Core package of FLR, fisheries modelling in R


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Documentation for package ‘FLCore’ version 2.5.20140904

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

FLCore-package Core package of FLR, fisheries modelling in R.

-- A --

ab2sv Stock-Recruitment models
ac FLCore-internal
AIC-method Akaike information criterion (AIC) method
apply-method Method apply
areaMeans Methods to compute sums, means and vars of FLQuant objects
areaMeans-method Methods to compute sums, means and vars of FLQuant objects
areaMeans-methods Methods to compute sums, means and vars of FLQuant objects
areaSums Methods to compute sums, means and vars of FLQuant objects
areaSums-method Methods to compute sums, means and vars of FLQuant objects
areaSums-methods Methods to compute sums, means and vars of FLQuant objects
areaVars Methods to compute sums, means and vars of FLQuant objects
areaVars-method Methods to compute sums, means and vars of FLQuant objects
areaVars-methods Methods to compute sums, means and vars of FLQuant objects
Arith-method Arithmetic methods for FLQuant objects
as.data.frame-FLCore Method as.data.frame
as.data.frame-method Method as.data.frame
as.FLBiol Old S3 coercion methods
as.FLBiol-method Old S3 coercion methods
as.FLBiol-methods Old S3 coercion methods
as.FLIndex Old S3 coercion methods
as.FLIndex-methods Old S3 coercion methods
as.FLQuant Old S3 coercion methods
as.FLQuant-method Old S3 coercion methods
as.FLQuant-methods Old S3 coercion methods
as.FLSR Old S3 coercion methods
as.FLSR-method Old S3 coercion methods
as.FLSR-methods Old S3 coercion methods
as.FLStock Old S3 coercion methods

-- B --

barchart-method Lattice plots
bevholt Stock-Recruitment models
bevholt.ar1 Stock-Recruitment models
bevholt.c.a Stock-Recruitment models
bevholt.c.b Stock-Recruitment models
bevholt.d Stock-Recruitment models
bevholt.ndc Stock-Recruitment models
Bevholt.SV Stock-Recruitment models
bevholt.sv Stock-Recruitment models
BIC-method Bayesian information criterion (BIC) method
bkey Generate key for bubbles plot
bkey-method Generate key for bubbles plot
bkey-methods Generate key for bubbles plot
bubbles Bubbles plot
bubbles-method Bubbles plot
bubbles-methods Bubbles plot
bwplot-method Lattice plots

-- C --

catch-method Class FLStock
catch-method Class FLStockLen
catch.n-method Class FLIndex
catch.n-method Class FLIndexBiomass
catch.n-method Class FLStock
catch.n-method Class FLStockLen
catch.n<--method Class FLIndex
catch.n<--method Class FLIndexBiomass
catch.n<--method Class FLStock
catch.n<--method Class FLStockLen
catch.wt-method Class FLIndex
catch.wt-method Class FLIndexBiomass
catch.wt-method Class FLStock
catch.wt-method Class FLStockLen
catch.wt<--method Class FLIndex
catch.wt<--method Class FLIndexBiomass
catch.wt<--method Class FLStock
catch.wt<--method Class FLStockLen
catch<--method Class FLStock
catch<--method Class FLStockLen
ccplot Catch-curves plot
ccplot-method Catch-curves plot
ccplot-methods Catch-curves plot
coerce-method Method as.data.frame
coerce-method Method coerce
computeCatch Methods to compute total catch, landings, discards and stock biomass
computeCatch-method Methods to compute total catch, landings, discards and stock biomass
computeCatch-methods Methods to compute total catch, landings, discards and stock biomass
computeDiscards Methods to compute total catch, landings, discards and stock biomass
computeDiscards-method Methods to compute total catch, landings, discards and stock biomass
computeDiscards-methods Methods to compute total catch, landings, discards and stock biomass
computeLandings Methods to compute total catch, landings, discards and stock biomass
computeLandings-method Methods to compute total catch, landings, discards and stock biomass
computeLandings-methods Methods to compute total catch, landings, discards and stock biomass
computeStock Methods to compute total catch, landings, discards and stock biomass
computeStock-method Methods to compute total catch, landings, discards and stock biomass
computeStock-methods Methods to compute total catch, landings, discards and stock biomass
convert6d FLCore-internal
convertFLPar FLCore-internal
convertFLPar-method FLCore-internal
convertFLPar-methods FLCore-internal
createFLAccesors Create accesor methods for a given class
cv Coefficient of Variation of FLR objects with multiple iterations
cv-method Coefficient of Variation of FLR objects with multiple iterations
cv-methods Coefficient of Variation of FLR objects with multiple iterations

