plotIndex: Plot Abundance Index

In scape: Statistical Catch-at-Age Plotting Environment

Description

Plot scape model fit to abundance index data.

Usage

plotIndex(model, what="s", 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.axis=0.8, cex.strip=0.8, col.strip="gray95",
          strip=strip.custom(bg=col.strip), 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="dimgray", lty.bar=1, plot=TRUE, ...)

Arguments

model	fitted scape model containing element CPUE and/or Survey.
what	what to plot: "c"[ommercial] or "s"[urvey] abundance index.
series	vector of strings indicating which gears or surveys to plot (all by default).
axes	whether to plot axis values.
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. Similar to the div argument in plotN and plotB.
bar	extent of error bars relative to standard error.
log	whether to log-transform values.
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.axis	size of tick labels.
cex.strip	size of strip labels.
col.strip	color of strip labels.
strip	logical flag (whether to plot strip labels), or a function passed to xyplot.
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	color of gridlines.
pch	symbol for points.
cex.points	size of points.
col.points	color of points and error bars.
lty.lines	line type of main lines.
lwd.lines	line width of main lines.
col.lines	color of main lines.
lty.bar	line type of error bars.
plot	whether to draw plot.
...	passed to xyplot, panel.xyplot, and panel.xYplot.

Value

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.

Note

The Args function from the gdata package is recommended for reviewing the arguments, instead of args.

See Also

xyplot, panel.xyplot, and panel.xYplot are the underlying drawing functions.

plotCA, plotCL, plotIndex, and plotLA plot model fit and data.

plotB, plotN, and plotSel plot derived quantities.

scape-package gives an overview of the package.

Examples

plotIndex(x.cod, xlab="Year", ylab="Survey abundance index",
          strip=FALSE)

plotIndex(x.oreo, "c", series="Series 1-1", xlim=c(1981,1990))

plotIndex(x.oreo, "c", xlim=list(c(1981,1990),c(1992,2002)),
          xlab="Year", ylab="Observed CPUE",
          col.points=c("salmon","seagreen"), lty.lines=0)

scape documentation built on Nov. 23, 2020, 5:08 p.m.