Core package of FLR, fisheries modelling in R.

Documentation for package `FLCore' version 1.1

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A B C D E F H I L M N P Q R S T U V W X Y misc

"aic<-"-methods	Accesor and replacement methods for slots of complex objects
"covar<-"-methods	Accesor and replacement methods for slots of complex objects
"desc<-"-methods	Accesor and replacement methods for slots of complex objects
"distribution<-"-methods	Accesor and replacement methods for slots of complex objects
"fec<-"-methods	Accesor and replacement methods for slots of complex objects
"harvest<-"-methods	Class FLStock for fish stock data and modelling output
"index.var<-"-methods	Accesor and replacement methods for slots of complex objects
"index<-"-methods	Accesor and replacement methods for slots of complex objects
"m<-"-methods	Accesor and replacement methods for slots of complex objects
"mcmc<-"-methods	Accesor and replacement methods for slots of complex objects
"model<-"-methods	Accesor and replacement methods for slots of complex objects
"n<-"-methods	Accesor and replacement methods for slots of complex objects
"name<-"-methods	Accesor and replacement methods for slots of complex objects
"params<-"-methods	Accesor and replacement methods for slots of complex objects
"quant<-"-methods	Quant, first dimension of FLQuant
"rec<-"-methods	Accesor and replacement methods for slots of complex objects
"rechat<-"-methods	Accesor and replacement methods for slots of complex objects
"residuals<-"-methods	Accesor and replacement methods for slots of complex objects
"se<-"-methods	Accesor and replacement methods for slots of complex objects
"spwn<-"-methods	Accesor and replacement methods for slots of complex objects
"ssb<-"-methods	Accesor and replacement methods for slots of complex objects
"units<-"-methods	Extract and modify the units slot of an object
"var<-"-methods	Class FLSR
"varacorr<-"-methods	Accesor and replacement methods for slots of complex objects
"wt<-"-methods	Accesor and replacement methods for slots of complex objects

-- A --

aic	Accesor and replacement methods for slots of complex objects
aic,FLSR-method	Class FLSR
aic-methods	Accesor and replacement methods for slots of complex objects
aic<-,FLSR,numeric-method	Class FLSR
apply,FLBiol,list,function-method	Class FLBiol
apply,FLIndex,list,function-method	Class FLIndex
apply,FLQuant,ANY,ANY-method	FLQuant class and methods
apply,FLStock,list,function-method	Class FLStock for fish stock data and modelling output
areaMeans	Common summary operations for FLQuants
areaSums	Common summary operations for FLQuants
as.data.frame,FLQuant,missing,missing-method	FLQuant class and methods
as.FLBiol	Method for creating an FLBiol object from other classes
as.FLBiol,FLBiol-method	Method for creating an FLBiol object from other classes
as.FLBiol-methods	Method for creating an FLBiol object from other classes
as.FLFleet	as.FLFleet method
as.FLFleet,FLStock-method	as.FLFleet method
as.FLFleet-method	as.FLFleet method
as.FLIndex	Method for creating an FLIndex object from other classes
as.FLIndex,FLFleet-method	Method for creating an FLIndex object from other classes
as.FLIndex-methods	Method for creating an FLIndex object from other classes
as.FLQuant	as.FLQuant
as.FLQuant,array-method	as.FLQuant
as.FLQuant,data.frame-method	as.FLQuant
as.FLQuant,FLQuant-method	as.FLQuant
as.FLQuant,matrix-method	as.FLQuant
as.FLQuant,vector-method	as.FLQuant
as.FLQuant-methods	as.FLQuant
as.FLStock	FLStock
as.FLStock,FLFleet-method	FLStock
as.FLStock,FLFleets-method	Class FLFleets
as.FLStock,FLStock-method	FLStock

-- B --

barchart,FLQuant-method	FLCore lattice methods
barchart,formula-method	FLCore lattice methods
bevholt	Stock-recruitment model function
bt4	FLCore datasets
bubbles	Lattice style bubble plots
bubbles,FLQuant-method	Lattice style bubble plots
bubbles,formula,FLQuant-method	Lattice style bubble plots
bubbles-methods	Lattice style bubble plots
bwplot,FLQuant-method	FLCore lattice methods
bwplot,formula-method	FLCore lattice methods

