All functions

SCAMCMC() getADMBCallArgs() getN()

MCMC settings class

SCAPars() stkmodel() n1model() srmodel() fmodel() qmodel() qMod() vmodel() vMod() srPars() srCovar() srFrml() fPars() fCovar() fFrml() qPars() qCovar() qFrml() vPars() vCovar() vFrml() m(<SCAPars>) wt(<SCAPars>) propagate(<SCAPars>) iter(<SCAPars>)

Model parameters class

a4aFit() a4aFit() clock() fitSumm() stock.n(<a4aFit>) harvest(<a4aFit>,<ANY>) catch.n(<a4aFit>) index(<a4aFit>) show(<a4aFit>) logLik(<a4aFit>) iter(<a4aFit>)

S4 class a4aFit

a4aFitMCMC() a4aFitMCMC() a4aFitSA(<a4aFitMCMC>) a4aFit(<a4aFitMCMC>) as.mcmc() burnin()

S4 class a4aFitMCMC

residuals(<a4aFit>)

S4 class a4aFitResiduals

a4aFitSA() a4aFitSA() a4aFit(<a4aFitSA>) pars() m(<a4aFitSA>) wt(<a4aFitSA>) qmodel(<a4aFitSA>) fmodel(<a4aFitSA>) srmodel(<a4aFitSA>) n1model(<a4aFitSA>) vmodel(<a4aFitSA>) stkmodel(<a4aFitSA>) show(<a4aFitSA>) submodels(<a4aFitSA>) iter(<a4aFitSA>) a4aFitSAs()

S4 class a4aFitSA

a4aGr() grMod() `grMod<-`() grInvMod() `grInvMod<-`() params(<a4aGr>) `params<-`(<a4aGr>,<FLPar>) distr(<a4aGr>) `distr<-`(<a4aGr>,<character>) vcov(<a4aGr>) `vcov<-`(<a4aGr>,<numeric>)

Individual growth class

a4aInternal()

Stock assessment model advanced method

a4aM() show(<a4aM>) shape() `shape<-`() level() `level<-`() trend() `trend<-`()

Natural mortality class

a4aStkParams() m(<a4aStkParams>) wt(<a4aStkParams>) mat(<a4aStkParams>) fMod() `fMod<-`() n1Mod() `n1Mod<-`() srMod() `srMod<-`() params(<a4aStkParams>) `params<-`(<a4aStkParams>,<FLPar>) coefficients() `coefficients<-`() distr(<a4aStkParams>) `distr<-`(<a4aStkParams>,<character>) vcov(<a4aStkParams>) `vcov<-`(<a4aStkParams>,<array>) propagate(<a4aStkParams>) iter(<a4aStkParams>)

Stock parameters class

`+`(<FLStock>,<a4aFit>) `+`(<FLIndices>,<a4aFit>)

+ methods

getYidx() is.empty() niters() dims(<a4aStkParams>)

Assorted methods needed by FLa4a

breakpts()

Breakpoints

bubbles(<a4aFitResiduals>,<missing>)

Bubbles plot of standardized log residuals

`formula<-`() coef() `coef<-`()

coefficients extract and replacement

collapseSeasons()

Collapse seasons

defaultFmod() defaultQmod() defaultN1mod() defaultVmod() defaultSRmod()

Default sub-models

a4aSCA()

deprecated

genFLIndex()

Methods to generate FLIndex objects

genFLQuant()

Methods to generate FLQuant objects

genFLStock()

Methods to generate FLStock objects

getADMBHessian() getADMBCovariance()

Get ADMB Hessian

getAcor()

compute log-correlation matrix

getCov()

Get covariance matrix

getK()

Get K

getTPL()

Get TPL with ADMB code

getX()

Get model matrix

hakeGSA7

hakeGSA7

hakeGSA7.idx

hakeGSA7.idx

index_cd_len

index_cd_len

index_pt_len

index_pt_len

index_sp_len

index_sp_len

l2a()

Method to convert length-based data to age-based

m(<a4aM>)

natural mortality

ma()

Model averaging (experimental)

`*`(<FLStock>,<a4aFitSA>) `*`(<FLStock>,<SCAPars>) `*`(<FLIndices>,<a4aFitSA>) `*`(<FLIndices>,<SCAPars>)

* methods

mvrnorm(<numeric>,<a4aM>,<missing>,<missing>,<missing>,<missing>)

natural mortality

mvrcop(<numeric>,<a4aGr>)

mvrcop

mvrcop()

Simulation using copula models

mvrnorm(<numeric>,<a4aGr>,<ANY>,<ANY>,<ANY>,<ANY>)

mvrnorm

mvrtriangle(<numeric>,<a4aGr>)

mvrtriangle

mvrtriangle()

Simulation with a copula model and triangular distributions

pars2dim()

Check that the second dimension in params is "iter"

plot(<a4aFitResiduals>,<missing>)

Plot of standardized log residuals

plot(<a4aFit>,<FLStock>)

plot for fitted catch-at-age

plot(<a4aFit>,<FLIndices>)

testing

predict(<a4aGr>)

predict for a4aGr

predict(<a4aFitSA>) predict(<SCAPars>)

Predict methods for SCA

qqmath(<a4aFitResiduals>,<missing>)

qqplot of standardized log residuals

`range<-`(<a4aM>,<ANY>,<numeric>)

range for a4aM objects

rfLen

redfish length data

rfLen.stk

rfLen.stk

rfTrawl.idx

rfTrawl.idx

rfTrawlJmp.idx

rfTrawlJmp.idx

rfTrawlTrd.idx

rfTrawlTrd.idx

sca()

Statistical catch-at-age method

shake_len

shake_len

simulate()

Simulation methods for SCA

southernHakeLen

Southern hake length data

stdlogres()

Standardized log residuals

submodel() params(<submodel>) sMod() iter(<submodel>) propagate(<submodel>) formula(<submodel>)

Submodel class

submodels() submodels() corBlocks() params(<submodels>) sMod(<submodels>) formula(<submodels>) `corBlocks<-`() `$<-`(<submodels>,<submodel>) `[[<-`(<submodels>,<character>,<missing>) `[[<-`(<submodels>,<numeric>,<missing>) propagate(<submodels>) iter(<submodels>)

Submodels class

vcov(<a4aFitSA>) vcov(<SCAPars>) vcov(<submodels>) vcov(<submodel>) `vcov<-`(<a4aFitSA>,<numeric>) `vcov<-`(<SCAPars>,<numeric>) `vcov<-`(<a4aStkParams>,<numeric>) `vcov<-`(<submodel>,<numeric>) `vcov<-`(<submodel>,<matrix>) `vcov<-`(<submodel>,<array>)

Variance-covariance matrix

wireframe(<FLQuant>,<missing>)

wireframe plot for FLQuant