A Simple and Robust Statistical Catch at Age Model


[Up] [Top]

Documentation for package ‘FLa4a’ version 1.1.2

Help Pages

A B C D F G H I L M N P Q R S T V W misc

-- A --

a4a a4a
a4aFit S4 class 'a4aFit'
a4aFit-class S4 class 'a4aFit'
a4aFit-method S4 class 'a4aFit'
a4aFit-method S4 class 'a4aFitSA'
a4aFit-methods S4 class 'a4aFit'
a4aFitMCMC S4 class 'a4aFitMCMC'
a4aFitMCMC-class S4 class 'a4aFitMCMC'
a4aFitMCMC-method S4 class 'a4aFitMCMC'
a4aFitMCMC-methods S4 class 'a4aFitMCMC'
a4aFitResiduals S4 class 'a4aFitResiduals'
a4aFitResiduals-class S4 class 'a4aFitResiduals'
a4aFitResiduals-methods S4 class 'a4aFitResiduals'
a4aFitSA S4 class 'a4aFitSA'
a4aFitSA-class S4 class 'a4aFitSA'
a4aFitSA-method S4 class 'a4aFitMCMC'
a4aFitSA-method S4 class 'a4aFitSA'
a4aFitSA-methods S4 class 'a4aFitSA'
a4aFitSAs S4 class 'a4aFitSA'
a4aFitSAs-class S4 class 'a4aFitSA'
a4aFitSAs-method S4 class 'a4aFitSA'
a4aFitSAs-methods S4 class 'a4aFitSA'
a4aGr Individual growth class
a4aGr-class Individual growth class
a4aGr-method Individual growth class
a4aGr-methods Individual growth class
a4aInternal Stock assessment model advanced method
a4aM Natural mortality class
a4aM-class Natural mortality class
a4aM-method Natural mortality class
a4aM-methods Natural mortality class
a4aSCA Statistical catch-at-age advanced method
a4aSCA-method Statistical catch-at-age advanced method
a4aSCA-methods Statistical catch-at-age advanced method
a4aStkParams Stock parameters class
a4aStkParams-class Stock parameters class
a4aStkParams-method Stock parameters class
a4aStkParams-methods Stock parameters class
addition + methods
as.mcmc S4 class 'a4aFitMCMC'
as.mcmc-method S4 class 'a4aFitMCMC'
as.mcmc-methods S4 class 'a4aFitMCMC'
assorted methods Assorted methods needed by FLa4a

-- B --

breakpts Breakpoints
breakpts-method Breakpoints
breakpts-methods Breakpoints
bubble plot of residuals Bubbles plot of standardized log residuals
bubbles-method Bubbles plot of standardized log residuals

-- C --

catch.n-method S4 class 'a4aFit'
clock S4 class 'a4aFit'
clock-method S4 class 'a4aFit'
clock-methods S4 class 'a4aFit'
coef coefficients extract and replacement
coef,a4aFitSA-methods coefficients extract and replacement
coef-method coefficients extract and replacement
coef<- coefficients extract and replacement
coef<-,a4aFitSA-methods coefficients extract and replacement
coef<--method coefficients extract and replacement
collapseSeasons Collapse seasons
covar-method Submodel class

-- D --

dims-method Assorted methods needed by FLa4a
distr-method Individual growth class
distr-method Stock parameters class
distr<--method Individual growth class
distr<--method Stock parameters class

-- F --

fCovar Model parameters class
fCovar-method Model parameters class
fCovar-methods Model parameters class
fFrml Model parameters class
fFrml-method Model parameters class
fFrml-methods Model parameters class
fitSumm S4 class 'a4aFit'
fitSumm-method S4 class 'a4aFit'
fitSumm-methods S4 class 'a4aFit'
fMod Stock parameters class
fMod-method Stock parameters class
fMod-methods Stock parameters class
fMod<- Stock parameters class
fMod<--method Stock parameters class
fMod<--methods Stock parameters class
fmodel Model parameters class
fmodel-method Model parameters class
fmodel-methods Model parameters class
fPars Model parameters class
fPars-method Model parameters class
fPars-methods Model parameters class

