R: Provides diagnostic plots to assess the convergence of the...
plot.ESS
R Documentation
Provides diagnostic plots to assess the convergence of the MCMC
procedure along the run
Description
The plot.ESS function provides a set of four plots
summarising the behaviour of all chains along the Evolutionary Monte
Carlo run. These plots are used to assess the convergence of
the algorithm and comprise: (i)- the history plot of the shrinkage factor
g, (ii)- the history plot of the model size in each chain,
(iii)- the history plot of the log posterior in each chain, and (iv)-
the history plot of each chain's temperature (during the burn-in
only, as temperatures are fixed at the end of the burn-in).
Usage
## S3 method for class 'ESS'
plot(x, ...)
Arguments
x
an object of class ESS.
...
additional arguments: range.SF range
value for the shrinkage factor plot (g);
range.MS range value for the model size plot;
range.LP range value for the log posterior plot.
# load an ESS object
modelY_Hopx <- example.as.ESS.object()
plot(modelY_Hopx)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(R2GUESS)
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
# maps v3.1: updated 'world': all lakes moved to separate new #
# 'lakes' database. Type '?world' or 'news(package="maps")'. #
Loading required package: MCMCpack
Loading required package: coda
Loading required package: MASS
##
## Markov Chain Monte Carlo Package (MCMCpack)
## Copyright (C) 2003-2016 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
##
## Support provided by the U.S. National Science Foundation
## (Grants SES-0350646 and SES-0350613)
##
Loading required package: mixOmics
Loading required package: lattice
Loading required package: ggplot2
Loaded mixOmics 6.0.0
Visit http://www.mixOmics.org for more details about our methods.
Any bug reports or comments? Notify us at mixomics at math.univ-toulouse.fr or https://bitbucket.org/klecao/package-mixomics/issues
Thank you for using mixOmics!
Attaching package: 'mixOmics'
The following object is masked from 'package:maps':
map
Loading required package: mvtnorm
Loading required package: snowfall
Loading required package: snow
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/R2GUESS/plot.ESS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.ESS
> ### Title: Provides diagnostic plots to assess the convergence of the MCMC
> ### procedure along the run
> ### Aliases: plot.ESS
>
> ### ** Examples
>
> # load an ESS object
> modelY_Hopx <- example.as.ESS.object()
The run is ok
You can now analyse the results
> plot(modelY_Hopx)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.