plotTrace {scapeMCMC} | R Documentation |
Plot Markov-chain Monte Carlo traces. This is a diagnostic plot for deciding whether a chain shows unwanted trends.
plotTrace(mcmc, axes=FALSE, same.limits=FALSE, between=list(x=axes,y=axes), div=1, span=1/4, log=FALSE, base=10, main=NULL, xlab=NULL, ylab=NULL, cex.main=1.2, cex.lab=1, cex.strip=0.8, cex.axis=0.8, las=0, tck=0.5, tick.number=5, lty.trace=1, lwd.trace=1, col.trace="grey", lty.median=1, lwd.median=1, col.median="black", lty.loess=2, lwd.loess=1, col.loess="black", plot=TRUE, ...)
mcmc |
MCMC chain(s) as a vector, data frame or mcmc
object. |
axes |
whether axis values should be plotted. |
same.limits |
whether panels should have same x-axis limits. |
between |
list with x and y indicating panel
spacing. |
div |
denominator to shorten values on the y axis. |
span |
smoothness parameter, passed to panel.loess |
log |
whether values should be log-transformed. |
base |
logarithm base. |
main |
main title. |
xlab |
x-axis title. |
ylab |
y-axis title. |
cex.main |
size of main title. |
cex.lab |
size of axis labels. |
cex.strip |
size of strip labels. |
cex.axis |
size of tick labels. |
las |
orientation of tick labels: 0=parallel, 1=horizontal, 2=perpendicular, 3=vertical. |
tck |
tick mark length. |
tick.number |
number of tick marks. |
lty.trace |
line type of trace. |
lwd.trace |
line width of trace. |
col.trace |
colour of trace. |
lty.median |
line type of median. |
lwd.median |
line width of median. |
col.median |
colour of median. |
lty.loess |
line type of loess. |
lwd.loess |
line width of loess. |
col.loess |
colour of loess. |
plot |
whether to draw plot. |
... |
passed to xyplot and panel.loess . |
When plot=TRUE
, a trellis plot is drawn and a data frame is
returned, containing the data used for plotting. When
plot=FALSE
, a trellis object is returned.
This function tries to draw the plot on a trellis device with a white background.
The Args
function from the gdata package is recommended
for reviewing the arguments, instead of args
.
Arni Magnusson arnima@u.washington.edu.
Lattice
, panel.loess
,
traceplot
, quantile
.
scapeMCMC-package
gives an overview of the package.
plotTrace(xmcmc$P, xlab="Iterations", ylab="Parameter value", layout=c(2,4)) plotTrace(xmcmc$P$R0, axes=TRUE, div=1000)