-- G --

genFLIndex Methods to generate FLIndex objects
genFLIndex-method Methods to generate FLIndex objects
genFLIndex-methods Methods to generate FLIndex objects
genFLQuant Methods to generate FLQuant objects
genFLQuant-method Methods to generate FLQuant objects
genFLQuant-methods Methods to generate FLQuant objects
genFLStock Methods to generate FLStock objects
genFLStock-method Methods to generate FLStock objects
genFLStock-methods Methods to generate FLStock objects
getAcor compute log-correlation matrix
getAcor-method compute log-correlation matrix
getAcor-methods compute log-correlation matrix
getADMBCallArgs MCMC settings class
getADMBCallArgs-method MCMC settings class
getADMBCovariance Get ADMB Hessian
getADMBHessian Get ADMB Hessian
getCov Get covariance matrix
getK Get K
getK-method Get K
getK-methods Get K
getN MCMC settings class
getN-method MCMC settings class
getN-methods MCMC settings class
getTPL Get TPL with ADMB code
getX Get model matrix
getX-method Get model matrix
getX-methods Get model matrix
getYidx Assorted methods needed by FLa4a
getYidx-method Assorted methods needed by FLa4a
getYidx-methods Assorted methods needed by FLa4a
grInvMod Individual growth class
grInvMod-method Individual growth class
grInvMod-methods Individual growth class
grInvMod<- Individual growth class
grInvMod<--method Individual growth class
grInvMod<--methods Individual growth class
grMod Individual growth class
grMod-method Individual growth class
grMod-methods Individual growth class
grMod<- Individual growth class
grMod<--method Individual growth class
grMod<--methods Individual growth class

-- H --

hakeGSA7 hakeGSA7
hakeGSA7.idx hakeGSA7.idx
harvest-method S4 class 'a4aFit'

-- I --

index-method S4 class 'a4aFit'
index_cd_len index_cd_len
index_pt_len index_pt_len
index_sp_len index_sp_len
is.empty Assorted methods needed by FLa4a
iter-method Model parameters class
iter-method S4 class 'a4aFit'
iter-method S4 class 'a4aFitSA'
iter-method Stock parameters class
iter-method Submodel class
iter-method Submodels class

-- L --

l2a Method to convert length-based data to age-based
l2a-method Method to convert length-based data to age-based
l2a-methods Method to convert length-based data to age-based
level Natural mortality class
level-method Natural mortality class
level-methods Natural mortality class
level<- Natural mortality class
level<--method Natural mortality class
level<--methods Natural mortality class
logLik-method S4 class 'a4aFit'

-- M --

m natural mortality
m-method Model parameters class
m-method S4 class 'a4aFitSA'
m-method Stock parameters class
m-method natural mortality
ma Model averaging (experimental)
ma-method Model averaging (experimental)
ma-methods Model averaging (experimental)
mcmc MCMC settings class
mcmc-method MCMC settings class
mcmc-methods MCMC settings class
model-method Submodel class
mvnorm natural mortality
mvrcop Simulation using copula models
mvrcop for a4aGr mvrcop
mvrcop-method mvrcop
mvrcop-method Simulation using copula models
mvrnorm for a4aGR mvrnorm
mvrnorm-method natural mortality
mvrnorm-method mvrnorm
mvrtriangle Simulation with a copula model and triangular distributions
mvrtriangle for a4aGr mvrtriangle
mvrtriangle-method mvrtriangle
mvrtriangle-method Simulation with a copula model and triangular distributions

-- N --

n1Mod Stock parameters class
n1Mod-method Stock parameters class
n1Mod-methods Stock parameters class
n1Mod<- Stock parameters class
n1Mod<--method Stock parameters class
n1Mod<--methods Stock parameters class
n1model Model parameters class
n1model-method Model parameters class
n1model-methods Model parameters class
niters Assorted methods needed by FLa4a
niters-method Assorted methods needed by FLa4a
niters-methods Assorted methods needed by FLa4a