-- D --

densityplot-method Lattice plots
desc-method Class FLBiol
desc-method Class FLIndex
desc-method Class FLIndexBiomass
desc-method Class FLStock
desc-method Class FLStockLen
desc<--method Class FLBiol
desc<--method Class FLIndex
desc<--method Class FLIndexBiomass
desc<--method Class FLStock
desc<--method Class FLStockLen
dimMeans Methods to compute sums, means and vars of FLQuant objects
dimMeans-method Methods to compute sums, means and vars of FLQuant objects
dimMeans-methods Methods to compute sums, means and vars of FLQuant objects
dimnames<--method Modify dimnames of an FLQuant
dims List with information on object dimensions
dims-method List with information on object dimensions
dims-methods List with information on object dimensions
dimSums Methods to compute sums, means and vars of FLQuant objects
dimSums-method Methods to compute sums, means and vars of FLQuant objects
dimSums-methods Methods to compute sums, means and vars of FLQuant objects
dimVars Methods to compute sums, means and vars of FLQuant objects
dimVars-method Methods to compute sums, means and vars of FLQuant objects
dimVars-methods Methods to compute sums, means and vars of FLQuant objects
discards-method Class FLStock
discards-method Class FLStockLen
discards.n-method Class FLStock
discards.n-method Class FLStockLen
discards.n<--method Class FLStock
discards.n<--method Class FLStockLen
discards.wt-method Class FLStock
discards.wt-method Class FLStockLen
discards.wt<--method Class FLStock
discards.wt<--method Class FLStockLen
discards<--method Class FLStock
discards<--method Class FLStockLen
distribution-method Class FLIndex
distribution-method Class FLIndexBiomass
distribution<--method Class FLIndex
distribution<--method Class FLIndexBiomass
dotplot-method Lattice plots

-- E --

effort-method Class FLIndex
effort-method Class FLIndexBiomass
effort<--method Class FLIndex
effort<--method Class FLIndexBiomass
expand Trim FLR objects using named dimensions
expand-method Trim FLR objects using named dimensions
expand-methods Trim FLR objects using named dimensions
Extract-FLCore Extract or Replace Parts of an FLR Object

