ocom: Optimized catch-only model

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

Optimized catch-only model

Description

Estimates biomass, fishing mortality, and stock status (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 natural mortality (M) estimate using the optimized catch-only model (OCOM) from Zhou et al. 2017.

Usage

ocom(year, catch, m)

Arguments

year	A time series of years
catch	A time series of catch
m	Natural mortality (1/yr)

Details

The "optimized catch-only model" (OCOM) developed by Zhou et al. 2017 employs a stock reduction analysis (SRA) using priors for r and stock depletion derived from natural mortality and saturation estimated using the Zhou-BRT method, respectively. The SRA employs a Schaefer biomass dynamics model and an algorithm for identifying feasible parameter combinations to estimate biomass, fishing mortality, and stock status (B/BMSY, F/FMSY) time series and biological/management quantities (i.e., r, K, MSY, BMSY, FMSY).

Value

A list with the following elements:

ref_pts	A data frame with estimates of r, k, MSY, BMSY, FMSY and final year saturation and confidence intervals
ref_ts	A data frame with time series of biomass, saturation, fishing mortality, B/BMSY, and F/FMSY estimates and 95% confidence intervals
b_ts	A data frame with time series of biomass estimates and expanded confidence intervals
s_ts	A data frame with time series of saturation estimates and expanded confidence intervals
f_ts	A data frame with time series of fishing mortality (F) estimates and expanded confidence intervals
bbmsy_ts	A data frame with time series of B/BMSY estimates and expanded confidence intervals
ffmsy_ts	A data frame with time series of F/FMSY estimates and expanded confidence intervals
b_trajs	A data frame with 1000 randomly selected biomass trajectories
s_trajs	A data frame with 1000 corresponding saturation trajectories
f_trajs	A data frame with 1000 corresponding fishing mortality (F) trajectories
bbmsy_trajs	A data frame with 1000 corresponding B/BMSY trajectories
ffmsy_trajs	A data frame with 1000 corresponding F/FMSY trajectories
krms_draws	A data frame with 10,000 draws underpinning the estimakes of r, k, MSY, and saturation
method	Name of the method

References

Zhou S, Punt AE, Smith ADM, Ye Y, Haddon M, Dichmont CM, Smith DC (2017) An optimised catch-only assessment method for data poor fisheries. ICES Journal of Marine Science: doi:10.1093/icesjms/fsx226. https://doi.org/10.1093/icesjms/fsx226

Examples

# Fit OCOM to catch time series and plot output
set.seed(1) # stochastic fitting
output <- ocom(year=TIGERFLAT$yr, catch=TIGERFLAT$catch, m=0.27)
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.