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Last data update: 2014.03.03

R: Length-frequency histogram with Gabelhouse lengths...

psdPlot

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 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 PSD category values.
`psd.lty`	A numeric that indicates the line type to use for the vertical lines at the PSD category values.
`psd.lwd`	A numeric that indicates the line width to use for the vertical lines at the PSD 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 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
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 <- Subset(df,mm>brks["stock"])
psdPlot(~mm,data=tmp,species="Yellow perch",w=10)
# ... without any sub-stock or stock fish
tmp <- Subset(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 <- Subset(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 <- Subset(df,mm<brks["stock"])
## Not run:  psdPlot(~mm,data=tmp,species="Yellow perch",w=10) 
par(op)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(FSA)


 ############################################
 ##      FSA package, version 0.8.7        ##
 ##    Derek H. Ogle, Northland College    ##
 ##                                        ##
 ## Run ?FSA for documentation.            ##
 ## Run citation('FSA') for citation ...   ##
 ##   please cite if used in publication.  ##
 ##                                        ##
 ## See derekogle.com/fishR/ for more      ##
 ##   thorough analytical vignettes.       ##
 ############################################


> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/FSA/psdPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: psdPlot
> ### Title: Length-frequency histogram with Gabelhouse lengths highlighted.
> ### Aliases: psdPlot
> ### Keywords: hplot
> 
> ### ** 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 <- Subset(df,mm>brks["stock"])
> psdPlot(~mm,data=tmp,species="Yellow perch",w=10)
> # ... without any sub-stock or stock fish
> tmp <- Subset(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 <- Subset(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 <- Subset(df,mm<brks["stock"])
> ## Not run:  psdPlot(~mm,data=tmp,species="Yellow perch",w=10) 
> par(op)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>