Last data update: 2014.03.03

 R: Moment Fractional Bayes Factor Stochastic Search with Local...
FBF_LSR Documentation

Moment Fractional Bayes Factor Stochastic Search with Local Prior for DAG Models

Description

Estimate the edge inclusion probabilities for a directed acyclic graph (DAG) from observational data, using the moment fractional Bayes factor approach with local prior.

Usage

FBF_LS(Corr, nobs, G_base, h, C, n_tot_mod)

Arguments

Corr

qxq correlation matrix.

nobs

Number of observations.

G_base

Base DAG.

h

Parameter prior.

C

Costant who keeps the probability of all local moves bounded away from 0 and 1.

n_tot_mod

Maximum number of different models which will be visited by the algorithm, for each equation.

Value

An object of class matrix with the estimated edge inclusion probabilities.

Author(s)

Davide Altomare (davide.altomare@gmail.com).

References

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

M_q=FBF_LS(Corr, nobs, matrix(0,q,q), 0, 0.01, 1000)

G_med=M_q
G_med[M_q>=0.5]=1
G_med[M_q<0.5]=0 #median probability DAG

sum(sum(abs(G_med-Gt))) #Structural Hamming Distance between the true DAG and the median 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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(FBFsearch)
Loading required package: Rcpp
Loading required package: RcppArmadillo
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/FBFsearch/FBF_LS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FBF_LS
> ### Title: Moment Fractional Bayes Factor Stochastic Search with Local
> ###   Prior for DAG Models
> ### Aliases: FBF_LS
> ### Keywords: multivariate models dag stochastic search
> 
> ### ** Examples
> 
> 
> data(SimDag6) 
> 
> Corr=dataSim6$SimCorr[[1]]
> nobs=50
> q=ncol(Corr)
> Gt=dataSim6$TDag
> 
> M_q=FBF_LS(Corr, nobs, matrix(0,q,q), 0, 0.01, 1000)

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; 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)
> 
> G_med=M_q
> G_med[M_q>=0.5]=1
> G_med[M_q<0.5]=0 #median probability DAG
> 
> sum(sum(abs(G_med-Gt))) #Structural Hamming Distance between the true DAG and the median probability DAG
[1] 0
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO