Individual growth class

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

a4aGr(object, ...)

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

grMod(object, ...)

# S4 method for a4aGr
grMod(object)

grMod(object) <- value

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

grInvMod(object, ...)

# S4 method for a4aGr
grInvMod(object)

grInvMod(object) <- value

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

# S4 method for a4aGr
params(object)

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

# S4 method for a4aGr
distr(object)

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

# S4 method for a4aGr
vcov(object)

# S4 method for 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")