psdVal: Finds Gabelhouse lengths (for PSD calculations) for a...

In fishR-Core-Team/FSA: Simple Fisheries Stock Assessment Methods

Finds Gabelhouse lengths (for PSD calculations) for a species.

Description

Returns a vector with the five Gabelhouse lengths for a chosen species.

Usage

psdVal(
  species = "List",
  group = NULL,
  units = c("mm", "cm", "in"),
  addLens = NULL,
  addNames = NULL,
  incl.zero = TRUE,
  showJustSource = FALSE
)

Arguments

species	A string that contains the species name for which to find Gabelhouse lengths. See details.
group	A string that contains the sub-group of species for which to find the Gabelhouse lengths; e.g., things like “landlocked”, “lentic”.
units	A string that indicates the units for the returned lengths. Choices are mm for millimeters (DEFAULT), cm for centimeters, and in for inches.
addLens	A numeric vector that contains minimum length definitions for additional categories. See details.
addNames	A string vector that contains names for the additional length categories added with addLens. See details.
incl.zero	A logical that indicates if a zero is included in the first position of the returned vector (DEFAULT) or not. This position will be named “substock”. See details.
showJustSource	A logical that indicates whether just the literature source information should be returned (TRUE) or not. If TRUE this will NOT return any of the Gabelhouse length information.

Details

Finds the Gabelhouse lengths from data(PSDlit) for the species given in species. The species name must be spelled exactly (including capitalization) as it appears in data(PSDlit). Type psdVal() to see the list of species and how they are spelled.

A zero is included in the first position of the returned vector if incl.zero=TRUE. This is useful when computing PSD values with a data.frame that contains fish smaller than the stock length.

Additional lengths may be added to the returned vector with addLens. Names for these lengths can be included as names in addLens or separately in addNames. If addNames is NULL and addLens is not named then the default category names will be the lengths from addLens. The addLens argument is useful for calculating PSD values that are different from the Gabelhouse lengths.

See examples and this article for a demonstration.

Value

A vector of minimum values for length categories for the chosen species.

IFAR Chapter

6-Size Structure.

Author(s)

Derek H. Ogle, [e-mail]

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

Examples

#===== List all available species in PSDlit
psdVal()

#===== Typical usages
psdVal("Bluegill")
psdVal("Bluegill",units="in")
psdVal("Bluegill",units="in",incl.zero=FALSE)
psdVal("Bluegill",showJustSource=TRUE)

#===== For species that have sub-groups
psdVal("Brown Trout",group="lentic")
psdVal("Brown Trout",group="lotic")
psdVal("Palmetto Bass",group="revised")
psdVal("Palmetto Bass",group="original")

#===== Adding user-defined categories
#-----   with lengths and names separately in addLens= and addNames=
psdVal("Bluegill",units="in",addLens=7)
psdVal("Bluegill",units="in",addLens=7,addNames="MinLen")
psdVal("Bluegill",units="in",addLens=c(7,9),addNames=c("MinSlot","MaxSlot"))
#-----   with a named vector in addLens=
psdVal("Bluegill",units="in",addLens=c("MinLen"=7))
psdVal("Bluegill",units="in",addLens=c("MinSlot"=7,"MaxSlot"=9))

fishR-Core-Team/FSA documentation built on June 14, 2025, 10:01 p.m.