plotN: Plot Numbers at Age

In arnima-github/scape: Statistical Catch-at-Age Plotting Environment

Plot Numbers at Age

Description

Plot scape model predicted numbers at age.

Usage

plotN(model, what="d", swap=FALSE, years=NULL, ages=NULL, axes=TRUE,
      same.limits=TRUE, div=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=(what=="b"), tck=c(1,what=="b")/2, tick.number=10, lty.grid=3,
      col.grid="white", pch=16, cex.points=1, col.points="black",
      ratio.bars=3, col.bars="gray", plot=TRUE, ...)

Arguments

model	fitted scape model.
what	what to plot: "d"[efault], "i"[nitial year], "l"[ast year], "r"[ecruitment], "p"[panels], "b"[ubble plot].
swap	whether to swap ages and years between axes or panels.
years	vector of numbers indicating which years to plot (all by default).
ages	vector of numbers indicating which ages to plot (all by default).
axes	whether to plot axis values.
same.limits	whether panels should have same y-axis limits.
div	denominator to shorten values on the y axis.
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.
ratio.bars	width of bars.
col.bars	color of bars.
plot	whether to draw plot.
...	passed to xyplot, panel.barchart, and panel.xyplot.

Details

The "d"[efault] plot is a combination of "i"[nitial year] and "r"[ecruitment].

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.barchart 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

plotN(x.cod, div=1000, xlab=c("Age (years)","Year"),
      ylab="Individuals (million)")

plotN(x.cod, "l", div=1000, xlab="Age", ylab="Individuals (million)")

plotN(x.cod, "r", age=3, div=1000, xlim=c(1967,2002))

plotN(x.cod, "p", div=1000, ages=3:10, xlim=c(2,11), xlab="Age",
      ylab="Individuals (million)", cex.strip=0.7, cex.axis=0.7,
      tck=0.5)

plotN(x.cod, "b", xlab="Age (years)", ylab="Year", cex.points=0.7)

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