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initializeSMARTchain

initializeSMARTchain[inputsnpls, nsq, nbp, initheta, inirho, inieps]
generates initial values for one MCMC chain, and returns {{theta, epsilon, rho}, treels, adpaptive parameters, snpls}. In the last column of snpls, the log likelihood given the initialized treels over-writes the values in inputsnpls.
  • The initheta = {shape, scale, min, max}, and the initial theta is sampled from the GammaDistribution [shape, scale], truncated to be in the range [min,max]. If scale=Infinity, it becomes the UniformDistribution [min, max].
  • The inirho = {shape, scale, min, max}, and the initial rho is sampled from the GammaDistribution [shape, scale], truncated to be in the range [min,max]. If scale=Infinity, it becomes the UniformDistribution [min, max].
  • The iniepsilon = {alpha, beta, min, max}, and the initial epsilon is sampled from the BetaDistribution [alpha, beta], truncated to be in the range [min,max].