-- C --

catch	Methods for estimating time series from dissagregated data
catch,FLCatch-method	Class FLCatch
catch,FLIndexCom-method	Class FLIndex
catch,FLQuant-method	FLQuant class and methods
catch,FLStock-method	Class FLStock for fish stock data and modelling output
catch.n	Accesor and replacement methods for slots of complex objects
catch.n,FLIndexSurvey-method	Class FLIndex
catch.n-methods	Accesor and replacement methods for slots of complex objects
catch.n<-,FLIndexSurvey,FLQuant-method	Class FLIndex
catch.wt	Accesor and replacement methods for slots of complex objects
catch.wt,FLIndexCom-method	Class FLIndex
catch.wt,FLIndexSurvey-method	Class FLIndex
catch.wt-methods	Accesor and replacement methods for slots of complex objects
catch.wt<-,FLIndexCom,FLQuant-method	Class FLIndex
catch.wt<-,FLIndexSurvey,FLQuant-method	Class FLIndex
catch<-,FLIndexCom,FLQuant-method	Class FLIndex
covar	Accesor and replacement methods for slots of complex objects
covar,FLSR-method	Class FLSR
covar-methods	Accesor and replacement methods for slots of complex objects
covar<-,FLSR,matrix-method	Class FLSR
createFLAccesors	Create accesor and replecement methods for slots of complex classes

-- D --

desc	Accesor and replacement methods for slots of complex objects
desc,FLBiol-method	Class FLBiol
desc,FLIndex-method	Class FLIndex
desc,FLSR-method	Class FLSR
desc-methods	Accesor and replacement methods for slots of complex objects
desc<-,FLBiol,character-method	Class FLBiol
desc<-,FLIndex,character-method	Class FLIndex
desc<-,FLSR,character-method	Class FLSR
dimnames<-,FLQuant-method	FLQuant class and methods
dims	Provide information onn the dimensions and range of an object
dims,FLIndex-method	Provide information onn the dimensions and range of an object
dims,FLQuant-method	Provide information onn the dimensions and range of an object
dims-methods	Provide information onn the dimensions and range of an object
discards	Methods for estimating time series from dissagregated data
discards,FLCatch-method	Class FLCatch
discards,FLQuant-method	FLQuant class and methods
discards,FLStock-method	Class FLStock for fish stock data and modelling output
distribution	Accesor and replacement methods for slots of complex objects
distribution,FLIndex-method	Class FLIndex
distribution-methods	Accesor and replacement methods for slots of complex objects
distribution<-,FLIndex,character-method	Class FLIndex
dotplot,FLQuant-method	FLCore lattice methods
dotplot,formula-method	FLCore lattice methods

-- E --

effort	Accesor and replacement methods for slots of complex objects
effort,FLIndexCom-method	Class FLIndex
effort,FLIndexSurvey-method	Class FLIndex
effort-methods	Accesor and replacement methods for slots of complex objects
effort<-,FLIndexCom,FLQuant-method	Class FLIndex
effort<-,FLIndexSurvey,FLQuant-method	Class FLIndex

