Class FLBiol

Description

This is a class for the modelling of age/length or biomass structured populations. It is in its structure a subset of the FLStock-class class, but lacks the harvesting information of that class. The slots are for mortality (natural or otherwise), fecundity/maturity/per capita birth rates, numbers, weight and mortality components before spawning/birthing period.

The non-accessor methods for this class calculate mature stock biomass/numbers of eggs/etc. and many life-history methods are available that calculate natural mortality (given certain information), the intrinsic rate of increase r (using various methods), or to apply a Leslie-transition matrix model for estimating the population dynamics.

Slots

n

for the numbers in the population. FLQuant.

m

for the mortality rate of the population. FLQuant.

wt

for the weight of the population. FLQuant.

fec

for the fecundity/maturity/per capita birth rate. FLQuant.

spwn

for the proportion of mortality before spawning/birth. FLQuant.

name

name of the object. character.

desc

brief description of the object. character.

range

range of the dimensions. numeric.

Extends

FLComp

Methods

as.FLBiol(FLCore) :

Coerces object ino an FLBiol object.

signature(object=missing)

as.FLSR(FLCore) :

Coerces an FLBiol into an FLSR object.

signature(object=missing)

coerce(methods) :

Describe method

signature(from=NULL,to=FLBiol,strict=missing)

coerce(methods) :

Describe method

signature(from=FLBiol,to=FLStock,strict=missing)

coerce(methods) :

Describe method

signature(from=FLStock,to=FLBiol,strict=missing)

fec(FLCore) :

accesses the fec slot.

signature(object=missing)

fec<-(FLCore) :

replacement method for this slot.

signature(object=FLBiol,value=FLQuant)

leslie(FLCore) :

applies a Leslie-transition matrix model for the FLBiol object.

signature(object=FLBiol,value=FLBiol)

m(FLCore) :

accesses the mortality slot.

signature(object=missing)

m<-(FLCore) :

replacement method for this slot.

signature(object=FLBiol,value=FLQuant)

n(FLCore) :

accesses the numbers slot.

signature(object=missing)

n<-(FLCore) :

replacement method for this slot.

signature(object=FLBiol,value=FLQuant)

plot(graphics) :

default plot method for FLBiol.

signature(x=FLBiol,y=missing)

spwn(FLCore) :

accesses the spwn slot.

signature(object=missing)

spwn<-(FLCore) :

replacement method for this slot.

signature(object=FLBiol,value=FLQuant)

ssb(FLCore) :

calculates the spawning stock biomass.

signature(object=missing)

wt(FLCore) :

accesses the weight slot.

signature(object=missing)

wt<-(FLCore) :

replacement method for this slot.

signature(object=FLBiol,value=FLQuant)

fbar(FLCore) :

calculates fbar

signature(object=FLBiol)

fbar(FLCore) :

calculates harvest, as fishing mortality. The ratio of F between the plusgroup, if specified, and the previous age, fratio, defaults to 1.

signature(object=FLBiol)

catch.n(FLCore) :

calculates catch by quant

signature(object=FLBiol)

Author(s)

The FLR Team

See Also

as.FLBiol, as.FLSR, coerce, fec, fec<-, m, m<-, n, n<-, plot, spwn, spwn<-, ssb, wt, wt<-, FLComp

Examples

# An FLBiol example dataser
data(ple4.biol)

summary(ple4.biol)