API for flr/FLa4a
A Simple and Robust Statistical Catch at Age Model

Global functions
$<-,submodels,submodel-method	Man page
*	Man page
*,FLIndices,SCAPars-method	Man page
*,FLIndices,a4aFitSA-method	Man page
*,FLStock,SCAPars-method	Man page
*,FLStock,a4aFitSA-method	Man page
+,FLIndices,a4aFit-method	Man page
+,FLStock,a4aFit-method	Man page
+,FLStocks,a4aFits-method	Man page
.onAttach	Source code
SCAMCMC	Man page
SCAMCMC,missing-method	Man page
SCAMCMC-class	Man page
SCAMCMC-methods	Man page
SCAPars	Man page
SCAPars,missing-method	Man page
SCAPars-class	Man page
SCAPars-methods	Man page
[[<-,submodels,character,missing-method	Man page
[[<-,submodels,numeric,missing-method	Man page
a4aFit	Man page
a4aFit,a4aFitMCMC-method	Man page
a4aFit,a4aFitSA-method	Man page
a4aFit-class	Man page
a4aFit-methods	Man page
a4aFitCatchDiagn	Man page
a4aFitCatchDiagn-class	Man page
a4aFitCatchDiagn-methods	Man page
a4aFitMCMC	Man page
a4aFitMCMC-class	Man page
a4aFitMCMC-methods	Man page
a4aFitMCMCs	Man page
a4aFitMCMCs,a4aFitMCMC-method	Man page
a4aFitMCMCs,list-method	Man page
a4aFitMCMCs,missing-method	Man page
a4aFitMCMCs-class	Man page
a4aFitMCMCs-methods	Man page
a4aFitResiduals	Man page
a4aFitResiduals-class	Man page
a4aFitResiduals-methods	Man page
a4aFitSA	Man page
a4aFitSA,a4aFitMCMC-method	Man page
a4aFitSA-class	Man page
a4aFitSA-methods	Man page
a4aFitSAs	Man page
a4aFitSAs,a4aFitSA-method	Man page
a4aFitSAs,list-method	Man page
a4aFitSAs,missing-method	Man page
a4aFitSAs-class	Man page
a4aFitSAs-methods	Man page
a4aFits	Man page
a4aFits,a4aFit-method	Man page
a4aFits,list-method	Man page
a4aFits,missing-method	Man page
a4aFits-class	Man page
a4aFits-methods	Man page
a4aGr	Man page
a4aGr,missing-method	Man page
a4aGr-class	Man page
a4aGr-methods	Man page
a4aInternal	Man page Source code
a4aM	Man page
a4aM,missing-method	Man page
a4aM-class	Man page
a4aM-methods	Man page
a4aSCA	Man page Source code
a4aSRmodelDefinitions	Source code
a4aStkParams	Man page
a4aStkParams,missing-method	Man page
a4aStkParams-class	Man page
a4aStkParams-methods	Man page
addition	Man page
as.mcmc	Man page
as.mcmc,a4aFitMCMC-method	Man page
as.mcmc-methods	Man page
assorted methods	Man page
bevholt	Source code
bevholtSV	Source code
breakpts	Man page
breakpts,numeric-method	Man page
breakpts-methods	Man page
bubble plot of residuals	Man page
bubbles,a4aFitResiduals,missing-method	Man page
burnin	Man page
burnin,a4aFitMCMC-method	Man page
burnin-methods	Man page
catch.n,a4aFit-method	Man page
check.executable	Source code
check_cv	Source code
clock	Man page
clock,a4aFit-method	Man page
clock-methods	Man page
coef	Man page
coef,SCAPars-method	Man page
coef,a4aFitSA-method	Man page
coef,a4aFitSA-methods	Man page
coef,a4aStkParams-method	Man page
coef,submodel-method	Man page
coef,submodels-method	Man page
coef<-	Man page
coef<-,SCAPars,numeric-method	Man page
coef<-,a4aFitSA,numeric-method	Man page
coef<-,a4aFitSA-methods	Man page
coef<-,a4aStkParams,FLPar-method	Man page
coef<-,a4aStkParams,matrix-method	Man page
coef<-,a4aStkParams,numeric-method	Man page
coef<-,submodel,FLPar-method	Man page
coef<-,submodel,numeric-method	Man page
coef<-,submodels,numeric-method	Man page
coefficients	Man page
coefficients,a4aStkParams-method	Man page
coefficients-methods	Man page
