R: Mortality estimates from the descending limb of a catch curve.

catch.curve {FSA}

R Documentation

Mortality estimates from the descending limb of a catch curve.

Description

Fits a linear model to the user-defined descending limb of a catch curve. A plot method shows the user-defined descending-limb highlighted, the linear model shown for the descending limb, and, optionally, the estimated instantaneous and annual mortality rates computed from the descending-limb.

Usage

catch.curve(age, catch, ages2use=age)

## S3 method for class 'CC':
plot(x,pos.est="bottomleft", ylab="log(Catch)", xlab="Age", col.pt="black",
     col.mdl="red",lwd=2,lty=1, ...)

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

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

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

## S3 method for class 'CC':
confint(object,parm=NULL,level=conf.level,conf.level=0.95,
        type=c("params","lm"), ...)

Arguments

`age`	A numerical vector of the assigned ages in the catch curve.
`catch`	A numerical vector of the catches or CPUEs for the ages in the catch curve.
`ages2use`	A numerical vector of the ages represented on the descending limb of the catch curve.
`object`	An object saved from the `catch.curve` call (i.e., of class `CC`).
`x`	An object saved from the `catch.curve` call (i.e., of class `CC`).
`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 (`"log(Catch)"` is the default).
`xlab`	A label for the x-axis (`"Age"` is the default).
`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.
`type`	a string used to indicate what type of summary should be returned. If `type="lm"` then summaries of the underlying linear model are returned. If `type="params"` then summaries of the Z and A parameters are returned.
`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

The default is to use all ages in the age vector. This is only appropriate if the age and catch vector contain only the ages and catches on the descending limb of the catch curve.

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 mortality rates from the plot.

Value

A list that contains the following items.

`age`	the original vector of assigned ages.
`catch`	the original vector of observed catches or CPUEs.
`age.e`	a vector of assigned ages for which the catch curve was fit.
`log.catch.e`	a vector of log catches or CPUEs for which the catch curve was fit.
`lm`	an `lm` object from the fit to the ages and log catches or CPUEs on the descending limb (i.e., in age.e and log.catch.e).

Author(s)

Derek H. Ogle, dogle@northland.edu

Examples

data(BrookTroutTH)
attach(BrookTroutTH)
cc <- catch.curve(age,catch,2:6)
par(mfrow=c(2,1))
plot(cc)
plot(cc,pos.est="topright")
summary(cc)
coef(cc)
confint(cc)
summary(cc,type="lm")
coef(cc,type="lm")
confint(cc,type="lm")
detach(BrookTroutTH)

[Package FSA version 0.0-13 Index]