-- F --

fbar Calculates mean harvest rate or fishing mortality
fbar-method Calculates mean harvest rate or fishing mortality
fbar-methods Calculates mean harvest rate or fishing mortality
fec-method Class FLBiol
fec<--method Class FLBiol
FLArray Class FLArray
FLArray-class Class FLArray
FLBiol Class FLBiol
FLBiol-class Class FLBiol
FLBiol-method Class FLBiol
FLBiol-methods Class FLBiol
FLBiols Class FLBiols
FLBiols-class Class FLBiols
FLBiols-method Class FLBiols
FLBiols-methods Class FLBiols
flc2flq Coerce FLCohort into FLQuant.
flc2flq-method Coerce FLCohort into FLQuant.
flc2flq-methods Coerce FLCohort into FLQuant.
FLCohort Class FLCohort
FLCohort-class Class FLCohort
FLCohort-method Class FLCohort
FLCohort-methods Class FLCohort
FLCohorts Class FLCohorts
FLCohorts-class Class FLCohorts
FLCohorts-method Class FLCohorts
FLCohorts-methods Class FLCohorts
FLComp Class FLComp
FLComp-class Class FLComp
FLCore Core package of FLR, fisheries modelling in R.
FLI Class FLI
FLIndex Class FLIndex
FLIndex Class FLIndexBiomass
FLIndex-method Class FLIndex
FLIndex-method Class FLIndexBiomass
FLIndex-methods Class FLIndex
FLIndex-methods Class FLIndexBiomass
FLIndexBiomass Class FLIndexBiomass
FLIndices Class FLIndices
FLIndices-class Class FLIndices
FLIndices-method Class FLIndices
FLIndices-methods Class FLIndices
FLlst Class FLlst
FLlst-class Class FLlst
FLlst-method Class FLlst
FLlst-methods Class FLlst
FLModel Class FLModel for statistical models
FLModel-class Class FLModel for statistical models
FLModel-method Class FLModel for statistical models
FLModel-methods Class FLModel for statistical models
FLPar Class FLPar
FLPar-class Class FLPar
FLPar-method Class FLPar
FLPar-methods Class FLPar
FLQuant Class FLIndex
FLQuant Class FLIndexBiomass
FLQuant FLQuant class for numerical data
FLQuant-class FLQuant class for numerical data
FLQuant-method FLQuant class for numerical data
FLQuant-methods FLQuant class for numerical data
FLQuantPoint Class FLQuantPoint
FLQuantPoint-accesors Method lowq
FLQuantPoint-class Class FLQuantPoint
FLQuantPoint-method Class FLQuantPoint
FLQuantPoint-methods Class FLQuantPoint
FLQuants Class FLQuants
FLQuants-class Class FLQuants
FLQuants-method Class FLQuants
FLQuants-methods Class FLQuants
FLSR Class FLSR
FLSR-class Class FLSR
FLSR-method Class FLSR
FLSR-methods Class FLSR
FLStock Class FLStock
FLStock-class Class FLStock
FLStock-method Class FLStock
FLStock-methods Class FLStock
FLStockLen Class FLStockLen
FLStockLen-class Class FLStockLen
FLStockLen-method Class FLStockLen
FLStockLen-methods Class FLStockLen
FLStocks Class FLStocks
FLStocks-class Class FLStocks
FLStocks-method Class FLStocks
FLStocks-methods Class FLStocks
fmle Method fmle
fmle-method Method fmle

-- G --

geomean Stock-Recruitment models
getPlural FLCore-internal

-- H --

halfwidth-method Class FLStockLen
halfwidth<--method Class FLStockLen
harvest-method Class FLStock
harvest-method Class FLStockLen
harvest-method Harvest calculations for FLBiol
harvest.spwn-method Class FLStock
harvest.spwn-method Class FLStockLen
harvest.spwn<--method Class FLStock
harvest.spwn<--method Class FLStockLen
harvest<--method Class FLStock
harvest<--method Class FLStockLen
histogram-method Lattice plots

-- I --

index-method Class FLIndex
index-method Class FLIndexBiomass
index.q-method Class FLIndex
index.q-method Class FLIndexBiomass
index.q<--method Class FLIndex
index.q<--method Class FLIndexBiomass
index.var-method Class FLIndex
index.var-method Class FLIndexBiomass
index.var<--method Class FLIndex
index.var<--method Class FLIndexBiomass
index<--method Class FLIndex
index<--method Class FLIndexBiomass
is.FLBiol Methods to determine the class of a given object
is.FLBiols Methods to determine the class of a given object
is.FLBiols-method Methods to determine the class of a given object
is.FLBiols-methods Methods to determine the class of a given object
is.FLIndices Methods to determine the class of a given object
is.FLIndices-method Methods to determine the class of a given object
is.FLIndices-methods Methods to determine the class of a given object
is.FLQuant Methods to determine the class of a given object
is.FLQuants Methods to determine the class of a given object
is.FLQuants-method Methods to determine the class of a given object
is.FLQuants-methods Methods to determine the class of a given object
is.FLStock Methods to determine the class of a given object
is.FLStocks Methods to determine the class of a given object
is.FLStocks-method Methods to determine the class of a given object
is.FLStocks-methods Methods to determine the class of a given object
iter Select or modify iterations of an FLR object
iter-method Select or modify iterations of an FLR object
iter-methods Select or modify iterations of an FLR object
iter<- Select or modify iterations of an FLR object
iter<--method Select or modify iterations of an FLR object
iter<--methods Select or modify iterations of an FLR object
iterMeans Methods to compute sums, means and vars of FLQuant objects
iterMeans-method Methods to compute sums, means and vars of FLQuant objects
iterMeans-methods Methods to compute sums, means and vars of FLQuant objects
iters Method iters
iters-method Method iters
iters-methods Method iters
iterVars Methods to compute sums, means and vars of FLQuant objects
iterVars-method Methods to compute sums, means and vars of FLQuant objects
iterVars-methods Methods to compute sums, means and vars of FLQuant objects

