BayesFactor {LaplacesDemon}  R Documentation 
Bayes Factor
Description
This function calculates Bayes factors for two or more fitted objects
of class demonoid
, iterquad
, laplace
, pmc
,
or vb
that were estimated respectively with the
LaplacesDemon
, IterativeQuadrature
,
LaplaceApproximation
, PMC
, or
VariationalBayes
functions, and indicates the strength
of evidence in favor of the hypothesis (that each model,
\mathcal{M}_i
, is better than another model,
\mathcal{M}_j
).
Usage
BayesFactor(x)
Arguments
x 
This is a list of two or more fitted objects of class

Details
Introduced by Harold Jeffreys, a 'Bayes factor' is a Bayesian
alternative to frequentist hypothesis testing that is most often used
for the comparison of multiple models by hypothesis testing, usually
to determine which model better fits the data (Jeffreys, 1961). Bayes
factors are notoriously difficult to compute, and the Bayes factor is
only defined when the marginal density of \textbf{y}
under
each model is proper (see is.proper
). However, the Bayes
factor is easy to approximate with the LaplaceMetropolis estimator
(Lewis and Raftery, 1997) and other methods of approximating the
logarithm of the marginal likelihood (for more information, see
LML
).
Hypothesis testing with Bayes factors is more robust than frequentist hypothesis testing, since the Bayesian form avoids model selection bias, evaluates evidence in favor of the null hypothesis, includes model uncertainty, and allows nonnested models to be compared (though of course the model must have the same dependent variable). Also, frequentist significance tests become biased in favor of rejecting the null hypothesis with sufficiently large sample size.
The Bayes factor for comparing two models may be approximated as the ratio of the marginal likelihood of the data in model 1 and model 2. Formally, the Bayes factor in this case is
B =
\frac{p(\textbf{y}\mathcal{M}_1)}{p(\textbf{y}\mathcal{M}_2)} =
\frac{\int
p(\textbf{y}\Theta_1,\mathcal{M}_1)p(\Theta_1\mathcal{M}_1)d\Theta_1}{\int
p(\textbf{y}\Theta_2,\mathcal{M}_2)p(\Theta_2\mathcal{M}_2)d\Theta_2}
where p(\textbf{y}\mathcal{M}_1)
is the marginal
likelihood of the data in model 1.
The IterativeQuadrature
,
LaplaceApproximation
, LaplacesDemon
,
PMC
, and VariationalBayes
functions each
return the LML
, the approximate logarithm of the
marginal likelihood of the data, in each fitted object of class
iterquad
, laplace
, demonoid
, pmc
, or
vb
. The BayesFactor
function calculates matrix B
,
a matrix of Bayes factors, where each element of matrix B
is a
comparison of two models. Each Bayes factor is calculated as the
exponentiated difference of LML
of model 1
(\mathcal{M}_1
) and LML
of model 2
(\mathcal{M}_2
), and the hypothesis for each element of
matrix B
is that the model associated with the row is greater
than the model associated with the column. For example, element
B[3,2]
is the Bayes factor that model 3 is greater than model
2. The 'Strength of Evidence' aids in the interpretation (Jeffreys,
1961).
A table for the interpretation of the strength of evidence for Bayes factors is available at https://web.archive.org/web/20150214194051/http://www.bayesianinference.com/bayesfactors.
Each Bayes factor, B
, is the posterior odds in favor of the
hypothesis divided by the prior odds in favor of the hypothesis, where
the hypothesis is usually
\mathcal{M}_1 > \mathcal{M}_2
. For example, when
B[3,2]=2
, the data favor \mathcal{M}_3
over
\mathcal{M}_2
with 2:1 odds.
It is also popular to consider the natural logarithm of the Bayes factor. The scale of the logged Bayes factor is the same above and below one, which is more appropriate for visual comparisons. For example, when comparing two Bayes factors at 0.5 and 2, the logarithm of these Bayes factors is 0.69 and 0.69.
Gelman finds Bayes factors generally to be irrelevant, because they
compute the relative probabilities of the models conditional on one
of them being true. Gelman prefers approaches that measure the
distance of the data to each of the approximate models (Gelman et al.,
2004, p. 180), such as with posterior predictive checks (see the
predict.iterquad
function regarding iterative
quadrature, predict.laplace
function in the context of
Laplace Approximation, predict.demonoid
function in the
context of MCMC, predict.pmc
function in the context
of PMC, or predict.vb
function in the context of
Variational Bayes). Kass et al. (1995) asserts this can be done
without assuming one model is the true model.
Value
BayesFactor
returns an object of class bayesfactor
that
is a list with the following components:
B 
This is a matrix of Bayes factors. 
