Consort {LaplacesDemon}  R Documentation 
Consort with Laplace's Demon
Description
This may be used to consort with Laplace's Demon regarding an object
of class demonoid
. Laplace's Demon will offer suggestions.
Usage
Consort(object)
Arguments
object 
This required argument is an object of class

Details
First, Consort
calls print.demonoid
, which prints most
of the components to the screen from the supplied object of class
demonoid
.
Second, Laplace's Demon considers a combination of five conditions
when making the largest part of its suggestion. These conditions are:
the algorithm, acceptance rate, MCSE, ESS, and stationarity. Other
things are considered as well, such as the recommended thinning value
is used to suggest a new number of iterations, how fast the algorithm
is expected to be, and if the condition of diminishing adaptation
(also called the vanishing adaptation condition) was met (for an
adaptive algorithm). Diminishing adaptation occurs only when the
absolute value of the proposed variances trends downward (toward zero)
over the course of all adaptations. When an algorithm is adaptive and
it does not have diminishing adaptations, the Consort
function
will suggest a different adaptive algorithm. The Periodicity
argument is suggested to be set equal to the value of
Rec.Thinning
.
Appeasement applies only when all parameters are continuous.The
Hangartner.Diagnostic
should be considered for discrete
parameters.
Appeasement Conditions
Algorithm: The final algorithm must be nonadaptive, so that the Markov property holds. This is conservative. A user may have an adaptive (nonfinal) algorithm in which adaptations in the latest update are stationary, or no longer diminishing. Laplace's Demon is unaware of previous updates, and conservatively interprets this as failing to meet the condition of diminishing adaptation, when the output may be satisfactory. On the other hand, if the adaptive algorithm has essentially stopped adapting, and if there is a nonadaptive version, then the user should consider switching to the nonadaptive algorithm. User discretion is advised.
Acceptance Rate: The acceptance rate is considered satisfactory if it is within the interval [15%,50%] for most algorithms. Some algorithms have different recommended intervals.
MCSE: The Monte Carlo Standard Error (MCSE) is considered satisfactory for each target distribution if it is less than 6.27% of the standard deviation of the target distribution. This allows the true mean to be within 5% of the area under a Gaussian distribution around the estimated mean. The
MCSE
function is used. Toft et al. (2007) propose a stricter criterion of 5%. The criterion of 6.27% for this stopping rule is arbitrary, and may be too lenient or strict, depending on the needs of the user. Nonetheless, it has performed well, and this type of stopping rule has been observed to perform better than MCMC convergence diagnostics (Flegal et al., 2008).ESS: The effective sample size (ESS) is considered satisfactory for each target distribution if it is at least 100, which is usually enough to describe 95% probability intervals (see
p.interval
andLPL.interval
for more information). TheESS
function is used. When this criterion is unmet, the name of the worst mixing chain in Summary1 appears.Stationarity: Each target distribution is considered satisfactory if it is estimated to be stationary with the
BMK.Diagnostic
function.
Bear in mind that the MCSE, ESS, and stationarity criteria are all univariate measures applied to each marginal posterior distribution. Multivariate forms are not included. By chance alone due to multiple independent tests, 5% of these diagnostics should indicate nonconvergence when 'convergence' exists. In contrast, even one nonconvergent nuisance parameter is associated with nonconvergence in all other parameters. Assessing convergence is difficult.
If all five conditions are satisfactory, then Laplace's Demon is appeased. Otherwise, Laplace's Demon will suggest and supply R code that is ready to be copy/pasted and executed.
To visualize the MCSEbased stopping rule, run the following code:
x < seq(from=3, to=3, by=0.1);
plot(x, dnorm(x,0,1), type="l");
abline(v=0.0627); abline(v=0.0627);
abline(v=2*0.0627, col="red"); abline(v=2*0.0627, col="red")
The black vertical lines show the standard error, and the red vertical lines show the 95% interval.
If the user has an object of class demonoid.hpc
, then the
Consort
function may be still be applied, but a particular
chain in the object must be specified as a component in a list. For
example, with an object called Fit
and a goal of consorting
over the second chain, the code would be: Consort(Fit[[2]])
.
The Demonic Suggestion is usually very helpful, but should not be
followed blindly. Do not let it replace critical thinking. For
example, Consort
may find that diminishing adaptation is unmet,
and recommend a different algorithm. However, the user may be
convinced that the current algorithm is best, and believe instead that
MCMC found a local solution, and is leaving it to find the global
solution, in which case adaptations may increase again. Diminishing
adaptation may have occurred in a previous run, and is not found in
the current run because adaptation is essentially finished. If either
of these is true, then it may be best to ignore the newly suggested
algorithm, and continue with the current algorithm. The suggested code
may be helpful, but it is merely a suggestion.
If achieving the appeasement of Laplace's Demon is difficult, consider ignoring the MCSE criterion and terminate when all other criteria have been met, placing special emphasis on ESS.
Author(s)
Statisticat, LLC. software@bayesianinference.com
References
Flegal, J.M., Haran, M., and Jones, G.L. (2008). "Markov chain Monte Carlo: Can We Trust the Third Significant Figure?". Statistical Science, 23, p. 250–260.
Toft, N., Innocent, G., Gettinby, G., and Reid, S. (2007). "Assessing the Convergence of Markov Chain Monte Carlo Methods: An Example from Evaluation of Diagnostic Tests in Absence of a Gold Standard". Preventive Veterinary Medicine, 79, p. 244–256.
See Also
BMK.Diagnostic
,
ESS
,
Hangartner.Diagnostic
,
LaplacesDemon
,
LaplacesDemon.hpc
,
LPL.interval
,
MCSE
, and
p.interval
.