bsm: Bayesian state-space surplus production model

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

Bayesian state-space surplus production 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 the Bayesian surplus production model from Froese et al. 2017.

Usage

bsm(year, catch, biomass, btype, 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, q.start = NA, q.end = NA, verbose = T)

Arguments

year	A time series of years
catch	A time series of catch
biomass	A time series of biomass or CPUE (specifiy type in btype)
btype	Biomass time series type: "CPUE" or "biomass" (at least 5 years required)
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)
q.start, q.end	A user-specified start and end year for estimating the catchability coefficient (optional)
verbose	Set to FALSE to suppress printed updates on model progress (default=TRUE)

Details

The Bayesian state-space surplus production model (BSM) developed by Froese et al. 2017 is fitted using a catch time series and any available (i.e., doesn't have to be complete) biomass or catch-per-unit-effort (CPUE) data. It extends the algorithms used to set bounds for r, K, and start, intermediate, and final year saturation in CMSY by deriving density distributions from these originally uniform bounds and by adding a prior for catchability, q. BSM 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).

This implementation of BSM is based on version "O 7q". BSM 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
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 BSM to catch time series and plot output
output <- bsm(year=SOLIRIS$yr, catch=SOLIRIS$ct, biomass=SOLIRIS$bt,
              btype="CPUE", 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.