plotCL: Plot Catch at Length

In scape: Statistical Catch-at-Age Plotting Environment

Description

Plot scape model fit to catch-at-length data.

Usage

plotCL(model, what="c", fit=TRUE, swap=FALSE, series=NULL, sex=NULL,
       years=NULL, lengths=NULL, axes=TRUE, same.limits=TRUE, log=FALSE,
       base=10, eps.log=1e-5, 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=!fit, tck=c(1,fit)/2,
       tick.number=5, lty.grid=3, col.grid="gray", pch=16,
       cex.points=0.5, col.points="black", lty.lines=1, lwd.lines=2,
       col.lines=c("red","blue"), plot=TRUE, ...)

Arguments

model	fitted scape model containing element CLc and/or CLs.
what	what to plot: "c"[ommercial] or "s"[urvey] catch at length.
fit	whether to overlay fitted values on observed data.
swap	whether to swap lengths and years between axes or panels.
series	string indicating which gear or survey to plot (first by default).
sex	string indicating which sex to plot (both by default).
years	vector of numbers indicating which years to plot plot (all by default).
lengths	vector of numbers indicating which lengths to plot (all by default).
axes	whether to plot axis values.
same.limits	whether panels should have same y-axis limits.
log	whether to log-transform values.
base	logarithm base.
eps.log	small number to add before log-transforming to avoid log 0.
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.
lty.lines	line type of main lines, possibly a vector where element 2 refers to males.
lwd.lines	line width of main lines, possibly a vector where element 2 refers to males.
col.lines	color of main lines, possibly a vector where element 2 refers to males.
plot	whether to draw plot.
...	passed to xyplot, panel.xyplot, panel.superpose, and panel.superpose.2.

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.superpose 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

plotCL(x.ling, fit=FALSE, strip=FALSE, series="1", sex="Female",
       xlab="Length (cm)", ylab="Year")

plotCL(x.oreo, xlab="Length (cm)", ylab="Proportion in catch")

plotCL(x.oreo, "s", layout=c(2,1), xlab="Length (cm)",
       ylab="Observed proportion in survey", cex.points=0.8,
       col.points=c("red","blue"), lty.lines=0)

plotCL(x.ling, fit=FALSE, series="2", xlab="Length (cm)",
       ylab="Observed proportion in trawl catch", tck=0.5)

plotCL(x.ling, series="2", swap=TRUE, lengths=70:150, lty.grid=0)

Example output

scape documentation built on Nov. 23, 2020, 5:08 p.m.