Plots to visualize age-length keys.

Source: R/alkPlot.R

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

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.

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.

IFAR Chapter

5-Age-Length Key.

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.

Author

Derek H. Ogle, derek@derekogle.com

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)

#>      age
#> LCat      4     5     6     7     8     9    10    11
#>   35  1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
#>   40  1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
#>   45  1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
#>   50  1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
#>   55  1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
#>   60  0.600 0.400 0.000 0.000 0.000 0.000 0.000 0.000
#>   65  0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000
#>   70  0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000
#>   75  0.000 0.889 0.111 0.000 0.000 0.000 0.000 0.000
#>   80  0.000 0.250 0.750 0.000 0.000 0.000 0.000 0.000
#>   85  0.000 0.000 0.909 0.091 0.000 0.000 0.000 0.000
#>   90  0.000 0.000 0.263 0.632 0.105 0.000 0.000 0.000
#>   95  0.000 0.000 0.059 0.706 0.176 0.000 0.059 0.000
#>   100 0.000 0.000 0.000 0.556 0.167 0.278 0.000 0.000
#>   105 0.000 0.000 0.000 0.286 0.429 0.143 0.143 0.000
#>   110 0.000 0.000 0.000 0.200 0.200 0.200 0.200 0.200
#>   115 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000

## 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))