Mean fishing mortality over a selected age range

Computes the arithmetic mean of the harvest() slot over a contiguous range of ages.

Usage

fbar(object, ...)

# S4 method for class 'FLStock'
fbar(object, min = range(object, "minfbar"), max = range(object, "maxfbar"))

# S4 method for class 'FLBiol'
fbar(object, minAge = dims(object)$min + 1, maxAge = dims(object)$max - 1, ...)

Arguments

object

An FLStock object.

min

Integer. Minimum age to include in the mean. Defaults to the value stored in range(object, "minfbar"); if that value is NA, the smallest age in the object (range(object, "min")) is used instead.

max

Integer. Maximum age to include in the mean. Defaults to the value stored in range(object, "maxfbar"); if that value is NA, the largest age in the object (range(object, "max")) is used instead.

minAge

Minimum age. Defaults to min + 1.

maxAge

Maximum age. Defaults to max - 1.

Value

An FLQuant with the quant dimension collapsed to one, containing the arithmetic mean of harvest() over ages min to max inclusive, as computed by quantMeans().

Details

Overriding min and max directly allows a one-off calculation over a different age range without modifying the object.

The method accepts both "f" and "hr" as valid units for the harvest() slot and applies quantMeans() identically in both cases.

Methods (by class)

• fbar(FLStock): The minfbar and maxfbar entries of the range slot are specific to the FLStock class, and define the reference age range for fishing-mortality calculations. These are set when the FLStock object is created or read, and can be altered using .

• fbar(FLBiol): For FLBiol objects, fbar is calculated from stock numbers (n) and natural mortality (m) by estimating fishing mortality from the cohort decline, i.e., F = log(nage/nage+1) - Mage

See also

harvest(), quantMeans(), base::range()

FLStock

Author

FLR Team

Examples

data(ple4)

# Default fbar using minfbar/maxfbar from range slot
fbar(ple4)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> age   1957  1958  1959  1960  1961  1962  1963  1964  1965  1966  1967  1968 
#>   all 0.242 0.279 0.311 0.324 0.325 0.336 0.367 0.394 0.388 0.362 0.348 0.354
#>      year
#> age   1969  1970  1971  1972  1973  1974  1975  1976  1977  1978  1979  1980 
#>   all 0.364 0.363 0.367 0.399 0.452 0.480 0.461 0.437 0.449 0.488 0.526 0.542
#>      year
#> age   1981  1982  1983  1984  1985  1986  1987  1988  1989  1990  1991  1992 
#>   all 0.541 0.526 0.515 0.523 0.551 0.586 0.616 0.630 0.622 0.606 0.600 0.607
#>      year
#> age   1993  1994  1995  1996  1997  1998  1999  2000  2001  2002  2003  2004 
#>   all 0.610 0.598 0.598 0.642 0.712 0.724 0.650 0.582 0.572 0.594 0.571 0.477
#>      year
#> age   2005  2006  2007  2008  2009  2010  2011  2012  2013  2014  2015  2016 
#>   all 0.387 0.333 0.296 0.255 0.216 0.196 0.198 0.207 0.210 0.205 0.201 0.199
#>      year
#> age   2017 
#>   all 0.199
#> 
#> units:  f 

# Override age range for a one-off calculation
fbar(ple4, min = 3, max = 6)
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> age   1957  1958  1959  1960  1961  1962  1963  1964  1965  1966  1967  1968 
#>   all 0.259 0.295 0.326 0.340 0.343 0.356 0.391 0.423 0.420 0.394 0.376 0.372
#>      year
#> age   1969  1970  1971  1972  1973  1974  1975  1976  1977  1978  1979  1980 
#>   all 0.373 0.372 0.381 0.420 0.478 0.506 0.478 0.446 0.455 0.497 0.538 0.558
#>      year
#> age   1981  1982  1983  1984  1985  1986  1987  1988  1989  1990  1991  1992 
#>   all 0.560 0.547 0.537 0.547 0.578 0.617 0.650 0.667 0.663 0.650 0.644 0.649
#>      year
#> age   1993  1994  1995  1996  1997  1998  1999  2000  2001  2002  2003  2004 
#>   all 0.651 0.645 0.652 0.700 0.772 0.787 0.717 0.648 0.625 0.625 0.582 0.481
#>      year
#> age   2005  2006  2007  2008  2009  2010  2011  2012  2013  2014  2015  2016 
#>   all 0.388 0.328 0.286 0.245 0.210 0.196 0.202 0.214 0.214 0.206 0.200 0.201
#>      year
#> age   2017 
#>   all 0.206
#> 
#> units:  f 

# Inspect the reference age range stored in the object
range(ple4, c("minfbar", "maxfbar"))
#> minfbar maxfbar 
#>       2       6