R: Operator parameters that control the operation of the MCMC
mcmc.operators
R Documentation
Operator parameters that control the operation of the MCMC
Description
These parameters, which are passed to the MCMC and MCMC_BB
functions, control the operation of the MCMC. They specify the number of
generations over which the MCMC runs; the scales of the tuning parameters (stp)
for all parameters updated via random-walk samplers; the save, print, and
sample frequency of the chain, and the output file names.
Usage
data(mcmc.operators)
Format
The format is:
List of 12
$ delta :
num 0.001
$ aD_stp :
num 0.0018
$ aE_stp :
num 0.04
$ a2_stp :
num 0.0035
$ phi_stp :
num 30
$ thetas_stp:
num 0.07
$ mu_stp :
num 0.17
$ ngen :
num 100
$ printfreq :
num 2
$ savefreq :
num 100
$ samplefreq:
num 5
$ prefix :
chr "example_"
Details
delta
The size of the "delta shift" on the off-diagonal elements of the
parametric covariance matrix, used to ensure its positive-definiteness (even,
for example, when there are separate populations sampled at the same
geographic/ecological coordinates). This value must be large enough that the
covariance matrix is positive-definite, but, if possible, should be smaller
than the smallest off-diagonal distance elements, lest it have an undue
impact on inference. If the user is concerned that the delta shift is too
large relative to the pairwise distance elements in D and E,
she should run subsequent analyses, varying the size of delta, to see if it
has an impact on model inference.
aD_stp
The scale of the tuning parameter on aD (alphaD). The scale of the
tuning parameter is the standard deviation of the normal distribution from
which small perturbations are made to those parameters updated via a
random-walk sampler. A larger value of the scale of the tuning parameter will
lead to, on average, larger proposed moves and lower acceptance rates (for
more on acceptance rates, see plot_acceptance_rate).
aE_stp
The scale of the tuning parameter on aE (alphaE). If there are
multiple ecological distances included in the analysis, there will be
multiple alphaE parameters (one for each matrix in the list of E). These may
be updated all with the same scale of a tuning parameter, or they can each
get their own, in which case aE_stp should be a vector of length equal to the
number of ecological distance variables.
a2_stp
The scale of the tuning parameter on a2 (alpha_2).
phi_stp
The scale of the tuning parameter on the phi parameters.
thetas_stp
The scale of the tuning parameter on the theta parameters.
mu_stp
The scale of the tuning parameter on mu.
ngen
The number of generations over which to run the MCMC (one parameter
is updated at random per generation, with mu, theta, and phi all counting,
for the purposes of updates, as one parameter).
printfreq
The frequency with which MCMC progress is printed to the
screen. If printfreq =1000, an update with the MCMC generation number
and the posterior probability at that generation will print to the screen
every 1000 generations.
savefreq
The frequency with which the MCMC saves its output as an R
object (savefreq =50,000 means that MCMC output is saved every 50,000
generations). If ngen is large, this saving process may be
computationally expensive, and so should not be performed too frequently.
However, users may wish to evalute MCMC performance while the chain is still
running, or may be forced to truncate runs early, and should therefore
specify a savefreq that is less than ngen. We recommend a
savefreq of between 1/10th and 1/20th of ngen.
samplefreq
The thinning of the MCMC chain (samplefreq = 1000 means
that the parameter values saved in the MCMC output are sampled once every
1000 generations). A higher samplefreq will decrease parameter
autocorrelation time. However, there is still information in autocorrelated
draws from the joint posterior, so the samplefreq should be viewed
merely as a computational convenience, to decrease the size of the MCMC
output objects.
prefix
If specified, this prefix will be added to all output file names.
Examples
## see command{MCMC} and command{MCMC_BB} for example usage.