scape (version 1.0-4)

plotIndex: 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.transform=FALSE, base.log=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.it=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.transform

whether values should be log-transformed.

base.log

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.it

whether to draw plot.

...

passed to xyplot.

Value

• When plot.it=TRUE, a trellis plot is drawn and a data frame is returned, containing the data used for plotting. When plot.it=FALSE, a trellis object is returned.

concept

Fisheries stock assessment

See Also

Fitted Coleraine models can be imported using importRes. Trellis plot details can be studied from the Lattice help page.

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)