FSA: psdPlot – R documentation

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FSA

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

Description

Constructs a length-frequency histogram with Gabelhouse lengths highlighted.

Usage

psdPlot(
  formula,
  data,
  species = "List",
  units = c("mm", "cm", "in"),
  startcat = 0,
  w = 1,
  justPSDQ = FALSE,
  main = "",
  xlab = "Length",
  ylab = "Number",
  xlim = NULL,
  ylim = c(0, max(h$counts) * 1.05),
  substock.col = "white",
  stock.col = "gray90",
  psd.col = "black",
  psd.lty = 2,
  psd.lwd = 1,
  show.abbrevs = TRUE,
  psd.add = TRUE,
  psd.pos = "topleft",
  psd.cex = 0.75,
  ...
)

Arguments

`formula`	A formula of the form `~length` where “length” generically represents a variable in `data` that contains length measurements. Note that this formula can only contain one variable.
`data`	A data.frame that minimally contains the length measurements given in the variable in the `formula`.
`species`	A string that contains the species name for which Gabelhouse length categories exist. See `psdVal` for details.
`units`	A string that indicates the type of units used for the length measurements. Choices are `mm` for millimeters (DEFAULT), `cm` for centimeters, and `in` for inches.
`startcat`	A number that indicates the beginning of the first length-class.
`w`	A number that indicates the width of length classes to create.
`justPSDQ`	A logical that indicates whether just stock and quality (for PSD-Q calculations) categories should be used. If `FALSE` (default) then the five Gabelhouse categories will be used.
`main`	A string that serves as the main label for the histogram.
`xlab`	A string that serves as the label for the x-axis.
`ylab`	A string that serves as the label for the y-axis.
`xlim`	A numeric vector of length two that indicates the minimum and maximum values (i.e., fish lengths) for the x-axis.
`ylim`	A numeric vector of length two that indicates the minimum and maximum values for the y-axis.
`substock.col`	A string that indicates the color to use for the bars representing under-stock size fish.
`stock.col`	A string that indicates the color to use for the bars representing stock size fish.
`psd.col`	A string that indicates the color to use for the vertical lines at the Gabelhouse length category values.
`psd.lty`	A numeric that indicates the line type to use for the vertical lines at the Gabelhouse length category values.
`psd.lwd`	A numeric that indicates the line width to use for the vertical lines at the Gabelhouse length category values.
`show.abbrevs`	A logical that indicates if the abbreviations for the Gabelhouse length categories should be added to the top of the plot.
`psd.add`	A logical that indicates if the calculated PSD values should be added to the plot (default is `TRUE`).
`psd.pos`	A string that indicates the position for where the PSD values will be shown. See details in `legend`.
`psd.cex`	A numeric value that indicates the character expansion for the PSD values text.
`...`	Arguments to be passed to the low-level plotting functions.

Details

Constructs a length-frequency histogram with the stock-sized fish highlighted, the Gabelhouse lengths marked by vertical lines, and the (traditional) PSD-X values superimposed.

The length of fish plotted on the x-axis can be controlled with xlim, however, the minimum value in xlim must be less than the stock length for that species.

Value

None. However, a graphic is produced.

IFAR Chapter

6-Size Structure.

Author(s)

Derek H. Ogle, derek@derekogle.com

References

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

Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS). Fisheries 31:86-87. [Was (is?) from http://pubstorage.sdstate.edu/wfs/415-F.pdf.]

Guy, C.S., R.M. Neumann, D.W. Willis, and R.O. Anderson. 2006. Proportional size distribution (PSD): A further refinement of population size structure index terminology. Fisheries 32:348. [Was (is?) from http://pubstorage.sdstate.edu/wfs/450-F.pdf.]

Willis, D.W., B.R. Murphy, and C.S. Guy. 1993. Stock density indices: development, use, and limitations. Reviews in Fisheries Science 1:203-222. [Was (is?) from http://web1.cnre.vt.edu/murphybr/web/Readings/Willis%20et%20al.pdf.]

Examples

## Random length data
# suppose this is yellow perch to the nearest mm
df <- data.frame(spec=rep("Yellow Perch",170),
                 mm=c(rnorm(100,mean=125,sd=15),rnorm(50,mean=200,sd=25),
                      rnorm(20,mean=300,sd=40)))

## Example graphics
op <- par(mar=c(3,3,2,1),mgp=c(1.7,0.5,0))
# Using 10-mm increments
psdPlot(~mm,data=df,species="Yellow perch",w=10)
psdPlot(~mm,data=df,species="Yellow perch",w=10,substock.col="gray90",
        stock.col="gray30")
# ... but without the PSD values
psdPlot(~mm,data=df,species="Yellow perch",w=10,psd.add=FALSE)
par(op)

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