Published March 23, 2021
| Version v3.2.0
Software
Open
rsetienne/DAISIE: v3.2.0
Creators
- 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.
ChangesDAISIE_loglikg_IW()
is now more efficient and numerically stable. Numerical integration is now done via C++ with packageodeint
.- 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 containingMinAge
sets a lower boundary for colonization in situations when the precise colonization time is unknown. This is interpreted byDAISIE_dataprep()
so that the information is passed on to the likelihood optimization functions. See theDAISIE_dataprep()
help page for more details. In the back-end this results in newstac
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 allDAISIE_calc_*_rate()
funcions andget_brts_mya()
. #126 - Made some functions internal, as they should be.
DAISIE_make_global()
andcreate_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
Files
(1.1 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/rsetienne/DAISIE/tree/v3.2.0 (URL)