plotIndex {scape}

Plot Abundance Index

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)