tracePlots: Traceplots for selected parameters

Description

This function draws traceplots of selected parameters from the MCMC simulations ran using NMixMCMC or GLMM_MCMC functions.

Usage

tracePlots(x, ...)
  # S3 method for default
tracePlots(x, ...)
  # S3 method for NMixMCMC
tracePlots(x, param=c("Emix", "SDmix", "Cormix", "K", "w", "mu", "sd", "gammaInv"),
    relabel=FALSE, order,
    auto.layout=TRUE, xlab="Iteration", ylab, col="slateblue", main="", ...)
  # S3 method for NMixMCMClist
tracePlots(x, param=c("Emix", "SDmix", "Cormix", "K", "w", "mu", "sd", "gammaInv"),
    relabel=FALSE,
    auto.layout=TRUE, xlab="Iteration", ylab, col=c("blue3", "red3"), main="", ...)
  # S3 method for GLMM_MCMC
tracePlots(x, param=c("Deviance", "Cond.Deviance",
    "alpha", "Eb", "SDb", "Corb", "sigma_eps",
    "w_b", "mu_b", "sd_b", "gammaInv_b", "gammaInv_eps"),
    relabel=FALSE, order,
    auto.layout=TRUE, xlab="Iteration", ylab, col="slateblue", main="", ...)
  # S3 method for GLMM_MCMClist
tracePlots(x, param=c("Deviance", "Cond.Deviance",
    "alpha", "Eb", "SDb", "Corb", "sigma_eps",
    "w_b", "mu_b", "sd_b", "gammaInv_b", "gammaInv_eps"),
    relabel=FALSE,                             
    auto.layout=TRUE, xlab="Iteration", ylab, col=c("blue3", "red3"), main="", ...)

Value

invisible(x)

Arguments

x

an object of appropriate class.

param

a character string which specifies which sort of parameters is to be plotted.

Emix: overall means (for each margin) of the normal mixture;

SDmix

overall standard deviations (for each margin) of the normal mixture;

Cormix

overall correlations (each pair) of the normal mixture;

K

number of mixture components;

w, w_b

weights of each of mixture components. If relabel is FALSE, weights are not re-labeled before plotting;

mu, mu_b

component means (each margin, each mixture component) of the normal mixture. The mixture means are shifted and scaled using x$scale$shift and x$scale$scale before plotting. If relabel is FALSE, means are not re-labeled before plotting;

sd, sd_b

component standard deviations (each margin, each mixture component) of the normal mixture. The mixture standard deviations are scaled using x$scale$scale before plotting. If relabel is FALSE, standard deviations are not re-labeled before plotting;

gammaInv, gammaInv_b, gammaInv_eps

variance hyperparameters;

Deviance

deviance (marginal, with random effects integrated out) of the GLMM;

Cond.Deviance

conditional deviance (given random effects) of the GLMM;

alpha

fixed effects of the fitted GLMM;

Eb

overall means (for each margin) of the random effects of the fitted GLMM;

SDb

overall standard deviations (for each margin) of the random effects of the fitted GLMM;

Corb

overall correlations (each pair) of the distribution of the random effects of the fitted GLMM.

sigma_eps

standard deviations of the error terms in the (mixed) models for continuous responses.

relabel

logical value. It indicates whether the chains with param being w, mu, sd, w_b, mu_b, sd_b should be re-labeled before plotting. Re-labelling is given by argument order. If order is missing then x$order or x$order_b determines re-labelling.

order

a matrix with $K$ columns and $M$ rows where $M$ is the length of MCMC. Each row of order must be a permutation of $(1, \ldots, K)$.

auto.layout

logical value. If TRUE, the plotting region is automatically divided to produce traceplots of all parameters. Note that layout must be set up automatically if there are more than 28 parameters to be plotted (often the case for correlations with param being Corb or for mixture means with param being mu_b).

xlab, ylab, col, main

arguments passed to plot function. They all can be of length one (the value is used on all plots) or of length equal to the number of parameters to be plotted.

...

other arguments passed to plot function.

Author

Arnošt Komárek arnost.komarek@mff.cuni.cz

Description

Usage

Value

Arguments

Author

See Also