Convert FLStock to FLSR

Create a stock-recruitment relationship object (FLSR) from an FLStock object. The method extracts recruitment and spawning stock biomass (SSB) data from an FLStock and constructs an FLSR object with properly lagged time series.

Usage

# S4 method for class 'FLStock'
as.FLSR(object, rec.age = dims(stock.n(object))$min, ...)

Arguments

object: An FLStock object to be converted
rec.age: Integer specifying the age at which recruitment is measured. Defaults to the minimum age class in the stock. Must be at least the minimum age class of the FLStock.
...: Additional arguments to be passed to the FLSR constructor, including model to specify the stock-recruitment model formula.

Value

An object of class FLSR containing:

rec: Recruitment time series as FLQuant, lagged by rec.age years
ssb: Spawning stock biomass time series as FLQuant
model: Stock-recruitment model formula
fitted: Empty FLQuant for fitted values
residuals: Empty FLQuant for residuals
name: Name inherited from the FLStock object
desc: Description indicating origin from FLStock

Details

The recruitment age (rec.age) is used to align the recruitment and SSB time series. Recruitment at age rec.age in year t is paired with SSB from year t-1. This ensures the stock-recruitment relationship reflects the biological process where recruitment depends on the parent stock biomass from the previous spawning season.

The time series are aligned as follows:

Recruitment data: uses age rec.age from years (1 + rec.age) to end
SSB data: uses years 1 to (total years - rec.age)

This ensures that recruitment observations are paired with the corresponding parent stock biomass from the appropriate lag years.

An error is raised if:

rec.age is less than the minimum age class
The FLStock recruitment time series is too short (less than rec.age + 1 years)

Author

The FLR Team

Examples

data(ple4)
# Create FLSR object with default recruitment age
sr <- as.FLSR(ple4, model=bevholt)

# Create FLSR object with recruitment age 2
sr2 <- as.FLSR(ple4, rec.age=2)

# Create FLSR with a specific model formula
sr_bh <- as.FLSR(ple4, model=rec~a*ssb/(b+ssb))