psdPlot {FSA}R Documentation

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)),
  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.]

See Also

See psdVal, psdCalc, psdAdd, PSDlit, lencat, tictactoe, lencat, and rcumsum for related functionality.

Examples

## Random length data
# suppose this is yellow perch to the nearest mm
mm <- c(rnorm(100,mean=125,sd=15),rnorm(50,mean=200,sd=25),
        rnorm(20,mean=300,sd=40))
# same data to the nearest 0.1 cm
cm <- mm/10
# same data to the nearest 0.1 in
inch <- mm/25.4
# put together as data.frame
df <- data.frame(mm,cm,inch)

## Example graphics
op <- par(mar=c(3,3,2,1),mgp=c(1.7,0.5,0))
# mm data using 10-mm increments
psdPlot(~mm,data=df,species="Yellow perch",w=10)
# cm data using 1-cm increments
psdPlot(~cm,data=df,species="Yellow perch",units="cm",w=1)
# inch data using 1-in increments
psdPlot(~inch,data=df,species="Yellow perch",units="in",w=1)
# same as first with some color changes
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)
# ... demonstrate use of xlim
psdPlot(~mm,data=df,species="Yellow perch",w=10,xlim=c(100,300))

## different subsets of fish
# ... without any sub-stock fish
brks <- psdVal("Yellow Perch")
tmp <- filterD(df,mm>brks["stock"])
psdPlot(~mm,data=tmp,species="Yellow perch",w=10)
# ... without any sub-stock or stock fish
tmp <- filterD(df,mm>brks["quality"])
psdPlot(~mm,data=tmp,species="Yellow perch",w=10)
# ... with only sub-stock, stock, and quality fish ... only PSD-Q
tmp <- filterD(df,mm<brks["preferred"])
psdPlot(~mm,data=tmp,species="Yellow perch",w=10)
# ... with only sub-stock fish (don't run ... setup to give an error)
tmp <- filterD(df,mm<brks["stock"])
## Not run:  psdPlot(~mm,data=tmp,species="Yellow perch",w=10) 
par(op)


[Package FSA version 0.8.26.9000 Index]