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[BUG] Cannot comupte probability with dnMultiSpeciesCoalescentUniformPrior #470

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thauffe opened this issue May 15, 2024 · 0 comments
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@thauffe
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thauffe commented May 15, 2024

Describe the bug

The probability of the tree object returned by the function dnMultiSpeciesCoalescentUniformPrior cannot be calculated.

To Reproduce

seed(73)
n_species <- 10
n_alleles <- 3

# species names
for (i in 1:n_species) {
    species[i] <- taxon(taxonName="Species_"+i, speciesName="Species_"+i)
}

# simulate an ultrametric species tree
spTree ~ dnBirthDeath(lambda=0.3, mu=0.2, rootAge=10, rho=1, samplingStrategy="uniform", condition="nTaxa", taxa=species)

# constant parameters for the inverse gamma distribution:
alpha <- abs(3.0)
beta <- abs(0.001)

#### taxa names
for (i in 1:n_species) {
    for (j in 1:n_alleles) {
        taxons[(i-1)*n_alleles+j] <- taxon(taxonName="Species_"+i+"_"+j, speciesName="Species_"+i)
    }
}

# simulate gene tree
geneTrees ~ dnMultiSpeciesCoalescentUniformPrior(speciesTree=spTree, max = 50, taxa=taxons)

# get probability
geneTrees.lnProbability()

Expected behavior

Returning a log probability

Screenshots

MSC_RB12

Computer info

Arch-based Linux with RB 1.2.3 (rapture-2578-gfc964c) compiled from scratch

Additional context
The reproducible example works for me under RB 1.1
MSC_RB11

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