Description Usage Format Details Author(s) References See Also Examples
Default controls of cubfits include for models, optimizations, MCMC, plotting, global variables, etc.
1 2 3 4 5 6 7 8 9 10 
All are in lists and contain several controlling options.
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 hyperparameters 
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. 
WeiChen Chen [email protected].
https://github.com/snoweye/cubfits/
init.function()
, cubfits()
,
cubpred()
, cubappr()
, and
mixnormerr.optim()
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  ## 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)

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