plotIndex: Plot Abundance Index
In arnima-github/scape: Statistical Catch-at-Age Plotting Environment

plotIndex

R Documentation

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.

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)

arnima-github/scape documentation built on Oct. 23, 2024, 9:59 a.m.