plotDens {scapeMCMC} | R Documentation |
Plot Markov-chain Monte Carlo density. This is an approximation of the posterior probability density function.
plotDens(mcmc, probs=c(0.025,0.975), points=FALSE, axes=TRUE, same.limits=FALSE, between=list(x=axes,y=axes), div=1, log=FALSE, base=10, main=NULL, xlab=NULL, ylab=NULL, cex.main=1.2, cex.lab=1, cex.strip=0.8, cex.axis=0.7, las=0, tck=0.5, tick.number=5, lty.density=1, lwd.density=3, col.density="black", lty.median=2, lwd.median=1, col.median="darkgrey", lty.outer=3, lwd.outer=1, col.outer="darkgrey", pch="|", cex.points=1, col.points="black", plot=TRUE, ...)
mcmc |
MCMC chain(s) as a vector, data frame or mcmc
object. |
probs |
vector of outer quantiles to draw, besides the median. |
points |
whether data points should be plotted along the x axis. |
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 x axis. |
log |
whether values should be log-transformed. |
base |
logarithm base. |
main |
main title. |
xlab |
x-axis label. |
ylab |
y-axis label. |
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.density |
line type of density curve. |
lwd.density |
line width of density curve. |
col.density |
colour of density curve. |
lty.median |
line type of median. |
lwd.median |
line width of median. |
col.median |
colour of median. |
lty.outer |
line type of outer quantiles. |
lwd.outer |
line width of outer quantiles. |
col.outer |
colour of outer quantiles. |
pch |
symbol for data points. |
cex.points |
size of data points. |
col.points |
colour of data points. |
plot |
whether to draw plot. |
... |
passed to densityplot and
panel.densityplot . |
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.densityplot
,
densplot
, quantile
.
scapeMCMC-package
gives an overview of the package.
plotDens(xmcmc$B$"2004", points=TRUE, div=1000, main="2004\n", xlab="Biomass age 4+ (1000 t)", tick.number=6, strip=FALSE) plotDens(xmcmc$P, xlab="Parameter value", ylab="Posterior density\n")