Controls {cubfits} | R Documentation |
Default Controlling Options
Description
Default controls of cubfits include for models, optimizations, MCMC, plotting, global variables, etc.
Usage
.cubfitsEnv
.CF.CT
.CF.CONF
.CF.GV
.CF.DP
.CF.OP
.CF.AC
.CF.PT
.CF.PARAM
.CO.CT
Format
All are in lists and contain several controlling options.
Details
See init.function()
for use cases of these objects.
-
.cubfitEnv
is a default environment to dynamically save functions and objects. -
.CF.CT
is main controls of models. It currently includesmodel
main models type.p
proposal for hyper-parameters type.Phi
proposal for Phi model.Phi
prior of Phi init.Phi
initial methods for Phi init.fit
how is coefficient proposed parallel
parallel functions adaptive
method for adaptive MCMC -
.CF.CONF
controls the initial and draw scaling. It currently includesscale.phi.Obs
if phi were scaled to mean 1 init.b.Scale
initial b scale init.phi.Scale
initial phi scale p.nclass
number of classes if mixture phi b.DrawScale
drawing scale for b if random walk p.DrawScale
drawing scale for p if random walk phi.DrawScale
random walk scale for phi phi.pred.DrawScale
random walk scale for phi.pred sigma.Phi.DrawScale
random walk scale for sigma.Phi bias.Phi.DrawScale
random walk scale for bias.Phi estimate.bias.Phi
if estimate bias of phi during MCMC compute.logL
if compute logL in each iteration -
.CF.GV
contains global variables for amino acids and codons. It currently includesamino.acid
amino acids amino.acid.3
amino acids synonymous.codon
synonymous codons of amino acids amino.acid.split
amino acid 'S' is split amino.acid.split.3
amino acid 'S' is split synonymous.codon.split
synonymous codons of split amino acid -
.CF.OP
controls optimizations. It currently includesoptim.method
method for optim
()stable.min.exp
minimum exponent stable.max.exp
maximum exponent E.Phi
expected Phi lower.optim
lower of derivative of logL(x) upper.optim
upper of derivative of logL(x) lower.integrate
lower of integration of L(x) upper.integrate
upper of integration of L(x) -
.CF.DP
is for dumping MCMC iterations. It currently includesdump
if dumping within MCMC iter
iterations per dumping prefix.dump
path and file names of dumping verbose
if verbose iterThin
iterations to thin chain report
iterations to report report.proc
iterations to report proc.time
() -
.CF.AC
controls adaptive MCMC. It currently includesrenew.iter
per renewing iterations target.accept.lower
target acceptant rate lower bound target.accept.upper
target acceptant rate upper bound scale.increase
increase scale size scale.decrease
decrease scale size sigma.lower
lower bound of relative scale size sigma.upper
upper bound of relative scale size -
.CF.PT
controls the plotting format. It currently includescolor
color for codons. -
.CF.PARAM
controls the parameters and hyperparameters of priors. It currently includesphi.meanlog
mean of phi in loca scale phi.sdlog
standard deviation of phi in loca scale -
.CO.CT
controls the constrained optimization function. It currently includesdebug
message printing level of debugging.
Author(s)
Wei-Chen Chen wccsnow@gmail.com.
References
https://github.com/snoweye/cubfits/
See Also
init.function()
, cubfits()
,
cubpred()
, cubappr()
, and
mixnormerr.optim()
.
Examples
## Not run:
suppressMessages(library(cubfits, quietly = TRUE))
.CF.CT
.CF.CONF
.CF.DP
.CF.GV
.CF.OP
.CF.AC
.CF.PT
.CF.PARAM
.CO.CT
ls(.cubfitsEnv)
init.function()
ls(.cubfitsEnv)
## End(Not run)