Controls: 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

Arguments

format

All are in lists and contain several controlling options.

Details

See init.function() for use cases of these objects.

.cubfitEnvis a default environment to dynamically save functions and objects.
.CF.CTis main controls of models. It currently includesll{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 ll{ 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 ll{ 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 ll{ 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 ll{ 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 ll{ 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 ll{ color color for codons. }

.CF.PARAM controls the parameters and hyperparameters of priors. It currently includes ll{ 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 ll{ debug message printing level of debugging. } https://github.com/snoweye/cubfits/ [object Object] init.function(), cubfits(), cubpred(), cubappr(), and mixnormerr.optim(). 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) datasets