VMCMC specifications

Information


Unique identifier OMICS_15716
Name VMCMC
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Takes as input Markov Chain Monte Carlo (MCMC) traces from various softwares.
Operating system Unix/Linux
Programming languages Java
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Lars Arvestad <>

Publication for VMCMC

VMCMC in publications

 (2)
PMCID: 5624502
PMID: 28983516
DOI: 10.1038/s41559-017-0280-x

[…] the markov chain is less efficient in traversing the posterior space. more formally, we use the mean of the mcmc sample (x̃) to estimate the posterior mean of any parameter. this has the variance (8)vmcmc=vind×[1+2(ρ1+ρ2+…)], where νind is the variance for an independent sample of the same size from the posterior distribution, and where ρk = corr(xt, xt + k) is the correlation between the values […]

PMCID: 5123345
PMID: 28185583
DOI: 10.1186/s12859-016-1268-2

[…] , three different convergence diagnostics were used to check for non-convergence of mcmc chains: geweke [], gelman-rubin [], and estimated sample size (ess) [], using vmcmc []. a burnin was chosen, for each mcmc trace, using the max-ess estimator []. each mcmc chain was run for 5·106 iterations and a thinning factor of 500 was used., to evaluate our method, […]


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VMCMC funding source(s)
This work was supported by the Higher Education Commission (HEC) of Pakistan, EuroSPIN (an Erasmus Mundus joint doctoral program) and Swedish e-Science Research Center (SeRC).

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