-- F --

fec	Accesor and replacement methods for slots of complex objects
fec,FLBiol-method	Class FLBiol
fec-methods	Accesor and replacement methods for slots of complex objects
fec<-,FLBiol,FLQuant-method	Class FLBiol
FLBiol	Class FLBiol
FLBiol-class	Class FLBiol
FLBiols	Class FLBiols
FLBiols-class	Class FLBiols
FLCatch	Class FLCatch
FLCatch-class	Class FLCatch
FLCore-accesors	Accesor and replacement methods for slots of complex objects
FLFleet	FLFleet class and methods
FLFleet-class	FLFleet class and methods
FLFleets	Class FLFleets
FLFleets-class	Class FLFleets
FLGenerics	FLCore S4 Generic Functions
FLGenerics-methods	FLCore S4 Generic Functions
FLIndex	Class FLIndex
FLIndex-class	Class FLIndex
FLIndexAcoustic	Class FLIndex
FLIndexAcoustic-class	Class FLIndex
FLIndexCom	Class FLIndex
FLIndexCom-class	Class FLIndex
FLIndexSurvey	Class FLIndex
FLIndexSurvey-class	Class FLIndex
FLIndices	Class FLIndices
FLIndices-class	Class FLIndices
FLQuant	FLQuant
FLQuant,array-method	FLQuant
FLQuant,FLQuant-method	FLQuant
FLQuant,matrix-method	FLQuant
FLQuant,missing-method	FLQuant
FLQuant,vector-method	FLQuant
FLQuant-class	FLQuant class and methods
FLQuant-methods	FLQuant
FLQuants	FLQuants
FLQuants-class	FLQuants
FLSR	Class FLSR
FLSR-class	Class FLSR
FLSR.control	Class FLSR.control
FLSR.control-class	Class FLSR.control
FLStock	Class FLStock for fish stock data and modelling output
FLStock-class	Class FLStock for fish stock data and modelling output
FLStocks	Class FLStocks
FLStocks-class	Class FLStocks

-- H --

harvest	Class FLStock for fish stock data and modelling output
harvest,FLStock-method	Class FLStock for fish stock data and modelling output
harvest-methods	Class FLStock for fish stock data and modelling output
harvest<-,FLStock,character-method	Class FLStock for fish stock data and modelling output
harvest<-,FLStock-method	Class FLStock for fish stock data and modelling output
histogram,FLQuant-method	FLCore lattice methods
histogram,formula-method	FLCore lattice methods

-- I --

index	Accesor and replacement methods for slots of complex objects
index,FLIndex-method	Class FLIndex
index-methods	Accesor and replacement methods for slots of complex objects
index.q	Accesor and replacement methods for slots of complex objects
index.q,FLIndexAcoustic-method	Class FLIndex
index.q,FLIndexCom-method	Class FLIndex
index.q,FLIndexSurvey-method	Class FLIndex
index.q-methods	Accesor and replacement methods for slots of complex objects
index.q<-,FLIndexAcoustic,FLQuant-method	Class FLIndex
index.q<-,FLIndexCom,FLQuant-method	Class FLIndex
index.q<-,FLIndexSurvey,FLQuant-method	Class FLIndex
index.var	Accesor and replacement methods for slots of complex objects
index.var,FLIndex-method	Class FLIndex
index.var-methods	Accesor and replacement methods for slots of complex objects
index.var<-,FLIndex,FLQuant-method	Class FLIndex
index<-,FLIndex,FLQuant-method	Class FLIndex
is.FLBiol	FLBiol
is.FLBiols	Checks for objects of class FLBiols
is.FLFleet	FLFleet
is.FLFleets	FLFleets
is.FLIndex	FLIndex
is.FLIndexAcoustic	FLIndex
is.FLIndexCom	FLIndex
is.FLIndexSurvey	FLIndex
is.FLIndices	FLIndices
is.FLQuant	as.FLQuant
is.FLSR	FLSR
is.FLStock	FLStock
is.FLStocks	FLStocks

-- L --

landings	Methods for estimating time series from dissagregated data
landings,FLCatch-method	Class FLCatch
landings,FLQuant-method	FLQuant class and methods
landings,FLStock-method	Class FLStock for fish stock data and modelling output

-- M --

m	Accesor and replacement methods for slots of complex objects
m,FLBiol-method	Class FLBiol
m-methods	Accesor and replacement methods for slots of complex objects
m<-,FLBiol,FLQuant-method	Class FLBiol
mcmc	Accesor and replacement methods for slots of complex objects
mcmc,FLSR-method	Class FLSR
mcmc-methods	Accesor and replacement methods for slots of complex objects
mcmc<-,FLSR,list-method	Class FLSR
model	Accesor and replacement methods for slots of complex objects
model,FLSR-method	Class FLSR
model-methods	Accesor and replacement methods for slots of complex objects
model<-,FLSR,character-method	Class FLSR

