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  • b1a1cf6c55edb267e0d2ad07bf620ed6acfc1acd
  • master default protected
  • fossilBM
  • mcmc.revell
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Created with Raphaël 2.2.07Aug15Jul1417Jun29May28adding a README filemastermasterNew version of the MCMC with the old lnLike function within Liam Revell code for the MCMCmcmc.revellmcmc.revellSolved an issue with the passing of ancestral states to the likelihood function. It now solves the overestimation of the sigma2 under MCMC...fossilBMfossilBMJonathan started to add the fossil constrains in the codeAdded Gibbs sampling instead of M-H sampling for the ancestral nodesFunctional version that estimates the ancestral states instead of using the contrast approach. MCMC implementation also availableInitial test by setting the internal nodes as variables in the estimation of BM. Seems to work so far.final version that works and is up-to-dateThere are mistakes in the formula from Novembre and Slatkin 2008. I changed the modification of S and the weighted average. Now it gives perfectly similar values than with the multinormal densityWorking now when assuming that the internal nodes are weighted averages from the two descendants. Crazy speed-ups vs fitBM...added a new function to calculate the probability with a known ancestor at a nodeadding some function to compute the likelihood of a continuous character under BM using the pruning algorithm