psdAdd: Creates a vector of Gabelhouse lengths for each species in an...

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

Creates a vector of Gabelhouse lengths for each species in an entire data frame.

Description

Creates a vector of the Gabelhouse lengths specific to a species for all individuals in an entire data frame.

Usage

psdAdd(len, ...)

## Default S3 method:
psdAdd(
  len,
  species,
  units = c("mm", "cm", "in"),
  use.names = TRUE,
  addSpec = NULL,
  addLens = NULL,
  verbose = TRUE,
  ...
)

## S3 method for class 'formula'
psdAdd(
  len,
  data = NULL,
  units = c("mm", "cm", "in"),
  use.names = TRUE,
  addSpec = NULL,
  addLens = NULL,
  verbose = TRUE,
  ...
)

Arguments

len	A numeric vector that contains lengths measurements or a formula of the form len~spec where “len” generically represents the length variable and “spec” generically represents the species variable. Note that this formula can only contain two variables and must have the length variable on the left-hand-side and the species variable on the right-hand-side.
...	Not used.
species	A character or factor vector that contains the species names. Ignored if len is a formula.
units	A string that indicates the type of units used for the lengths. Choices are mm for millimeters (DEFAULT), cm for centimeters, and in for inches.
use.names	A logical that indicates whether the vector returned is numeric (=FALSE) or string (=TRUE; default) representations of the Gabelhouse lengths. See details.
addSpec	A character vector of species names for which addLens will be provided.
addLens	A numeric vector of lengths that should be used in addition to the Gabelhouse lengths for the species in addSpec. See examples.
verbose	A logical that indicates whether detailed messages about species without Gabelhouse lengths or with no recorded values should be printed or not.
data	A data.frame that minimally contains the length measurements and species names if len is a formula.

Details

This computes a vector that contains the Gabelhouse lengths specific to each species for all individuals in an entire data frame. The vector can be appended to an existing data.frame to create a variable that contains the Gabelhouse lengths for each individual. The Gabelhouse length value will be NA for each individual for which Gabelhouse length definitions do not exist in PSDlit. Species names in the data.frame must be the same as those used in PSDlit. See the examples for one method for changing species names to something that this function will recognize.

Individuals shorter than “stock” length will be listed as substock if use.names=TRUE or 0 if use.names=FALSE.

Additional lengths to be used for a species may be included by giving a vector of species names in addSpec and a corresponding vector of additional lengths in addLens. Note, however, that use.names will be reset to FALSE if addSpec and addLens are specified, as there is no way to order the names for all species when additional lengths are used.

Value

A numeric or factor vector that contains the Gabelhouse length categories.

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

psdVal, psdCalc, psdPlot, PSDlit, and wrAdd for related functions. See mapvalues for help in changing species names to match those in PSDlit.

Examples

## Create random data for three species
# only for repeatability
set.seed(345234534)
dbg <- data.frame(species=factor(rep(c("Bluegill"),30)),
                  tl=round(rnorm(30,130,50),0))
dbg$wt <- round(4.23e-06*dbg$tl^3.316+rnorm(30,0,10),1)
dlb <- data.frame(species=factor(rep(c("Largemouth Bass"),30)),
                  tl=round(rnorm(30,350,60),0))
dlb$wt <- round(2.96e-06*dlb$tl^3.273+rnorm(30,0,60),1)
dbt <- data.frame(species=factor(rep(c("Bluefin Tuna"),30)),
                  tl=round(rnorm(30,1900,300),0))
dbt$wt <- round(4.5e-05*dbt$tl^2.8+rnorm(30,0,6000),1)
df <- rbind(dbg,dlb,dbt)
str(df)

## Examples (non-dplyr)
# Add variable using category names -- formula notation
df$PSD <- psdAdd(tl~species,data=df)
head(df)
# Add variable using category names -- non-formula notation
df$PSD1 <- psdAdd(df$tl,df$species)
head(df)
# Add variable using length values as names
df$PSD2 <- psdAdd(tl~species,data=df,use.names=FALSE)
head(df)
# Add additional length and name for Bluegill
df$PSD3 <- psdAdd(tl~species,data=df,addSpec="Bluegill",addLens=175)
head(df)
# Add add'l lengths and names for Bluegill and Largemouth Bass from a data.frame
addls <- data.frame(species=c("Bluegill","Largemouth Bass","Largemouth Bass"),
                    lens=c(175,254,356))
df$psd4 <- psdAdd(tl~species,data=df,addSpec=addls$species,addLens=addls$lens)
head(df)

## All of the above but using dplyr
if (require(dplyr)) {
  df <- df %>%
    mutate(PSD1A=psdAdd(tl,species)) %>%
    mutate(PSD2A=psdAdd(tl,species,use.names=FALSE)) %>%
    mutate(psd3a=psdAdd(tl,species,addSpec="Bluegill",addLens=175)) %>%
    mutate(psd4a=psdAdd(tl,species,addSpec=addls$species,addLens=addls$lens))
}
df

fishR-Core-Team/FSA documentation built on Jan. 22, 2025, 7:49 p.m.