psdVal {FSA} | R Documentation |
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 |
units |
A string that indicates the units for the returned lengths. Choices are |
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 |
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 ( |
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, DerekOgle51@gmail.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 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))