depletion {FSA}R Documentation

Computes the Leslie or Delury population estimate from catch and effort data.

Description

Computes the Leslie or Delury estimates of population size and catchability coefficient from paired catch and effort data. The Ricker modification may also be used.

Usage

depletion(catch,effort,type=c("Leslie","Delury"),ricker.mod=FALSE)

## S3 method for class 'Depletion':
plot(x,pos.est="topright",xlab=NULL,ylab=NULL,pch=19,col.pt="black",
     col.mdl="red",lwd=2,lty=1,...)

## S3 method for class 'Depletion':
summary(object,type=c("params","lm"),...)

## S3 method for class 'Depletion':
coef(object,type=c("params","lm"),...)

## S3 method for class 'Depletion':
anova(object,...)

## S3 method for class 'Depletion':
confint(object,parm=c("both","all","q","No","lm"),level=conf.level,
        conf.level=0.95,...)

Arguments

catch Vector of catches of fish at each time.
effort Vector of efforts expended at each time.
type A string identifying which depletion method to use (in depletion or a string indicating the type of summary or coefficients to extract. In the latter case, if type="params" (the default) then results for No and q are returned. If type="lm" then results for the underlying linear model are returned..
ricker.mod A logical indicating whether to use the modification proposed by Ricker (=TRUE) or not (=FALSE, default).
object An object saved from the removal call (i.e., of class Depletion).
x An object saved from the depletion call (i.e., of class Depletion).
pos.est A string to identify where to place the estimated mortality rates on the graph. See details.
ylab A label for the y-axis.
xlab A label for the x-axis.
pch A numeric used to indicate the type of plotting character.
col.pt a string used to indicate the color of the plotted points.
col.mdl a string used to indicate the color of the fitted line.
lwd a numeric used to indicate the line width of the fitted line.
lty a numeric used to indicate the type of line used for the fitted line.
parm a specification of which parameters are to be given confidence intervals, either a vector of numbers or a vector of names. If missing, all parameters are considered.
level Same as conf.level but used for compatability with generic confint function.
conf.level a number representing the level of confidence to use for constructing confidence intervals.
... Additional arguments for methods.

Details

Fits a linear regression model to catch-per-unit-effort on cumulative catch. The catchability coefficient is estimated from the negative of the slope and the initial population size is estimated from dividing the intercept by the catchability coefficient.

Standard errors for the catchability and population size estimates are computed using formulas from Seber (1982).

Confidence intervals are computed using standard large-sample normal distribution theory with regression error df.

The pos.est= argument can be set to one of "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" or "center" for positioning the estimated mortality rates on the plot. Typically "bottomleft" (DEFAULT) and "topright" will be “out-of-the-way” placements. Set pos.est to NULL to remove the estimated population size and catchability coefficient from the plot.

Value

A list with the following items

type a string indicating whether the "Leslie" or "Delury" model was used.
catch the original vector of catches.
effort the orginal vector of efforts.
cpe a computed vector of catch-per-unit-effort for each time.
K or E a computed vector of cumulative catch (K; Leslie method) or effort (E; Delury method).
lm the lm object from the fit of log(CPE) on K (Leslie method) or E (Delury method).
est A 2x2 matrix that contains the estimates and standard errors for No and q.

Author(s)

Derek H. Ogle, dogle@northland.edu

References

Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada.

Seber, G.A.F. 1982. The Estimation of Animal Abundance. Edward Arnold, second edition.

See Also

leslie.sim, leslie.sim2, removal

Examples

data(SMBassLS)
attach(SMBassLS)

# Leslie model examples
l1 <- depletion(catch,effort,"Leslie")
plot(l1)
confint(l1)
summary(l1)
summary(l1,type="lm")
l2 <- depletion(catch,effort,"L",ricker.mod=TRUE)
plot(l2)
confint(l2)

# Delury model examples
d1 <- depletion(catch,effort,"Delury")
plot(d1)
confint(d1)
summary(d1)
summary(d1,type="lm")
d2 <- depletion(catch,effort,"D",ricker.mod=TRUE)
plot(d2)
confint(d2)

detach(SMBassLS)
[Package FSA version 0.0-13 Index]