In smartell/CatchMSY: Catch-MSY method for estimating MSY-based reference points

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

Summary

In this vignette I use the Namimian Hake as an example of how to use this package using:

1. only catch data
2. catch data and relative abundance
3. catch data, relative abundance, and changes in mean size of the catch

First, we'll have a look at the input data and the Stock ID object sID. To create a new stock ID object we use the function new_sID. The data for this example were taken from chapter 10 in the Ecological Detective (Hilborn and Mangel, 1997).

    library(catchMSY)
    data(NamibianHake)
    names(hake)
    head(hake$data)

Given a valid `sID' object, you can quickly run the age-structured model and preview the results.

    hake <- runModel(hake)
    str(hake)

library(catchMSY)
data(NamibianHake)
knitr::kable(head(hake$data, 10))

Input data and Stock ID

The stock ID object for this example is included in the catchMSY package, and the default values for new_sID were used to set up the initial stock ID object. Here is the structure of that object.

The catchMSY package is intended to be used to determine MSY-based reference points.

The catchMSY package is based on the initial work for Martell and Froese (2012). "A simple method for estimating MSY from catch and resilience".

This is a simple example based on the Namibian hake dataset published in the ecoloigical detective (Hilborn and Mangle, 1997).

Steps:

• assemble a time-series data file for your stock.
• create a stockID object

stockID object (sID)

Describe the contaents of an 'sID' object.

library(catchMSY)
library(ggplot2)


# load the hake sID object
data(NamibianHake)

# run the age structured model.
hake <- runModel(hake)

# plot the biomass
qplot(hake$year,hake$bt,geom="line")

References

Hilborn, R. and Mangel, M. (1997). The ecological detective: confronting models with data. Princeton Univ Pr.

Martell, S. and Froese, R. (2012). A simple method for estimating msy from catch and resilience. Fish and Fisheries.

smartell/CatchMSY documentation built on May 30, 2019, 3:07 a.m.