Pas-Kapli / mptp

mPTP - a tool for single-locus species delimitation
GNU Affero General Public License v3.0
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Implement basic bayesian method #19

Closed xflouris closed 8 years ago

xflouris commented 9 years ago

Implement a Bayesian approach to estimating the prior distribution using a uniform hyperprior

We have decided to focus on a very basic bayesian space exploration for now as described in many textbooks:

  1. Generate an initial delimitation.
  2. throw a coin to decide whether we are (a) turning a speciation node to a coalescent or (b) a coalescent root to a speciation.
  3. Select a node from either (a) the list of speciation nodes or (b) the list of coalescent roots
  4. Change it to a speciation or coalescent node, and compute the new likelihood
  5. Based on the Metropolis-Hastings ratio compute the probability of accepting this new delimitation
  6. generate a random number between 0 and 1 to decide whether to accept this new delimitation
  7. repeat from 2

We will implement both version (multi and single)

xflouris commented 8 years ago

finished.