FSA: alkPlot – R documentation

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FSA

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`.

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.

Value

None, but a plot is constructed.

IFAR Chapter

5-Age-Length Key.

Author(s)

Derek H. Ogle, derek@derekogle.com

References

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

Examples

## Make an example age-length key
WR.age <- filterD(WR79, !is.na(age))
WR.age$LCat <- lencat(WR.age$len,w=5)
raw <- xtabs(~LCat+age,data=WR.age)
WR.key <- prop.table(raw, margin=1)
round(WR.key,3)

## 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,"lines")
alkPlot(WR.key,"splines")
alkPlot(WR.key,"splines",span=0.2)
alkPlot(WR.key,"bubble")
alkPlot(WR.key,"bubble",col=rgb(0,0,0,0.5))

FSA

Simple Fisheries Stock Assessment Methods

v0.8.32

GPL (>= 2)

Authors

Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>), Powell Wheeler [aut], Alexis Dinno [aut] (Provided base functionality of dunnTest())

Initial release

2021-1-15