a4aGr-class: Individual growth class

In flr/FLa4a: A Simple and Robust Statistical Catch at Age Model

Individual growth class

Description

Class definition (slots), constructors, accessors, replacement (when relevant) and common methods.

Usage

a4aGr(object, ...)

## S4 method for signature 'missing'
a4aGr(object, ...)

grMod(object, ...)

## S4 method for signature 'a4aGr'
grMod(object)

grMod(object) <- value

## S4 replacement method for signature 'a4aGr,formula'
grMod(object) <- value

grInvMod(object, ...)

## S4 method for signature 'a4aGr'
grInvMod(object)

grInvMod(object) <- value

## S4 replacement method for signature 'a4aGr,formula'
grInvMod(object) <- value

## S4 method for signature 'a4aGr'
params(object)

## S4 replacement method for signature 'a4aGr,FLPar'
params(object) <- value

## S4 method for signature 'a4aGr'
distr(object)

## S4 replacement method for signature 'a4aGr,character'
distr(object) <- value

## S4 method for signature 'a4aGr'
vcov(object)

## S4 replacement method for signature 'a4aGr,numeric'
vcov(object) <- value

Arguments

object	object of relevant class (see signature of method)
...	additional argument list that might never be used
value	the new object

Slot

grMod

the formula for the growth model, e.g. von Bertallanffy

grInvMod

the formula for the inverse of the growth model, having length as the independent variable

params

an FLPar object with the parameters of the model; must match the equations in the models

vcov

an array with the variance covariance matrix of the parameters

distr

a character with the parameters' statistical distribution; it must match a known distribution for R (e.g. "norm" for gaussian), so that rnorm can be called

Accessors

All slots in the class have accessor and replacement methods defined that allow retrieving and substituting individual slots.

The values passed for replacement need to be of the class of that slot. A numeric vector can also be used when replacing FLQuant slots, and the vector will be used to substitute the values in the slot, but not its other attributes.

Constructor

A construction method exists for this class that can take named arguments for any of its slots. All slots are then created to match the requirements of the class validity. If an unnamed FLQuant object is provided, this is used for sizing, but not for populating any slot.

Examples

mm <- matrix(NA, ncol=3, nrow=3)
diag(mm) <- c(50, 0.001,0.001)
mm[upper.tri(mm)] <- mm[lower.tri(mm)] <- c(0.1,0.01,0.00004)
md <- ~linf*(1-exp(-k*(t-t0)))
imd <- ~t0-1/k*log(1-len/linf)
prs <- FLPar(linf=58.5, k=0.086, t0=0.001, units=c("cm","yr^-1","yr"))
vbObj <- a4aGr(grMod=md, grInvMod=imd, params=prs, vcov=mm, distr="norm")

flr/FLa4a documentation built on Dec. 21, 2024, 9:28 p.m.