_bashforth_moulton_X" to the list of available
    numeric integrators for parameter estimation.