-- J --

jacknife Jacknife resampling
jacknife-method Jacknife resampling
jacknife-methods Jacknife resampling

-- L --

landings-method Class FLStock
landings-method Class FLStockLen
landings.n-method Class FLStock
landings.n-method Class FLStockLen
landings.n<--method Class FLStock
landings.n<--method Class FLStockLen
landings.wt-method Class FLStock
landings.wt-method Class FLStockLen
landings.wt<--method Class FLStock
landings.wt<--method Class FLStockLen
landings<--method Class FLStock
landings<--method Class FLStockLen
lapply-method Method lapply
lattice-FLCore Lattice plots
leslie Method for calculating Leslie matrix dynamics of an FLBiol object
leslie-method Method for calculating Leslie matrix dynamics of an FLBiol object
leslie-methods Method for calculating Leslie matrix dynamics of an FLBiol object
logl.ar1 Stock-Recruitment models
lower Methods upper and lower
lower-method Methods upper and lower
lower<- Methods upper and lower
lower<--method Methods upper and lower
lowess-method Method lowess
lowq Method lowq
lowq-method Method lowq
lowq-methods Method lowq
lowq<- Method lowq
lowq<--method Method lowq
lowq<--methods Method lowq

-- M --

m-method Class FLBiol
m-method Class FLStock
m-method Class FLStockLen
m.spwn-method Class FLStock
m.spwn-method Class FLStockLen
m.spwn<--method Class FLStock
m.spwn<--method Class FLStockLen
m<--method Class FLBiol
m<--method Class FLStock
m<--method Class FLStockLen
mat-method Class FLStock
mat-method Class FLStockLen
mat<--method Class FLStock
mat<--method Class FLStockLen
mcf Method mcf
mcf-method Method mcf
mcf-methods Method mcf
mean-method Method lowq
mean-method Method mean
mean.lifespan Method for calculating mean lifespan, given the natural mortality
mean.lifespan-method Method for calculating mean lifespan, given the natural mortality
mean.lifespan-methods Method for calculating mean lifespan, given the natural mortality
mean<- Method lowq
mean<--method Method lowq
mean<--methods Method lowq
median-method Method lowq
median-method Method median
median<- Method lowq
median<--method Method lowq
median<--methods Method lowq
mergeFLStock Merging FLStock objects
missing Class FLIndex
missing Class FLIndexBiomass
model.frame-method Method model.frame

-- N --

n-method Class FLBiol
n<--method Class FLBiol
name-method Class FLBiol
name-method Class FLIndex
name-method Class FLIndexBiomass
name-method Class FLStock
name-method Class FLStockLen
name<--method Class FLBiol
name<--method Class FLIndex
name<--method Class FLIndexBiomass
name<--method Class FLStock
name<--method Class FLStockLen
names-method Method names
names<--method Method names
nls-FLCore Method nls
nls-method Method nls
nsher FLCore datasets

-- P --

ple4 FLCore datasets
ple4.biol FLCore datasets
ple4.index FLCore datasets
ple4.indices FLCore datasets
ple4sex FLCore datasets
plot-method Method plot
predict-method Method predict
print-method Method print
propagate Extend an FLQuant along the iter dimension
propagate-method Extend an FLQuant along the iter dimension
propagate-methods Extend an FLQuant along the iter dimension
pv Population variability
pv-method Population variability
pv-methods Population variability

