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Published March 23, 2021 | Version v3.2.0
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rsetienne/DAISIE: v3.2.0

  • 1. @tece-lab, University of Groningen
  • 2. University of Groningen

Description

N.B.: MacOS users may experience issues when installing DAISIE, especially when on MacOS Big Sur. If that is you case, please see here for detailed installation instructions.

Changes
  • DAISIE_loglikg_IW() is now more efficient and numerically stable. Numerical integration is now done via C++ with package odeint.
  • Add relaxed rate capabilities (both inference and simulations). Relaxed rate models allow for parameters to not be static, but to be sampled by specific probability distributions.
  • Introduce MinAge data status in DAISIE data objects. A status containing MinAge sets a lower boundary for colonization in situations when the precise colonization time is unknown. This is interpreted by DAISIE_dataprep() so that the information is passed on to the likelihood optimization functions. See the DAISIE_dataprep() help page for more details. In the back-end this results in new stac values 8 and 9.
  • Bug fix of "bug 2" in the bug report manuscript. This bug was present in DAISIE_ONEcolonist() when recolonization occurs. It has now been fixed so that the colonization and branching times are stored in the way that we now think is the best for it to be dealt with in the likelihood code. In recolonization cases, $other_clades_same_ancestor renamed to $all_colonisations. #125
  • Fix bug which occurs rarely, when computing log conditional probabilities. Only applicable to ML code running with cond.
  • Removed deprecated legacy functions. Removed all functions named DAISIE_*_VERSION_NUMBER() and all DAISIE_calc_*_rate() funcions and get_brts_mya(). #126
  • Made some functions internal, as they should be. DAISIE_make_global() and create_island() are now internal. #127
  • @HHildenbrandt is now an author.
  • Added @xieshu95's and @joshwlambert's ORCIDs.
  • Added a NEWS.md file to track changes to the package.

Files

rsetienne/DAISIE-v3.2.0.zip

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