plotIndex {scape}R Documentation

Plot Abundance Index

Description

Plot scape model fit to abundance index data

Usage

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, ...)

Arguments

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.

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

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.

Author(s)

Arni Magnusson arnima@u.washington.edu.

See Also

Lattice, xyplot, panel.xyplot, panel.xYplot, plotCI.

scape-package gives an overview of the package.

Examples

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)

[Package scape version 1.0-8 Index]