psdCalc | R Documentation |
Convenience function for calculating (traditional) PSD-X and (incremental) PSD X-Y values for all Gabelhouse lengths and increments thereof.
psdCalc(
formula,
data,
species,
group = NULL,
units = c("mm", "cm", "in"),
method = c("multinomial", "binomial"),
conf.level = 0.95,
addLens = NULL,
addNames = NULL,
justAdds = FALSE,
what = c("all", "traditional", "incremental", "none"),
drop0Est = TRUE,
showIntermediate = FALSE,
digits = 0
)
formula |
A formula of the form |
data |
A data.frame that minimally contains the observed lengths given in the variable in |
species |
A string that contains the species name for which Gabelhouse lengths exist. See |
group |
A string that contains the sub-group of |
units |
A string that indicates the type of units used for the lengths. Choices are |
method |
A character that identifies the confidence interval method to use. See details in |
conf.level |
A number that indicates the level of confidence to use for constructing confidence intervals (default is |
addLens |
A numeric vector that contains minimum lengths for additional categories. See |
addNames |
A string vector that contains names for the additional lengths added with |
justAdds |
A logical that indicates whether just the values related to the lengths in |
what |
A string that indicates the type of PSD values that will be printed. See details. |
drop0Est |
A logical that indicates whether the PSD values that are zero should be dropped from the output. |
showIntermediate |
A logical that indicates whether the number of fish in the category and the number of stock fish (i.e., “intermediate” values) should be included in the returned matrix. Default is to not include these values. |
digits |
A numeric that indicates the number of decimals to round the result to. Default is zero digits following the recommendation of Neumann and Allen (2007). |
Computes the (traditional) PSD-X and (incremental) PSD X-Y values, with associated confidence intervals, for each Gabelhouse length. All PSD-X and PSD X-Y values are printed if what="all"
(DEFAULT), only PSD-X values are printed if what="traditional"
, only PSD X-Y values are printed if what="incremental"
, and nothing is printed (but the matrix is still returned) if what="none"
.
Confidence intervals can be computed with either the multinomial (DEFAULT) or binomial distribution as set in method
See details in psdCI
for more information.
This function may be used for species for which Gabelhouse length categories are not defined. In this case do not include a name in species
, but define at least two lengths in addLens
where the first category MUST be called “stock”.
See examples and this article for a demonstration.
A matrix with columns that contain the computed PSD-X or PSD X-Y values and associated confidence intervals. If showIntermediate=TRUE
then the number of fish in the category and the number of stock fish will also be shown.
Point estimate calculations match those constructed "by hand."
6-Size Structure.
Derek H. Ogle, DerekOgle51@gmail.com
Ogle, D.H. 2016. Introductory Fisheries Analyses with RChapman & 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. Anderson2006Proportional 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.]
Neumann, R.M. and Allen, M.S. 2007. Size structure. In Guy, C.S. and Brown, M.L., editors, Analysis and Interpretation of Freshwater Fisheries Data, Chapter 9, pages 375-421. American Fisheries Society, Bethesda, MD.
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 psdVal
, psdPlot
, psdAdd
, PSDlit
, tictactoe
, lencat
, and rcumsum
for related functionality.
#===== Random length data for Yellow Perch (for example) to the nearest mm
set.seed(633437)
yepdf <- data.frame(yepmm=round(c(rnorm(100,mean=125,sd=15),
rnorm(50,mean=200,sd=25),
rnorm(20,mean=270,sd=40)),0),
species=rep("Yellow Perch",170))
#===== Simple (typical) uses with just Gabelhouse lengths
#----- All results
psdCalc(~yepmm,data=yepdf,species="Yellow Perch")
#----- Just the traditional indices
psdCalc(~yepmm,data=yepdf,species="Yellow Perch",what="traditional")
#----- Just the incremental indices
psdCalc(~yepmm,data=yepdf,species="Yellow Perch",what="incremental")
#===== Add a custom length of interest (to the Gabelhouse lengths)
psdCalc(~yepmm,data=yepdf,species="Yellow Perch",addLens=150)
#----- Additional lengths can be named
psdCalc(~yepmm,data=yepdf,species="Yellow Perch",addLens=c("minLen"=150))
psdCalc(~yepmm,data=yepdf,species="Yellow Perch",
addLens=c("minLen"=150,"maxslot"=275))
#----- Can return just those results that include the additional lengths
psdCalc(~yepmm,data=yepdf,species="Yellow Perch",
addLens=c("minSlot"=150,"maxSlot"=275),justAdds=TRUE)
psdCalc(~yepmm,data=yepdf,species="Yellow Perch",
addLens=c("minSlot"=150,"maxSlot"=275),justAdds=TRUE,what="traditional")
#===== Can show intermediate values (num in category and in stock)
psdCalc(~yepmm,data=yepdf,species="Yellow Perch",showInterm=TRUE)
#===== Some species require use of group (e.g., treat these as if Brown Trout)
psdCalc(~yepmm,data=yepdf,species="Brown Trout",group="lotic")
psdCalc(~yepmm,data=yepdf,species="Brown Trout",group="lentic")
#===== For species not in PSDlit ... don't include species and use addLens
# Note that these are same data as above, but treated as different species
psdCalc(~yepmm,data=yepdf,addLens=c("stock"=130,"quality"=200,"preferred"=250,
"memorable"=300,"trophy"=380))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.