-- N --

n	Accesor and replacement methods for slots of complex objects
n,FLBiol-method	Class FLBiol
n-methods	Accesor and replacement methods for slots of complex objects
n<-,FLBiol,FLQuant-method	Class FLBiol
name	Accesor and replacement methods for slots of complex objects
name,FLBiol-method	Class FLBiol
name,FLIndex-method	Class FLIndex
name,FLSR-method	Class FLSR
name-methods	Accesor and replacement methods for slots of complex objects
name<-,FLBiol,character-method	Class FLBiol
name<-,FLIndex,character-method	Class FLIndex
name<-,FLSR,character-method	Class FLSR
names,FLQuant-method	FLQuant class and methods

-- P --

params	Accesor and replacement methods for slots of complex objects
params,FLSR-method	Class FLSR
params-methods	Accesor and replacement methods for slots of complex objects
params<-,FLSR,matrix-method	Class FLSR
params<-,FLSR,vector-method	Class FLSR
params<-,FLSR-method	Class FLSR
ple4	FLCore datasets
ple4sex	FLCore datasets
plot,FLBiol,missing-method	Class FLBiol
plot,FLCatch,missing-method	Class FLCatch
plot,FLFleet,missing-method	FLFleet class and methods
plot,FLIndex,missing-method	Class FLIndex
plot,FLQuant,missing-method	FLQuant class and methods
plot,FLSR,missing-method	Class FLSR
plot,FLStock,missing-method	Class FLStock for fish stock data and modelling output
predict,FLSR-method	Class FLSR
project,FLStock,FLSTF.control-method	Class FLStock for fish stock data and modelling output

-- Q --

qhstk	Stock-recruitment model function
quant	Quant, first dimension of FLQuant
quant,FLQuant-method	FLQuant class and methods
quant-methods	Quant, first dimension of FLQuant
quant<-,FLQuant-method	FLQuant class and methods
quantMeans	Common summary operations for FLQuants
quantSums	Common summary operations for FLQuants
quantTotals	Common summary operations for FLQuants

-- R --

read.FLIndex	Import FLIndices data from a file
read.FLIndices	Import FLIndices data from a file
read.FLStock	Import stock data from a file
read.VPAFile	Import stock data from a file
rec	Accesor and replacement methods for slots of complex objects
rec,FLSR-method	Class FLSR
rec-methods	Accesor and replacement methods for slots of complex objects
rec<-,FLSR,FLQuant-method	Class FLSR
rechat	Accesor and replacement methods for slots of complex objects
rechat,FLSR-method	Class FLSR
rechat-methods	Accesor and replacement methods for slots of complex objects
rechat<-,FLSR,FLQuant-method	Class FLSR
residuals	Accesor and replacement methods for slots of complex objects
residuals,FLSR-method	Class FLSR
residuals-methods	Accesor and replacement methods for slots of complex objects
residuals<-,FLSR,FLQuant-method	Class FLSR
revenue	Calculate the revenue of a fleet
revenue,FLFleet-method	FLFleet class and methods
ricker	Stock-recruitment model function

