AIFFD Box 6.7 Vignette

The analysis in this box very closely follows the techniques shown in the Box 6.3 and Box 6.4 vignettes. Thus, many of the details are not described in detail here.

Required Packages and Setting Options

> library(FSA)    # chapman.robson, catch.curve

Preparing Data

The data for this box was entered directly into R:

> d <- data.frame(age=1:6,catch=c(65,66,27,6,4,1))
> d
  age catch
1   1    65
2   2    66
3   3    27
4   4     6
5   5     4
6   6     1

Chapman-Robson Method

Note that the authors suggest that age-2 and older fish are recruited to the gear.

> cr1 <- chapman.robson(d$age, d$catch, 2:6)
> summary(cr1)
Intermediate Statistics
n=104; T=55

Estimates with Standard Errors
   Estimate Std. Err.
S 34.810127 3.8018331
Z  1.055262 0.1092163
> confint(cr1)
     95% LCI   95% UCI
S 27.3586707 42.261582
Z  0.8412018  1.269322
> plot(cr1)

Catch-Curve Method

Note that the authors also note (correctly) that the last age should not be used because of the very small sample size.

> cc1 <- catch.curve(d$age, d$catch, 2:5)
> summary(cc1)
    Estimate Std. Error  t value   Pr(>|t|)
Z  0.9914159  0.1433995 6.913662 0.02028661
A 62.8949035         NA       NA         NA
> confint(cc1)
     95% LCI   95% UCI
Z  0.3744175  1.608414
A 31.2310244 79.979516
> plot(cc1)