R: Computes Chapman-Robson estimates of S and Z.

chapman.robson {FSA}

R Documentation

Computes Chapman-Robson estimates of S and Z.

Description

Computes the Chapman-Robson estimates of annual survival rate (S) and instantaneous mortality rate (Z), along with associated standard errors, from catch-at-age data on the descending limb of a catch-curve.

Usage


chapman.robson(age, catch, ages2use=age)

## S3 method for class 'CR':
plot(x,pos.est="bottomleft",ylab="Catch",xlab="Age",col.pt="black",...)

## S3 method for class 'CR':
summary(object, ...)

## S3 method for class 'CR':
confint(object,parm=c("all","both","S","Z"),level=conf.level,
       conf.level=0.95, ...)

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 `chapman.robson` call (i.e., of class `CR`).
`x`	An object saved from the `chapman.robson` call (i.e., of class `CR`).
`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.
`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 with 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 used to estimate mortalities.
`catch.e`	a vector of catches or CPUEs used to estimate mortalities.
`age.r`	a vector of recoded ages used to estimate mortalities. See references.
`n`	a numeric holding the intermediate calcualtion of n. See references.
`T`	a numeric holding the intermediate calcualtion of T. See references.
`est`	A 2x2 matrix that contains the estimates and standard errors for S and Z.

Author(s)

Derek H. Ogle, dogle@northland.edu

References

D.G. Chapman and D.S. Robson. 1960. The analysis of a catch curve. Biometrics. 16:354-368.

D.S. Robson and D.G. Chapman. 1961. Catch curves and mortality rates. Transactions of the American Fisheries Society. 90:181-189.

Examples

data(BrookTroutTH)
attach(BrookTroutTH)
cr <- chapman.robson(age,catch,2:6)
summary(cr)
confint(cr)
detach(BrookTroutTH)

[Package FSA version 0.0-13 Index]