coefficients<-	Man page
coefficients<-,a4aStkParams,FLPar-method	Man page
coefficients<--methods	Man page
collapseSeasons	Man page
computeCatchDiagnostics	Man page
computeCatchDiagnostics,a4aFit-method	Man page
corBlock-methods	Man page
corBlocks	Man page
corBlocks,submodels-method	Man page
corBlocks<-	Man page
corBlocks<-,submodels,list-method	Man page
defaultFmod	Man page Source code
defaultN1mod	Man page Source code
defaultQmod	Man page Source code
defaultSRmod	Man page Source code
defaultSubModels	Man page
defaultVmod	Man page Source code
deprecated	Man page
dims,a4aStkParams-method	Man page
distr,a4aGr-method	Man page
distr,a4aStkParams-method	Man page
distr<-,a4aGr,character-method	Man page
distr<-,a4aStkParams,character-method	Man page
dps567	Man page
dps567.idx	Man page
dropMatrixIter	Source code
fCovar	Man page
fCovar,SCAPars-method	Man page
fCovar-methods	Man page
fFrml	Man page
fFrml,SCAPars-method	Man page
fFrml-methods	Man page
fMod	Man page
fMod,a4aStkParams-method	Man page
fMod-methods	Man page
fMod<-	Man page
fMod<-,a4aStkParams,formula-method	Man page
fMod<--methods	Man page
fPars	Man page
fPars,SCAPars-method	Man page
fPars-methods	Man page
fitADMB	Source code
fitSumm	Man page
fitSumm,a4aFit-method	Man page
fitSumm-methods	Man page
flqFromRange	Source code
fmodel	Man page
fmodel,SCAPars-method	Man page
fmodel,a4aFitSA-method	Man page
fmodel-methods	Man page
formula,submodel-method	Man page
formula,submodels-method	Man page
formula<-	Man page
formula<-,submodel,formula-method	Man page
genFLIndex	Man page
genFLIndex,FLQuant-method	Man page
genFLIndex-methods	Man page
genFLQuant	Man page
genFLQuant,FLQuant-method	Man page
genFLQuant,a4aStkParams-method	Man page
genFLQuant,submodel-method	Man page
genFLQuant,submodels-method	Man page
genFLQuant-methods	Man page
genFLStock	Man page
genFLStock,FLStock,FLQuant,FLQuant,missing-method	Man page
genFLStock,FLStock,FLQuant,missing,FLQuant-method	Man page
genFLStock,FLStock,missing,FLQuant,FLQuant-method	Man page
genFLStock-methods	Man page
geomean	Source code
getADMBCallArgs	Man page
getADMBCallArgs-methods	Man page
getADMBCovariance	Man page Source code
getADMBHessian	Man page Source code
getAcor	Man page
getAcor,FLQuant-method	Man page
getAcor-methods	Man page
getCov	Man page Source code
getK	Man page
getK,a4aGr-method	Man page
getK-methods	Man page
getN	Man page
getN,SCAMCMC-method	Man page
getN-methods	Man page
getTPL	Man page Source code
getX	Man page
getX,formula-method	Man page
getX-methods	Man page
getYidx	Man page
getYidx,FLQuant-method	Man page
getYidx-methods	Man page
geta4aSRmodel	Source code
grInvMod	Man page
grInvMod,a4aGr-method	Man page
grInvMod-methods	Man page
grInvMod<-	Man page
grInvMod<-,a4aGr,formula-method	Man page
grInvMod<--methods	Man page
grMod	Man page
grMod,a4aGr-method	Man page
grMod-methods	Man page
grMod<-	Man page
grMod<-,a4aGr,formula-method	Man page
grMod<--methods	Man page
hakeGSA7	Man page
hakeGSA7.idx	Man page
harvest,a4aFit,ANY-method	Man page
hke1567	Man page
hke1567.idx	Man page
hockey	Source code
index,a4aFit-method	Man page
index_cd_len	Man page
index_pt_len	Man page
index_sp_len	Man page
is.empty	Man page Source code
isPresenta4aSRmodel	Source code
iter,SCAPars-method	Man page
iter,a4aFit-method	Man page
iter,a4aFitSA-method	Man page
iter,a4aStkParams-method	Man page
