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Adds a dedicated verification
folder containing only the Matlab code
needed to verify Lumiere with an implementation independent of Beast.
Run verification.m
to output the MFBD likelihood for a simple, but
non-trivial case of a phylogenetic tree with only two tips, and export
a Beast input file beast_config.xml
with the same parameters that can
be run with Lumiere to compare the result.
The code here is based on the content of the sim
folder. Components
not needed for this verification were removed. The remaining code was
cleaned up and refactored.
Functional changes:
beast.util
,
which might be exactly the same, though Matlab also has 'simdTwister'
a.k.a. "SIMD-oriented Fast Mersenne Twister", so this can be questioned.Refactoring changes include:
{{alignment}}
. This makes the code that exports the Beast
file more flexible and robust. Also avoid creating other output
files that are never actually needed.handle
.
This lets us use a sane method call syntax such as obj.set(value)
.
With Matlab's default class implementation, objects are (inexplicably)
immutable, which leads to unnecessarily confusing syntax like
obj = set(obj, value)
.string
type (marked by literals in
"double quotes"
) rather than the traditional character vector (literals
in 'single quotes'
) as much as possible. It's the better abstraction
for strings and was arguably introduced when MathWorks finally realized
that Matlab sucks at handling strings.