Core package of FLR, fisheries modelling in R.


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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