-- S --

se	Accesor and replacement methods for slots of complex objects
se,FLSR-method	Class FLSR
se-methods	Accesor and replacement methods for slots of complex objects
se<-,FLSR,numeric-method	Class FLSR
seasonMeans	Common summary operations for FLQuants
seasonSums	Common summary operations for FLQuants
segreg	Stock-recruitment model function
sel.pattern	Accesor and replacement methods for slots of complex objects
sel.pattern,FLIndexCom-method	Class FLIndex
sel.pattern-methods	Accesor and replacement methods for slots of complex objects
sel.pattern<-,FLIndexCom,FLQuant-method	Class FLIndex
setPlusGroup	setPlusgroup for FLStock
setunits,FLBiol-method	Class FLBiol
setunits,FLStock-method	Class FLStock for fish stock data and modelling output
show,FLBiols-method	Class FLBiols
show,FLQuant-method	FLQuant class and methods
show,FLSR.control-method	Class FLSR.control
sop	Calculates the sum of products correction
spwn	Accesor and replacement methods for slots of complex objects
spwn,FLBiol-method	Class FLBiol
spwn-methods	Accesor and replacement methods for slots of complex objects
spwn<-,FLBiol,FLQuant-method	Class FLBiol
sr	Stock-recruitment model function
srlkhd	Likelihood of the S-R parameters
ssb	Method for calculating Spawning Stock Biomass
ssb,FLSR-method	Class FLSR
ssb,FLStock-method	Class FLStock for fish stock data and modelling output
ssb-methods	Accesor and replacement methods for slots of complex objects
ssb<-,FLSR,FLQuant-method	Class FLSR
steepvirginbiom	Change to steepness/virgin biomass parameterisation
stripplot,FLQuant-method	FLCore lattice methods
stripplot,formula-method	FLCore lattice methods
summary,FLBiol-method	Class FLBiol
summary,FLBiols-method	Class FLBiols
summary,FLCatch-method	Class FLCatch
summary,FLFleet-method	FLFleet class and methods
summary,FLFleets-method	Class FLFleets
summary,FLIndex-method	Class FLIndex
summary,FLIndices-method	Class FLIndices
summary,FLQuant-method	FLQuant class and methods
summary,FLSR-method	Class FLSR
summary,FLSR.control-method	Class FLSR.control
summary,FLStock-method	Class FLStock for fish stock data and modelling output
summary,FLStocks-method	Class FLStocks

-- T --

transform,FLBiol-method	Class FLBiol
transform,FLCatch-method	Class FLCatch
transform,FLFleet-method	FLFleet class and methods
transform,FLIndex-method	Class FLIndex
transform,FLStock-method	Class FLStock for fish stock data and modelling output
trim	Method for trimming FLQuant objects.
trim,FLQuant-method	FLQuant class and methods
trim-methods	Method for trimming FLQuant objects.

-- U --

unitMeans	Common summary operations for FLQuants
units	Extract and modify the units slot of an object
units,FLQuant-method	Extract and modify the units slot of an object
units-methods	Extract and modify the units slot of an object
units<-,FLQuant-method	Extract and modify the units slot of an object
unitSums	Common summary operations for FLQuants
update,FLStock-method	Class FLStock for fish stock data and modelling output

-- V --

var,FLSR,missing,missing,missing-method	Class FLSR
var<-,FLSR,numeric-method	Class FLSR
varacorr	Accesor and replacement methods for slots of complex objects
varacorr,FLSR-method	Class FLSR
varacorr-methods	Accesor and replacement methods for slots of complex objects
varacorr<-,FLSR,numeric-method	Class FLSR

-- W --

window	window for FLQuants based classes
window,FLBiol-method	window for FLQuants based classes
window,FLCatch-method	window for FLQuants based classes
window,FLFleet-method	window for FLQuants based classes
window,FLIndex-method	window for FLQuants based classes
window,FLIndices-method	window for FLQuants based classes
window,FLQuant-method	window for FLQuants based classes
window,FLStock-method	window for FLQuants based classes
window-methods	window for FLQuants based classes
write.FLStock	Write FLStock data to a file
wt	Accesor and replacement methods for slots of complex objects
wt,FLBiol-method	Class FLBiol
wt-methods	Accesor and replacement methods for slots of complex objects
wt<-,FLBiol,FLQuant-method	Class FLBiol

-- X --

xyplot,FLQuant-method	FLCore lattice methods
xyplot,FLQuants-method	FLCore lattice methods
xyplot,formula-method	FLCore lattice methods

-- Y --

yearMeans	Common summary operations for FLQuants
yearSums	Common summary operations for FLQuants
yearTotals	Common summary operations for FLQuants

-- misc --

[,FLQuant-method	FLQuant class and methods
[<-,FLQuant-method	FLQuant class and methods