plotCumu {scapeMCMC} | R Documentation |
Plot Markov-chain Monte Carlo cumulative quantiles. This is a diagnostic plot for deciding whether the chain has converged.
plotCumu(mcmc, probs=c(0.025,0.975), div=1, log=FALSE, base=10, main=NULL, xlab="Iterations", ylab="Value", lty.median=1, lwd.median=2, col.median="black", lty.outer=2, lwd.outer=1, col.outer="black", ...)
mcmc |
MCMC chain(s) as a vector, data frame or mcmc
object. |
probs |
outer quantiles to draw, a vector of length 2. |
div |
denominator to shorten values on the y axis. |
log |
whether values should be log-transformed. |
base |
logarithm base. |
main |
main title. |
xlab |
x-axis label. |
ylab |
y-axis label. |
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. |
... |
passed to cumuplot() , title() and
axis() . |
Null, but a plot is drawn on the current graphics device.
The Args
function from the gdata package is recommended
for reviewing the arguments, instead of args
.
Arni Magnusson arnima@u.washington.edu.
scapeMCMC-package
gives an overview of the package.
plotCumu(xmcmc$P$R0, main="R0") plotCumu(xmcmc$P$cSfull, main="cSfull") plotCumu(xmcmc$P, probs=c(0.25,0.50,0.75), ann=FALSE, axes=FALSE)