plotIndex {scape} | R Documentation |
Plot scape
model fit to abundance index data
plotIndex(model, what="c", series=NULL, axes=TRUE, same.limits=FALSE, between=list(x=axes,y=axes), ylim=NULL, q=1, bar=1, log=FALSE, base=10, main="", xlab="", ylab="", cex.main=1.2, cex.lab=1, cex.strip=0.8, cex.axis=0.8, las=1, tck=c(1,0)/2, tick.number=5, lty.grid=3, col.grid="white", pch=16, cex.points=1.2, col.points="black", lty.lines=1, lwd.lines=4, col.lines="dimgrey", lty.bar=1, plot=TRUE, ...)
model |
fitted scape model containing element CPUE
and/or Survey . |
what |
what should be plotted: "c" [ommercial] or
"s" [urvey] abundance index. |
series |
vector of strings indicating which gears or surveys should be plotted (first by default). |
axes |
whether axis values should be plotted. |
same.limits |
whether panels should have same y-axis limits. |
between |
list with x and y indicating panel
spacing. |
ylim |
vector with lower and upper y-axis limits. |
q |
denominator to scale the y axis, e.g. to vulnerable biomass. |
bar |
extent of error bars relative to standard error. |
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.grid |
line type of gridlines. |
col.grid |
colour of gridlines. |
pch |
symbol for points. |
cex.points |
size of points. |
col.points |
colour of points, possibly a vector. |
lty.lines |
line type of main lines. |
lwd.lines |
line width of main lines. |
col.lines |
colour of main lines, possibly a vector. |
lty.bar |
line type of error bars. |
plot |
whether to draw plot. |
... |
passed to xyplot , panel.xyplot , and
panel.xYplot . |
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
, xyplot
,
panel.xyplot
,
panel.xYplot
, plotCI
.
scape-package
gives an overview of the package.
plotIndex(x.cod, "s", xlab="Year", ylab="Survey abundance index", strip=FALSE) plotIndex(x.oreo, xlim=list(c(1981,1990),c(1992,2002)), xlab="Year", ylab="Observed CPUE", col.points=c("peru","red"), lty.lines=0)