HHSD is a python pipeline for hierarchical heuristic species delimitation using genomic sequence data under the multispecies coalescent model. It drives data analysis using the program bpp.
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Rework to gdi estimation and gdi_threshold syntax #7
1) The gdi is now estimated using a Monte Carlo algorithm that samples 1000 values from the posterior of the numeric parameters $\Theta$. This allows us to give a a more accurate estimation of $P(gdi|\Theta)$. The reported mean and 2.5% + 97.5% HPD gdi values are now calculated from this distribution, rather than crudely derived from point estimates on the parameters $\Theta$.
2) The user is able to specify concretely how differences in the gdi values of a population pair should be reconciled using the gdi_threshold parameter. Possible examples include:
gdi_threshold = leq 0.2, leq 1.0, which specifies that a merge will be accepted if at least one gdi is <=0.2, while the second gdi can be anything.
gdi_threshold = gt 0.7, gt 0.7, which specifies that a split will be accepted only if both gdi values are > 0.7
3) The manual was updated, and a new example dataset replaces the old datasets.
1) The gdi is now estimated using a Monte Carlo algorithm that samples 1000 values from the posterior of the numeric parameters $\Theta$. This allows us to give a a more accurate estimation of $P(gdi|\Theta)$. The reported mean and 2.5% + 97.5% HPD gdi values are now calculated from this distribution, rather than crudely derived from point estimates on the parameters $\Theta$.
2) The user is able to specify concretely how differences in the gdi values of a population pair should be reconciled using the
gdi_thresholdparameter. Possible examples include:gdi_threshold = leq 0.2, leq 1.0, which specifies that a merge will be accepted if at least one gdi is <=0.2, while the second gdi can be anything.gdi_threshold = gt 0.7, gt 0.7, which specifies that a split will be accepted only if both gdi values are > 0.73) The manual was updated, and a new example dataset replaces the old datasets.