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,
dat = NULL
)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
speciesfor 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
mmfor millimeters (DEFAULT),cmfor centimeters, andinfor 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. IfTRUEthis will NOT return any of the Gabelhouse length information.- dat
Data.frame of Gabelhouse length categories for all species. Defaults to `PSDlit` and is generally not used by the user (this simplifies use of this function in
psdAdd).
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.
Some species have length categories separated by sub-group. For example, length categories exist for both lentic and lotic populations of Brown Trout. The length values for a sub-group may be obtained by either including the species name in species and the sub-group name in group or by using the combined species and sub-group name, with the sub-group name in parentheses, in species. Both methods are demonstrated in the examples. Note that an error is returned if a species has sub-groups but neither method is used to define the sub-group.#'
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.
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.]
Author
Derek H. Ogle, DerekOgle51@gmail.com
Examples
#===== List all available species in PSDlit
psdVal()
#>
#> Species name must be one of following. Be careful of spelling and capitalization.
#> [1] "Alabama Bass" "Arctic Grayling"
#> [3] "Bighead Carp" "Bigmouth Buffalo"
#> [5] "Black Bullhead" "Black Carp"
#> [7] "Black Crappie" "Blue Catfish"
#> [9] "Bluegill" "Brook Trout"
#> [11] "Brook Trout (lentic)" "Brook Trout (lotic)"
#> [13] "Brook Trout (overall)" "Brown Bullhead"
#> [15] "Brown Trout" "Brown Trout (lentic)"
#> [17] "Brown Trout (lotic)" "Bull Trout"
#> [19] "Burbot" "Chain Pickerel"
#> [21] "Channel Catfish" "Chinook Salmon"
#> [23] "Chinook Salmon (landlocked)" "Common Carp"
#> [25] "Cutthroat Trout" "Cutthroat Trout (lentic)"
#> [27] "Cutthroat Trout (lotic)" "Flathead Catfish"
#> [29] "Flier" "Freshwater Drum"
#> [31] "Gizzard Shad" "Golden Trout"
#> [33] "Goldeye" "Grass Carp"
#> [35] "Green Sunfish" "Kokanee"
#> [37] "Lake Chubsucker" "Lake Trout"
#> [39] "Largemouth Bass" "Longear Sunfish"
#> [41] "Longnose Gar" "Muskellunge"
#> [43] "Muskellunge (female)" "Muskellunge (male)"
#> [45] "Muskellunge (overall)" "Northern Pike"
#> [47] "Northern Pikeminnow" "Northern Snakehead"
#> [49] "Paddlefish" "Paddlefish (female)"
#> [51] "Paddlefish (male)" "Paddlefish (overall)"
#> [53] "Pallid Sturgeon" "Palmetto Bass"
#> [55] "Palmetto Bass (original)" "Pumpkinseed"
#> [57] "Rainbow Trout" "Rainbow Trout (lentic)"
#> [59] "Rainbow Trout (lotic)" "Redbreast Sunfish"
#> [61] "Redear Sunfish" "River Carpsucker"
#> [63] "Rock Bass" "Ruffe"
#> [65] "Sauger" "Saugeye"
#> [67] "Shoal Bass" "Shorthead Redhorse"
#> [69] "Silver Carp" "Smallmouth Bass"
#> [71] "Smallmouth Buffalo " "Splake"
#> [73] "Spotted Bass" "Spotted Bass (original)"
#> [75] "Spotted Gar" "Spotted Sunfish"
#> [77] "Striped Bass" "Striped Bass (landlocked)"
#> [79] "Striped Bass X White Bass" "Suwannee Bass"
#> [81] "Utah Chub" "Walleye"
#> [83] "Walleye (30-149 mm)" "Walleye (overall)"
#> [85] "Warmouth" "White Bass"
#> [87] "White Catfish" "White Crappie"
#> [89] "White Perch" "White Sucker"
#> [91] "Yellow Bass" "Yellow Bullhead"
#> [93] "Yellow Perch"
#===== Typical usages
psdVal("Bluegill")
#> substock stock quality preferred memorable trophy
#> 0 80 150 200 250 300
psdVal("Bluegill",units="in")
#> substock stock quality preferred memorable trophy
#> 0 3 6 8 10 12
psdVal("Bluegill",units="in",incl.zero=FALSE)
#> stock quality preferred memorable trophy
#> 3 6 8 10 12
psdVal("Bluegill",showJustSource=TRUE)
#> species source
#> 9 Bluegill Gabelhouse (1984a)
#===== For species that have sub-groups
#----- using group= argument
psdVal("Brown Trout",group="lentic")
#> substock stock quality preferred memorable trophy
#> 0 200 300 400 500 600
psdVal("Brown Trout",group="lotic")
#> substock stock quality preferred memorable trophy
#> 0 150 230 300 380 460
#----- group combined in species name, so no group= use
psdVal("Brown Trout (lentic)")
#> substock stock quality preferred memorable trophy
#> 0 200 300 400 500 600
#===== For species with revised values
psdVal("Palmetto Bass")
#> substock stock quality preferred memorable trophy
#> 0 250 410 510 610 710
psdVal("Palmetto Bass (original)")
#> substock stock quality preferred memorable trophy
#> 0 200 300 380 510 630
#===== Adding user-defined categories
#----- with lengths and names separately in addLens= and addNames=
psdVal("Bluegill",units="in",addLens=7)
#> substock stock quality 7 preferred memorable trophy
#> 0 3 6 7 8 10 12
psdVal("Bluegill",units="in",addLens=7,addNames="MinLen")
#> substock stock quality MinLen preferred memorable trophy
#> 0 3 6 7 8 10 12
psdVal("Bluegill",units="in",addLens=c(7,9),addNames=c("MinSlot","MaxSlot"))
#> substock stock quality MinSlot preferred MaxSlot memorable trophy
#> 0 3 6 7 8 9 10 12
#----- with a named vector in addLens=
psdVal("Bluegill",units="in",addLens=c("MinLen"=7))
#> substock stock quality MinLen preferred memorable trophy
#> 0 3 6 7 8 10 12
psdVal("Bluegill",units="in",addLens=c("MinSlot"=7,"MaxSlot"=9))
#> substock stock quality MinSlot preferred MaxSlot memorable trophy
#> 0 3 6 7 8 9 10 12