c2_convergence: Cedric Convergence Utilities

In snoweye/cubfits: Codon Usage Bias Fits

Description

This utility function provides convergence related functions by Cedric.

Usage

  cubmultichain(cubmethod, reset.qr, seeds=NULL,
                teston=c("phi", "sphi"), swap=0, swapAt=0.05, monitor=NULL, 
                min=0, max=160000, nchains=2, conv.thin=10,
                eps=0.1, ncores=2, ...)
                          
  cubsinglechain(cubmethod, frac1=0.1, frac2=0.5, reset.qr,
                 seed=NULL, teston=c("phi", "sphi"), monitor=NULL, 
                 min=0, max=160000, conv.thin=10, eps=1, ...)

Arguments

cubmethod	String to choose method. Options are "cubfits", "cubappr", "cubpred"
reset.qr	recalculate QR decomposition matrix of covariance matrix until reset.qr samples are reached
swap	proportion of b matrix parameters to be swaped between convergence checks
swapAt	difference (L1-norm) between two consequtive convergence test leading to a swap in the b matrix
seeds	Vector of seed for random number generation
seed	Seed for random number generation
teston	Select data to test convergence on
monitor	A function to monitor the progress of the MCMC. The fucntions expects the result object and for cubmultichain an index i. (cubmultichain call: monitor(x,i), cubsinglechain call: monitor(x))
min	Minimum samples to be obtained. eps is ignored until number of samples reaches min
max	Maximum samples to be obtained. eps is ignored after max samples is obtained
eps	Convergence criterium
conv.thin	thinning of samples before performing convergence test
nchains	number of chains to run in parallel
ncores	number of cores to use for parallel execution of chains
frac1	fraction of samples at the beginning of set for Geweke test
frac2	fraction of samples at the end of set for Geweke test
...	named arguments for functions "cubfits", "cubappr" or "cubpred"

Details

under development

Value

under development

Author(s)

Cedric Landerer [e-mail].

References

https://github.com/clandere/cubfits/

See Also

cubfits, cubappr, cubpred

Examples

## Not run: 
suppressMessages(library(cubfits, quietly = TRUE))


## End(Not run)

snoweye/cubfits documentation built on Nov. 9, 2021, 3:39 a.m.