-- Q --

qapply Method qapply
qapply-method Method qapply
qapply-methods Method qapply
quant Method quant
quant-method Method quant
quant-methods Method quant
quant<- Method quant
quant<--method Method quant
quant<--methods Method quant
quantile-method Method quantile
quantMeans Methods to compute sums, means and vars of FLQuant objects
quantMeans-method Methods to compute sums, means and vars of FLQuant objects
quantMeans-methods Methods to compute sums, means and vars of FLQuant objects
quantSums Methods to compute sums, means and vars of FLQuant objects
quantSums-method Methods to compute sums, means and vars of FLQuant objects
quantSums-methods Methods to compute sums, means and vars of FLQuant objects
quantTotals Method quantTotals
quantTotals-method Method quantTotals
quantTotals-methods Method quantTotals
quantVars Methods to compute sums, means and vars of FLQuant objects
quantVars-method Methods to compute sums, means and vars of FLQuant objects
quantVars-methods Methods to compute sums, means and vars of FLQuant objects

-- R --

r Intrinsic rate of increase from an FLBiol object
r-method Intrinsic rate of increase from an FLBiol object
r-methods Intrinsic rate of increase from an FLBiol object
range-method Class FLBiol
range-method Class FLIndex
range-method Class FLIndexBiomass
range-method Class FLStock
range-method Class FLStockLen
range-method Method range
range-methods Method range
range<- Method range
range<--method Class FLBiol
range<--method Class FLIndex
range<--method Class FLIndexBiomass
range<--method Class FLStock
range<--method Class FLStockLen
range<--method Method range
range<--methods Method range
read.FLIndex Input/Output of FLR objects
read.FLIndices Input/Output of FLR objects
read.FLStock Input/Output of FLR objects
readFLIndex Input/Output of FLR objects
readFLIndices Input/Output of FLR objects
readFLStock Input/Output of FLR objects
readVPAFile Input/Output of FLR objects
rgamma-method Method rgamma
ricker Stock-Recruitment models
ricker.ar1 Stock-Recruitment models
ricker.c.a Stock-Recruitment models
ricker.c.b Stock-Recruitment models
ricker.d Stock-Recruitment models
Ricker.SV Stock-Recruitment models
ricker.sv Stock-Recruitment models
rlnorm-method Method rlnorm
rnorm-method Method rnorm
rpois-method Method rpois

-- S --

sd-method Standard deviation of an FLModel object
seasonMeans Methods to compute sums, means and vars of FLQuant objects
seasonMeans-method Methods to compute sums, means and vars of FLQuant objects
seasonMeans-methods Methods to compute sums, means and vars of FLQuant objects
seasonSums Methods to compute sums, means and vars of FLQuant objects
seasonSums-method Methods to compute sums, means and vars of FLQuant objects
seasonSums-methods Methods to compute sums, means and vars of FLQuant objects
seasonVars Methods to compute sums, means and vars of FLQuant objects
seasonVars-method Methods to compute sums, means and vars of FLQuant objects
seasonVars-methods Methods to compute sums, means and vars of FLQuant objects
segreg Stock-Recruitment models
sel.pattern-method Class FLIndex
sel.pattern-method Class FLIndexBiomass
sel.pattern<--method Class FLIndex
sel.pattern<--method Class FLIndexBiomass
setPlusGroup Method setPlusGroup
setPlusGroup-method Method setPlusGroup
setPlusGroup-methods Method setPlusGroup
shepherd Stock-Recruitment models
shepherd.ar1 Stock-Recruitment models
shepherd.d Stock-Recruitment models
shepherd.d.ar1 Stock-Recruitment models
shepherd.ndc Stock-Recruitment models
shepherd.ndc.ar1 Stock-Recruitment models
show-method Method show
sop Calculates the sum of products correction
splom-method Method splom
spr0 Method spr0
spr0-method Method spr0
spr0-methods Method spr0
spwn-method Class FLBiol
spwn<--method Class FLBiol
sr Stock-recruitment model function
SRModelName Convenience function to identify an SR model by its formula
SRModels Stock-Recruitment models
ssb Method ssb
ssb-method Method ssb
ssb-methods Method ssb
ssbpurec Method ssbpurec
ssbpurec-method Method ssbpurec
ssbpurec-methods Method ssbpurec
ssn Method ssn
ssn-method Method ssn
ssn-methods Method ssn
stock-method Class FLStock
stock-method Class FLStockLen
stock.n-method Class FLStock
stock.n-method Class FLStockLen
stock.n<--method Class FLStock
stock.n<--method Class FLStockLen
stock.wt-method Class FLStock
stock.wt-method Class FLStockLen
stock.wt<--method Class FLStock
stock.wt<--method Class FLStockLen
stock<--method Class FLStock
stock<--method Class FLStockLen
stripplot-method Lattice plots
summary-method Method summary
survprob Calculating survival probabilties given mortality in the FLBiol object
survprob-method Calculating survival probabilties given mortality in the FLBiol object
survprob-methods Calculating survival probabilties given mortality in the FLBiol object
sv2ab Stock-Recruitment models
sweep-method Sweep out FLQuant Summaries