iter,submodel-method	Man page
iter,submodels-method	Man page
l2a	Man page
l2a,FLIndex,a4aGr-method	Man page
l2a,FLQuant,a4aGr-method	Man page
l2a,FLStockLen,a4aGr-method	Man page
l2a-methods	Man page
level	Man page
level,a4aM-method	Man page
level-methods	Man page
level<-	Man page
level<-,a4aM-method	Man page
level<--methods	Man page
list2df	Source code
logLik,a4aFit-method	Man page
m	Man page
m,SCAPars-method	Man page
m,a4aFitSA-method	Man page
m,a4aM-method	Man page
m,a4aStkParams-method	Man page
ma	Man page
ma,a4aFitSAs-method	Man page
ma-methods	Man page
make.df	Source code
mat,a4aStkParams-method	Man page
missing-method	Man page Man page
mut09	Man page
mut09.idx	Man page
mvnorm	Man page
mvrEmpT	Source code
mvrcop	Man page
mvrcop for a4aGr	Man page
mvrcop,numeric,FLModelSim-method	Man page
mvrcop,numeric,a4aGr-method	Man page
mvrnorm for a4aGR	Man page
mvrnorm,numeric,a4aGr,ANY,ANY,ANY,ANY-method	Man page
mvrnorm,numeric,a4aGr-method	Man page
mvrnorm,numeric,a4aM,missing,missing,missing,missing-method	Man page
mvrtriangle	Man page
mvrtriangle for a4aGr	Man page
mvrtriangle,numeric,FLModelSim-method	Man page
mvrtriangle,numeric,a4aGr-method	Man page
n1Mod	Man page
n1Mod,a4aStkParams-method	Man page
n1Mod-methods	Man page
n1Mod<-	Man page
n1Mod<-,a4aStkParams,formula-method	Man page
n1Mod<--methods	Man page
n1model	Man page
n1model,SCAPars-method	Man page
n1model,a4aFitSA-method	Man page
n1model-methods	Man page
niters	Man page
niters,FLModelSim-method	Man page
niters,a4aGr-method	Man page
niters-methods	Man page
none	Source code
par2mat	Source code
params,a4aGr-method	Man page
params,a4aStkParams-method	Man page
params,submodel-method	Man page
params,submodels-method	Man page
params<-,a4aGr,FLPar-method	Man page
params<-,a4aStkParams,FLPar-method	Man page
pars	Man page
pars,a4aFitSA-method	Man page
pars-methods	Man page
pars2dim	Man page
pars2dim,FLModelSim-method	Man page
pars2dim,FLPar-method	Man page
pars2dim-methods	Man page
plot for fitted catch-at-age	Man page
plot for fitted indices-at-age	Man page
plot metrics of multiple fits	Man page Man page
plot of catch residuals	Man page
plot of residuals	Man page
plot,a4aFit,FLIndices-method	Man page
plot,a4aFit,FLStock-method	Man page
plot,a4aFitCatchDiagn,missing-method	Man page
plot,a4aFitMCMCs,	Man page
plot,a4aFitResiduals,missing-method	Man page
plot,a4aFits,	Man page
predict for a4aGr	Man page
predict for sca	Man page
predict,SCAPars-method	Man page
predict,a4aFitSA-method	Man page
predict,a4aGr-method	Man page
predict.stkpars	Source code
predict.submod	Source code
predict.submods	Source code
propagate,SCAPars-method	Man page
propagate,a4aStkParams-method	Man page
propagate,submodel-method	Man page
propagate,submodels-method	Man page
qCovar	Man page
qCovar,SCAPars-method	Man page
qCovar-methods	Man page
qFrml	Man page
qFrml,SCAPars-method	Man page
qFrml-methods	Man page
qMod	Man page
qMod,SCAPars-method	Man page
qMod-methods	Man page
qPars	Man page
qPars,SCAPars-method	Man page
qPars-methods	Man page
qmodel	Man page
qmodel,SCAPars-method	Man page
qmodel,a4aFitSA-method	Man page
qmodel-methods	Man page
qqmath,a4aFitResiduals,missing-method	Man page
qqplot of residuals	Man page
quant2mat	Source code
rMod-methods	Man page
range<-,a4aM,ANY,numeric-method	Man page
