// library(ascii)
// setwd("c://aaaWork//web//fishR//bookex//AIFFD//Box6_7")
// Sweave("Box6_7a.Rnw",driver=RweaveAsciidoc)









AIFFD Box 6.7  Vignette
=======================
:Author:    Derek H. Ogle
:Email:     dogle@northland.edu
:Date:      29-June-2009
:Revision:  1

The analysis in this box very closely follows the techniques shown in the link:../Box6_3/Box6_3a.html[Box 6.3] and link:../Box6_4/Box6_4a.html[Box 6.4] vignettes.  Thus, many of the details are not described in detail here.

== Required Packages and Setting Options
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> library(FSA)    # chapman.robson, catch.curve

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== Preparing Data
The data for this box was entered directly into R:
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> 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)

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image::Box6_7a-004.png[]

== 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)

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image::Box6_7a-005.png[]