pope: Pope's Cohort Analysis

In hafroAssmt: Hafro Assessment Toolbox

Description

Perform Pope's approximate cohort analysis on a matrix of catch-at-age numbers.

Usage

pope(catage, surv, M=0.2)

Arguments

catage	Catch-at-age matrix, years in rows and ages in columns.
surv	Vector of survivors, of length equal to columns in catage), to the year following the newest catch.
M	Natural mortality rate, constant.

Details

The currently implemented assumption is that the whole catch is taken mid-year and the backwards calculation is initiated assuming that catch-at-oldest-age is the cohort's remainder. Natural mortality rate, in this simple model from all causes other than fishing, is assumed constant, defaults to a value once derived from a question mark. The vector of survivors has to be taken from other sources (a simple one would be from some type of ADAPT tuning).

Value

A matrix of numbers at age.

Author(s)

Sigurdur Thor Jonsson.

References

Pope, J.G. 1972. An investigation of the accuracy of virtual population analysis using cohort analysis. ICNAF Research Bulletin 9:65–74.

See Also

n2f evaluates F from numbers at age.

hafroAssmt-package gives an overview of the package.

Examples

# Prepare a matrix of catch-at-age from the data.frame 'catage'
catageMat <- tapply(catage$ObsCno, list(catage$year,catage$age), sum)

# Supply a vector of survivors
surv <- c(33845, 31405, 12389, 4199, 5001, 5306, 1141, 2179, 1244, 629,
          213, 111)

# Estimate numbers
Nmat <- pope(catageMat, surv)

# Time series of numbers-at-youngest-age
Nmat[,1]

# Estimate fishing mortalities
Fmat <- n2f(Nmat)

# Arithmetic mean F for a reference age range
# Note matrices have named dimensions
apply(Fmat[,colnames(Fmat) %in% 4:9], 1, mean)

hafroAssmt documentation built on May 2, 2019, 5:47 p.m.