replaceZeros	Man page
replaceZeros,FLI-method	Man page
replaceZeros,FLIndices-method	Man page
replaceZeros,FLQuant-method	Man page
replaceZeros,FLStock-method	Man page
replaceZeros-methods	Man page
residuals,a4aFit-method	Man page
rfLen	Man page
rfLen.stk	Man page
rfTrawl.idx	Man page
rfTrawlJmp.idx	Man page
rfTrawlTrd.idx	Man page
ricker	Source code
sMod	Man page
sMod,submodel-method	Man page
sMod,submodels-method	Man page
sMod-methods	Man page
sca	Man page
sca,FLStock,FLIndex-method	Man page
sca,FLStock,FLIndices-method	Man page
sca-methods	Man page
sca.sa	Man page Source code
scas	Source code
scax	Man page
sep.sa	Man page Source code
shake_len	Man page
shape	Man page
shape,a4aM-method	Man page
shape-methods	Man page
shape<-	Man page
shape<-,a4aM-method	Man page
shape<--methods	Man page
show,a4aFit-method	Man page
show,a4aFitSA-method	Man page
show,a4aM-method	Man page
simulate	Man page
simulate,SCAPars-method	Man page
simulate,a4aFitSA-method	Man page
simulate,a4aStkParams-method	Man page
simulate,submodel-method	Man page
simulate,submodels-method	Man page
southernHakeLen	Man page
srCovar	Man page
srCovar,SCAPars-method	Man page
srCovar-methods	Man page
srFrml	Man page
srFrml,SCAPars-method	Man page
srFrml-methods	Man page
srMod	Man page
srMod,a4aStkParams-method	Man page
srMod<-	Man page
srMod<-,a4aStkParams,formula-method	Man page
srMod<--methods	Man page
srPars	Man page
srPars,SCAPars-method	Man page
srPars-methods	Man page
srmodel	Man page
srmodel,SCAPars-method	Man page
srmodel,a4aFitSA-method	Man page
srmodel-methods	Man page
stdlogres	Man page
stdlogres,FLQuant,FLQuant-method	Man page
stdlogres-methods	Man page
stkmodel	Man page
stkmodel,SCAPars-method	Man page
stkmodel,a4aFitSA-method	Man page
stkmodel-methods	Man page
stock.n,a4aFit-method	Man page
submodel	Man page
submodel,missing-method	Man page
submodel-class	Man page
submodel-methods	Man page
submodels	Man page
submodels,a4aFitSA-method	Man page
submodels-class	Man page
submodels-methods	Man page
trend	Man page
trend,a4aM-method	Man page
trend-methods	Man page
trend<-	Man page
trend<-,a4aM-method	Man page
trend<--methods	Man page
vCovar	Man page
vCovar,SCAPars-method	Man page
vCovar-methods	Man page
vFrml	Man page
vFrml,SCAPars-method	Man page
vFrml-methods	Man page
vMod	Man page
vMod,SCAPars-method	Man page
vMod-methods	Man page
vPars	Man page
vPars,SCAPars-method	Man page
vPars-methods	Man page
valida4aGr	Source code
valida4aM	Source code
vcov	Man page
vcov,SCAPars-method	Man page
vcov,a4aFitSA-method	Man page
vcov,a4aGr-method	Man page
vcov,a4aStkParams-method	Man page
vcov,submodel-method	Man page
vcov,submodels-method	Man page
vcov<-,SCAPars,numeric-method	Man page
vcov<-,a4aFitSA,numeric-method	Man page
vcov<-,a4aGr,numeric-method	Man page
vcov<-,a4aStkParams,array-method	Man page
vcov<-,a4aStkParams,numeric-method	Man page
vcov<-,submodel,array-method	Man page
vcov<-,submodel,matrix-method	Man page
vcov<-,submodel,numeric-method	Man page
vmodel	Man page
vmodel,SCAPars-method	Man page
vmodel,a4aFitSA-method	Man page
vmodel-methods	Man page
wireframe plot for FLQuant	Man page
wireframe,FLQuant,missing-method	Man page
wireframe,FLQuant-method	Man page
write.t	Source code
write.t.sparse	Source code
wt,SCAPars-method	Man page
wt,a4aFitSA-method	Man page
wt,a4aStkParams-method	Man page