R: Moment Fractional Bayes Factor Stochastic Search with Global...
FBF_GS
R Documentation
Moment Fractional Bayes Factor Stochastic Search with Global Prior for Gaussian DAG Models
Description
Estimate the edge inclusion probabilities for a Gaussian DAG with q nodes from observational data, using the moment fractional Bayes factor approach with global prior.
D. Altomare, G. Consonni and L. La Rocca (2013). Objective Bayesian search of Gaussian directed acyclic graphical models for ordered variables with non-local priors. Biometrics.
Examples
data(SimDag6)
Corr=dataSim6$SimCorr[[1]]
nobs=50
q=ncol(Corr)
Gt=dataSim6$TDag
Res_search=FBF_GS(Corr, nobs, matrix(0,q,q), 1, 0.01, 1000, 10)
M_q=Res_search$M_q
M_G=Res_search$M_G
M_P=Res_search$M_P
G_med=M_q
G_med[M_q>=0.5]=1
G_med[M_q<0.5]=0 #median probability DAG
G_high=M_G[1:q,1:q] #Highest Posterior Probability DAG (HPP)
pp_high=M_P[1] #Posterior Probability of the HPP
sum(sum(abs(G_med-Gt))) #Structural Hamming Distance between the true DAG and the median probability DAG
sum(sum(abs(G_high-Gt))) #Structural Hamming Distance between the true DAG and the highest probability DAG
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(FBFsearch)
Loading required package: Rcpp
Loading required package: RcppArmadillo
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/FBFsearch/FBF_GS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FBF_GS
> ### Title: Moment Fractional Bayes Factor Stochastic Search with Global
> ### Prior for Gaussian DAG Models
> ### Aliases: FBF_GS
> ### Keywords: multivariate models dag stochastic search
>
> ### ** Examples
>
>
> data(SimDag6)
>
> Corr=dataSim6$SimCorr[[1]]
> nobs=50
> q=ncol(Corr)
> Gt=dataSim6$TDag
>
> Res_search=FBF_GS(Corr, nobs, matrix(0,q,q), 1, 0.01, 1000, 10)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
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warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
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warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
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warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
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warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
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warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
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warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
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warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed; change inv(sympd(X)) to inv_sympd(X)
warning: sympd() is deprecated and will be removed;