zbrt: Zhou-BRT catch-only stock assessment model

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

Zhou-BRT catch-only stock assessment model

Description

Estimates saturation (B/K) and stock status (B/BMSY) time series from a time series of catch using the boosted regression tree (BRT) model from Zhou et al. 2017. Note: B/BMSY is equal to saturation times two.

Usage

zbrt(year, catch)

Arguments

year	A time series of years
catch	A time series of catch

Details

Zhou et al. 2017 use boosted regression tree models (Zhou-BRT) trained on the RAM Legacy Database to estimate saturation (i.e., 1 - depletion = 0.5*B/BMSY) from 56 catch history statistics, the most important of which are linear regression coefficients for the whole catch time series, the subseries before and after the maximum catch, and in recent years. Ultimately, saturation is estimated as the average of the saturation values predicted by two reduced and bias-corrected BRT models (8 and 38 predictors each). B/BMSY is estimated as saturation doubled.

Value

A list with the following elements:

ts	A data frame with a time series of saturation and B/BMSY estimates. S8 and S38 correspond to the saturation estimates from the 8- and 38-predictor models, respectively. S, the best estimate of saturation, is the mean of these two predictions. B/BMSY is this estimate doubled (B/BMSY = S * 2). High and low values correspond to the upper and lower 95% confidence intervals, respectively.
method	Name of the method

References

Zhou S, Punt AE, Yimin Y, Ellis N, Dichmont CM, Haddon M, Smith DC, Smith ADM (2017) Estimating stock depletion level from patterns of catch history. Fish and Fisheries. http://onlinelibrary.wiley.com/doi/10.1111/faf.12201/abstract

Examples

# Fit zBRT model to catch time series and plot output
output <- zbrt(year=TIGERFLAT$yr, catch=TIGERFLAT$catch)
plot_dlm(output)

# Extract time series from output
ts <- output[["ts"]]

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