Hypothesis 
This is the hypothesis, and is stated as 'row > column', indicating
that the model associated with the row of an element in matrix

Strength.of.Evidence 
This is the strength of evidence in favor of the hypothesis. 
Posterior.Probability 
This is a vector of the posterior probability of each model, given flat priors. 
Author(s)
Statisticat, LLC.
References
Gelman, A., Carlin, J., Stern, H., and Rubin, D. (2004). "Bayesian Data Analysis, Texts in Statistical Science, 2nd ed.". Chapman and Hall, London.
Jeffreys, H. (1961). "Theory of Probability, Third Edition". Oxford University Press: Oxford, England.
Kass, R.E. and Raftery, A.E. (1995). "Bayes Factors". Journal of the American Statistical Association, 90(430), p. 773–795.
Lewis, S.M. and Raftery, A.E. (1997). "Estimating Bayes Factors via Posterior Simulation with the LaplaceMetropolis Estimator". Journal of the American Statistical Association, 92, p. 648–655.
See Also
is.bayesfactor
,
is.proper
,
IterativeQuadrature
,
LaplaceApproximation
,
LaplacesDemon
,
LML
,
PMC
,
predict.demonoid
,
predict.iterquad
,
predict.laplace
,
predict.pmc
,
predict.vb
, and
VariationalBayes
.
Examples
# The following example fits a model as Fit1, then adds a predictor, and
# fits another model, Fit2. The two models are compared with Bayes
# factors.
library(LaplacesDemon)
############################## Demon Data ###############################
data(demonsnacks)
J < 2
y < log(demonsnacks$Calories)
X < cbind(1, as.matrix(log(demonsnacks[,10]+1)))
X[,2] < CenterScale(X[,2])
######################### Data List Preparation #########################
mon.names < "LP"
parm.names < as.parm.names(list(beta=rep(0,J), sigma=0))
pos.beta < grep("beta", parm.names)
pos.sigma < grep("sigma", parm.names)
PGF < function(Data) {
beta < rnorm(Data$J)
sigma < runif(1)
return(c(beta, sigma))
}
MyData < list(J=J, PGF=PGF, X=X, mon.names=mon.names,
parm.names=parm.names, pos.beta=pos.beta, pos.sigma=pos.sigma, y=y)
########################## Model Specification ##########################
Model < function(parm, Data)
{
### Parameters
beta < parm[Data$pos.beta]
sigma < interval(parm[Data$pos.sigma], 1e100, Inf)
parm[Data$pos.sigma] < sigma
### LogPrior
beta.prior < sum(dnormv(beta, 0, 1000, log=TRUE))
sigma.prior < dhalfcauchy(sigma, 25, log=TRUE)
### LogLikelihood
mu < tcrossprod(Data$X, t(beta))
LL < sum(dnorm(Data$y, mu, sigma, log=TRUE))
### LogPosterior
LP < LL + beta.prior + sigma.prior
Modelout < list(LP=LP, Dev=2*LL, Monitor=LP,
yhat=rnorm(length(mu), mu, sigma), parm=parm)
return(Modelout)
}
############################ Initial Values #############################
Initial.Values < GIV(Model, MyData, PGF=TRUE)
######################## Laplace Approximation ##########################
Fit1 < LaplaceApproximation(Model, Initial.Values, Data=MyData,
Iterations=10000)
Fit1
############################## Demon Data ###############################
data(demonsnacks)
J < 3
y < log(demonsnacks$Calories)
X < cbind(1, as.matrix(demonsnacks[,c(7,8)]))
X[,2] < CenterScale(X[,2])
X[,3] < CenterScale(X[,3])
######################### Data List Preparation #########################
mon.names < c("sigma","mu[1]")
parm.names < as.parm.names(list(beta=rep(0,J), sigma=0))
pos.beta < grep("beta", parm.names)
pos.sigma < grep("sigma", parm.names)
PGF < function(Data) return(c(rnormv(Data$J,0,10), rhalfcauchy(1,5)))
MyData < list(J=J, PGF=PGF, X=X, mon.names=mon.names,
parm.names=parm.names, pos.beta=pos.beta, pos.sigma=pos.sigma, y=y)
############################ Initial Values #############################
Initial.Values < GIV(Model, MyData, PGF=TRUE)
######################## Laplace Approximation ##########################
Fit2 < LaplaceApproximation(Model, Initial.Values, Data=MyData,
Iterations=10000)
Fit2
############################# Bayes Factor ##############################
Model.list < list(M1=Fit1, M2=Fit2)
BayesFactor(Model.list)