FLIndex-class {FLCore}R Documentation

Class FLIndex

Description

A class designed to hold data and parameters related to abundance indices

Objects from the Class

Objects can be created by calls of the form new("FLIndex", ...), through the creator function FLIndex().

Creator Function

The function FLIndex() creates a new FLIndex object. To initialise the object, an FLQuant should be provided for the index slot. An empty FLQuant can be used to create an empty FLIndex of the right dimensions, as in

FLIndex(index=FLQuant(dim=c(5,10,1,1,1)))

By using the class argument, objects can be created of the derived FLIndex classes. This can also be achieved by using the corresponding creator functions: FLIndexCom(), FLIndexSurvey() and FLIndexAcoustic().

Slots

Objects of the FLIndex class contain the following slots:

name:
The name of the index or fleet
desc:
Description of the index
range:
Year and age range, and specified plus group age. A vector of length 5.
distribution:
A character string for the probability density function assumed for the error estructure
index:
An "FLQuant" for the index (CPUE or other) in numbers, either quant (i.e., age) structured, or not.
index.var:
An "FLQuant" for the index variance

The FLIndexCom class, designed for indices based on commercial catch data, adds the following slots:

catch:
An "FLQuant" for the catch
catch.wt:
An "FLQuant" for the weight-at-age (or length) in the catch
effort:
An "FLQuant" for the effort time series. The units slot should indicate the units used to measure it (days, hooks per line,...)
sel.pattern:
An "FLQuant" for the selection pattern.
index.q:
An "FLQuant" for the index catchability.

The FLIndexSurvey class, designed for indices based on catch surveys, adds the following slots:

catch.n:
An "FLQuant" for the catch by age or quant
catch.wt:
An "FLQuant" for the weight-at-age (or length) in the catch
effort:
An "FLQuant" for the effort time series. The units slot should indicate the units used to measure it (days, hooks per line,...)
index.q:
An "FLQuant" for the index catchability.

The FLIndexAcoustic class, designed for indices based on acoustic surveys, adds the following slots to be basic class:

index.q:
An "FLQuant" for the index catchability.

Methods

apply
signature(X = "FLIndex", MARGIN = "list", FUN = "function"): ...
dims
signature(obj = "FLIndex"): ...
plot
signature(x = "FLIndex", y = "missing"): ...
summary
signature(object = "FLIndex"): ...
transform
signature(x = "FLIndex"): ...
window
signature(x = "FLIndex"): ...

Author(s)

FLR Team

See Also

FLIndices-class

Examples

fi <- FLIndex(name = 'index', desc = 'An index', index=FLQuant(dim=c(5,10,1,1,1)))
summary(fi)
fi <- FLIndex(name = 'index', desc = 'An index', index=FLQuant(dim=c(5,10,1,1,1)), class="FLIndexCom")
summary(fi)

[Package FLCore version 1.1 Index]