cmsy2: CMSY catch-only stock assessment model

In cfree14/datalimited2: More Stock Assessment Methods for Data-limited Fisheries

CMSY catch-only stock assessment model

Description

Estimates biomass, fishing mortality, and stock status (i.e., B/BMSY, F/FMSY) time series and biological/management quantities (i.e., r, K, MSY, BMSY, FMSY) from a time series of catch and a resilience estimate using CMSY from Froese et al. 2017.

Usage

cmsy2(year, catch, resilience = NA, r.low = NA, r.hi = NA, stb.low = NA,
  stb.hi = NA, int.yr = NA, intb.low = NA, intb.hi = NA,
  endb.low = NA, endb.hi = NA, verbose = T)

Arguments

year	A time series of years
catch	A time series of catch
resilience	Resilience of the stock: "High", "Medium", "Low", or "Very low" (optional if r.low and r.hi are specified)
r.low, r.hi	A user-specified prior on the species intrinsic growth rate, r (optional if resilience is specified)
stb.low, stb.hi	A user-specified prior on biomass relative to unfished biomass at the beginning of the catch time series (optional)
int.yr	A user-specified year of intermediate biomass (optional)
intb.low, intb.hi	A user-specified prior on biomass relative to unfished biomass in the year of intermediate biomass (optional)
endb.low, endb.hi	A user-specified prior on biomass relative to unfished biomass at the end of the catch time series (optional)
verbose	Set to FALSE to suppress printed updates on model progress (default=TRUE)

Details

The CMSY model developed by Froese et al. 2017 employs a stock reduction analysis using priors for r based on resilience, K based on maximum catch and the r priors, and start, intermediate, and final year saturation based on a set of simple rules. It also allows users to revise the default priors based on expert knowledge. The SRA employs a Schaefer biomass dynamics model and an algorithm for identifying feasible parameter combinations to estimate biomass, fishing mortality, and stock status (i.e., B/BMSY, F/FMSY) time series and biological/management quantities (i.e., r, K, MSY, BMSY, FMSY).

This implementation of CMSY is based on version "O 7q". CMSY is constantly being improved so please consult the original authors about where to find the most up-to-date method.

Value

A list with the following elements:

ref_pts	A data frame with biological quantity and reference point estimates with 95% confidence intervals
ref_ts	A data frame with B/BMSY, F/FMSY, biomass, and fishing mortality time series with 95% confidence intervals
priors	A data frame with the priors used in the analysis
r_viable	A vector with the viable r values
k_viable	A vector with the viable K values
bt_viable	A data frame with the biomass trajectories produced by the viable r/K pairs
method	Name of the method

References

Froese R, Demirel N, Coro G, Kleisner KM, Winker H (2017) Estimating fisheries reference points from catch and resilience. Fish and Fisheries 18(3): 506-526. http://onlinelibrary.wiley.com/doi/10.1111/faf.12190/abstract

Examples

# Fit cMSY to catch time series and plot output
output <- cmsy2(year=SOLIRIS$yr, catch=SOLIRIS$ct, r.low=0.18, r.hi=1.02)
plot_dlm(output)

# Extract reference points and time series from output
ref_pts <- output[["ref_pts"]]
ref_ts <- output[["ref_ts"]]

cfree14/datalimited2 documentation built on Aug. 21, 2023, 2:26 p.m.