Controls {cubfits}

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 includes

  model	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 includes

  scale.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 includes

  amino.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 includes

  optim.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 includes

  dump	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 includes

  renew.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 includes

  color

  color for codons.

• .CF.PARAM controls the parameters and hyperparameters of priors. It currently includes

  phi.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 includes

  debug

  message printing level of debugging.

Author(s)

Wei-Chen Chen [e-mail].

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)