FLBiol-class: Class FLBiol

In FLCore: Core package of FLR, fisheries modelling in R.

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, 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

Constructor

The FLBiol(object, ...) constructor method allows simple creation of new FLBiol objects with the methods described below.

object

An initial FLQuant only used for sizing.

plusgroup

The age/length to be considered as plusgroup.

...

Extra objects to be allocated to given slots.

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)

FLCore documentation built on May 2, 2019, 5:46 p.m.