plotQuant {scapeMCMC} | R Documentation |
Plot quantiles of multiple Markov-chain Monte Carlo chains, using bars, boxes, or lines.
plotQuant(mcmc, style="boxes", probs=c(0.025,0.975), axes=TRUE, names=NULL, ylim=NULL, yaxs="i", div=1, log=FALSE, base=10, main=NULL, xlab=NULL, ylab=NULL, cex.axis=0.8, las=1, tck=-0.015, tick.number=8, lty.median=1, lwd.median=1+2*(style!="boxes"), col.median="black", lty.outer=1+2*(style=="lines"), lwd.outer=1, col.outer="darkgrey", boxfill="darkgrey", boxwex=0.7, mai=c(0.8,1,1,0.6), mgp=list(bottom=c(2,0.4,0),left=c(3,0.6,0),top=c(0,0.6,0), right=c(0,0.6,0)), ...)
mcmc |
MCMC chains as a data frame or mcmc object. |
style |
how quantiles should be drawn: "bars" ,
"boxes" , or "lines" . |
probs |
outer quantiles to draw, a vector of length 2. |
axes |
numeric vector indicating which axis labels should be
drawn: 1=bottom, 2=left, 3=top, 4=right, or TRUE to display
all (default). |
names |
x-axis labels. |
ylim |
y-axis limits. |
yaxs |
y-axis style: "i" to truncate exactly at limits
(default) or "r" to extend the axis slightly beyond the
limits. |
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. |
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.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. |
boxfill |
colour of boxes. |
boxwex |
relative width of boxes. |
mai |
margins around plot as a vector of four numbers (bottom, left, top, right). |
mgp |
margins around axis titles, labels, and lines as a list of four vectors (bottom, left, top, right). |
... |
passed to plot , bxp , plotCI ,
lines , matplot , axis , and title . |
List containing:
x |
midpoint coordinates on the x axis. |
y |
quantile coordinates on the y axis. |
The Args
function from the gdata package is recommended
for reviewing the arguments, instead of args
.
Arni Magnusson arnima@u.washington.edu.
bxp
, plotCI
,
matplot
, quantile
.
scapeMCMC-package
gives an overview of the package.
plotQuant(xmcmc$B, style="lines", div=1000, xlab="Year", ylab="Biomass age 4+ (1000 t)") plotQuant(xmcmc$R, names=substring(names(xmcmc$R),3), div=1000, xlab="Year", ylab="Recruitment (million one-year-olds)")