FSA (version 0.8.11)

alkPlot: Plots to visualize age-length keys.

Description

Various plots to visualize the proportion of fish of certain ages within length intervals in an age-length key.

Usage

alkPlot(key, type = c("barplot", "area", "lines", "splines", "bubble"), xlab = "Length", ylab = ifelse(type != "bubble", "Proportion", "Age"), xlim = NULL, ylim = NULL, showLegend = FALSE, lbl.cex = 1.25, leg.cex = 1, lwd = 2, span = 0.25, pal = paletteChoices(), grid = TRUE, col = "gray80", buf = 0.45, add = FALSE, ...)

Arguments

key

A numeric matrix that contains the age-length key.

type

A string that indicates the type of plot to construct. See details.

xlab, ylab

A string that contains the label for the x- or y-axis.

xlim, ylim

A numeric of length 2 that provide the limits for the x-axis or y-axis.

showLegend

A logical that indicates whether a legend should be displayed (not implemented for type="bubble"). See examples.

lbl.cex

A numeric character expansion value for labels inside the bars when type="barplot" or on the lines when type="lines" or type="splines". Only used if showLegend=FALSE.

leg.cex

A numeric character expansion value for labels on the legend when showLegend=TRUE.

lwd

A numeric that indicates the line width when type="lines" or type="splines".

span

A numeric that indicates the span value to use in loess when type="splines".

pal

A string that indicates the palette to generate colors for the bars, areas, lines, or spline lines. The name of a palette must be one of “rich”, “cm”, “default”, “grey”, “gray”, “heat”, “jet”, “rainbow”, “topo”, or “terrain”. See chooseColors.

grid

A logical that indicates whether a grid should be placed under the bubbles when type="bubble" or a character or appropriate vector that identifies a color for the grid. See examples.

col

A string that indicates the color of the bubbles when type="bubble".

buf

A single numeric that indicates the relative width of the bubbles when type="bubble". A value of 0.5 means that two full-width bubbles would touch each other either in the x- or y-direction (i.e., this would represent half of the minimum of the physical distance between values one-unit apart on the x- and y-axes). Set this to a value less than 0.5 so that the bubbles will not touch (the default is 0.45).

add

A logical that indicates whether the data should be added to an already existing plot. May be useful for visually comparing age-length keys. Only implemented when type="bubble".

...

Additional arguments to pass to plot or barplot.

Value

None, but a plot is constructed.

IFAR Chapter

5-Age-Length Key.

Details

A variety of plots can be used to visualize the proportion of fish of certain ages within length intervals of an age-length key. The types of plots are described below and illustrated in the examples.

• A “stacked” bar chart where vertical bars over length intervals sum to 1 but are segmented by the proportion of each age in that length interval is constructed with type="barplot". The ages will be labeled in the bar segments unless showLegend=TRUE is used.
• A “stacked” area chart similar to the bar chart described above is constructed with type="area".
• A plot with (differently colored) lines that connect the proportions of ages within each length interval is constructed with type="lines".
• A plot with (differently colored) lines, as estimated by loess splines, that connect the proportions of ages within each length interval is constructed with type="splines".
• A “bubble” plot where circles whose size is proportional to the proportion of fish of each age in each length interval is constructed with type="bubble". The color of the bubbles can be controlled with col= and an underlying grid for ease of seeing the age and length interval for each bubble can be controlled with grid=. Bubbles from a second age-length key can be overlaid on an already constructed bubble plot by using add=TRUE in a second call to alkPlot.

Note that all plots are “vertically conditional” -- i.e., each represents the proportional ages WITHIN each length interval.

References

Ogle, D.H. 2016. Introductory Fisheries Analyses with R. Chapman & Hall/CRC, Boca Raton, FL.

See Also

See alkIndivAge for using an age-length key to assign ages to individual fish.

Examples

## Make an example age-length key
data(WR79)
WR.age <- subset(WR79, !is.na(age))      # isolate the age sample
WR.age$LCat <- lencat(WR.age$len,w=5)    # add length intervals (width=5)
raw <- xtabs(~LCat+age,data=WR.age)      # create age-length key
( WR.key <- prop.table(raw, margin=1) )

## Various visualizations of the age-length key
alkPlot(WR.key,"barplot")
alkPlot(WR.key,"barplot",pal="gray")
alkPlot(WR.key,"barplot",showLegend=TRUE)
alkPlot(WR.key,"area")
alkPlot(WR.key,"area",showLegend=TRUE)
alkPlot(WR.key,"area",pal="gray")
alkPlot(WR.key,"lines")
alkPlot(WR.key,"lines",pal="gray")
alkPlot(WR.key,"lines",showLegend=TRUE)
alkPlot(WR.key,"splines")
alkPlot(WR.key,"splines",span=0.2)
alkPlot(WR.key,"splines",pal="gray",showLegend=TRUE)
alkPlot(WR.key,"bubble")
alkPlot(WR.key,"bubble",grid=FALSE)
alkPlot(WR.key,"bubble",grid="blue")
alkPlot(WR.key,"bubble",grid=rgb(0,0,0,0.2),col=rgb(0,0,0,0.5))