-- T --

transform-method Transform elements of a complex FLR object
trim Trim FLR objects using named dimensions
trim-method Trim FLR objects using named dimensions
trim-methods Trim FLR objects using named dimensions
type-method Class FLIndex
type-method Class FLIndexBiomass
type<--method Class FLIndex
type<--method Class FLIndexBiomass

-- U --

unitMeans Methods to compute sums, means and vars of FLQuant objects
unitMeans-method Methods to compute sums, means and vars of FLQuant objects
unitMeans-methods Methods to compute sums, means and vars of FLQuant objects
units-method units attribute for FLQuant objects
units<--method units attribute for FLQuant objects
unitSums Methods to compute sums, means and vars of FLQuant objects
unitSums-method Methods to compute sums, means and vars of FLQuant objects
unitSums-methods Methods to compute sums, means and vars of FLQuant objects
unitVars Methods to compute sums, means and vars of FLQuant objects
unitVars-method Methods to compute sums, means and vars of FLQuant objects
unitVars-methods Methods to compute sums, means and vars of FLQuant objects
uom uom Units of Measurement
update-method Method update
upper Methods upper and lower
upper-method Methods upper and lower
upper<- Methods upper and lower
upper<--method Methods upper and lower
uppq Method lowq
uppq-method Method lowq
uppq-methods Method lowq
uppq<- Method lowq
uppq<--method Method lowq
uppq<--methods Method lowq

-- V --

var-method Method lowq
var-method Variance of an FLPar
var<- Method lowq
var<--method Method lowq
var<--methods Method lowq

-- W --

window-method Extract time (year) windows of an FLR object
wireframe 3D plot for FLQuant objects
wireframe-method 3D plot for FLQuant objects
writeFLStock Input/Output of FLR objects
wt-method Class FLBiol
wt<--method Class FLBiol

-- X --

xyplot-method Lattice plots

-- Y --

yearMeans Methods to compute sums, means and vars of FLQuant objects
yearMeans-method Methods to compute sums, means and vars of FLQuant objects
yearMeans-methods Methods to compute sums, means and vars of FLQuant objects
yearSums Methods to compute sums, means and vars of FLQuant objects
yearSums-method Methods to compute sums, means and vars of FLQuant objects
yearSums-methods Methods to compute sums, means and vars of FLQuant objects
yearTotals Method quantTotals
yearTotals-method Method quantTotals
yearTotals-methods Method quantTotals
yearVars Methods to compute sums, means and vars of FLQuant objects
yearVars-method Methods to compute sums, means and vars of FLQuant objects
yearVars-methods Methods to compute sums, means and vars of FLQuant objects

-- misc --

$<--method Extract or Replace Parts of an FLR Object
+-method Merging FLStock objects
[-method Extract or Replace Parts of an FLR Object
[<--method Extract or Replace Parts of an FLR Object
[[<--method Extract or Replace Parts of an FLR Object