-- P --

params-method Individual growth class
params-method Stock parameters class
params-method Submodel class
params<--method Individual growth class
params<--method Stock parameters class
pars S4 class 'a4aFitSA'
pars-method S4 class 'a4aFitSA'
pars-methods S4 class 'a4aFitSA'
pars2dim Check that the second dimension in params is "iter"
pars2dim-method Check that the second dimension in params is "iter"
pars2dim-methods Check that the second dimension in params is "iter"
plot for fitted catch-at-age plot for fitted catch-at-age
plot for fitted indices-at-age testing
plot of residuals Plot of standardized log residuals
plot-method Plot of standardized log residuals
plot-method plot for fitted catch-at-age
plot-method testing
predict for a4aGr predict for 'a4aGr'
predict for sca Predict methods for SCA
predict-method predict for 'a4aGr'
predict-method Predict methods for SCA

-- Q --

qCovar Model parameters class
qCovar-method Model parameters class
qCovar-methods Model parameters class
qFrml Model parameters class
qFrml-method Model parameters class
qFrml-methods Model parameters class
qmodel Model parameters class
qmodel-method Model parameters class
qmodel-methods Model parameters class
qPars Model parameters class
qPars-method Model parameters class
qPars-methods Model parameters class
qqmath-method qqplot of standardized log residuals
qqplot of residuals qqplot of standardized log residuals

-- R --

range<--method range for a4aM objects
residuals-method S4 class 'a4aFitResiduals'
rfLen redfish length data
rfLen.stk rfLen.stk
rfTrawl.idx rfTrawl.idx
rfTrawlJmp.idx rfTrawlJmp.idx
rfTrawlTrd.idx rfTrawlTrd.idx
rMod Stock parameters class
rMod-method Stock parameters class
rMod-methods Stock parameters class
rMod<- Stock parameters class
rMod<--method Stock parameters class
rMod<--methods Stock parameters class

-- S --

sca Statistical catch-at-age method
sca-method Statistical catch-at-age method
sca-methods Statistical catch-at-age method
SCAMCMC MCMC settings class
SCAMCMC-class MCMC settings class
SCAMCMC-method MCMC settings class
SCAMCMC-methods MCMC settings class
SCAPars Model parameters class
SCAPars-class Model parameters class
SCAPars-method Model parameters class
SCAPars-methods Model parameters class
shake_len shake_len
shape Natural mortality class
shape-method Natural mortality class
shape-methods Natural mortality class
shape<- Natural mortality class
shape<--method Natural mortality class
shape<--methods Natural mortality class
show-method S4 class 'a4aFit'
show-method S4 class 'a4aFitSA'
show-method Natural mortality class
simulate Simulation methods for SCA
simulate-method Simulation methods for SCA
southernHakeLen Southern hake length data
srCovar Model parameters class
srCovar-method Model parameters class
srCovar-methods Model parameters class
srFrml Model parameters class
srFrml-method Model parameters class
srFrml-methods Model parameters class
srmodel Model parameters class
srmodel-method Model parameters class
srmodel-methods Model parameters class
srPars Model parameters class
srPars-method Model parameters class
srPars-methods Model parameters class
stdlogres Standardized log residuals
stdlogres-method Standardized log residuals
stdlogres-methods Standardized log residuals
stkmodel Model parameters class
stkmodel-method Model parameters class
stkmodel-methods Model parameters class
stock.n-method S4 class 'a4aFit'
submodel Submodel class
submodel-class Submodel class
submodel-method Submodel class
submodel-methods Submodel class
submodels Submodels class
submodels-class Submodels class
submodels-method S4 class 'a4aFitSA'
submodels-method Submodels class
submodels-methods Submodels class

-- T --

trend Natural mortality class
trend-method Natural mortality class
trend-methods Natural mortality class
trend<- Natural mortality class
trend<--method Natural mortality class
trend<--methods Natural mortality class

-- V --

vcov Variance-covariance matrix
vcov-method Individual growth class
vcov-method Stock parameters class
vcov-method Variance-covariance matrix
vcov<--method Individual growth class
vcov<--method Stock parameters class
vcov<--method Variance-covariance matrix
vCovar Model parameters class
vCovar-method Model parameters class
vCovar-methods Model parameters class
vFrml Model parameters class
vFrml-method Model parameters class
vFrml-methods Model parameters class
vmodel Model parameters class
vmodel-method Model parameters class
vmodel-methods Model parameters class
vPars Model parameters class
vPars-method Model parameters class
vPars-methods Model parameters class

-- W --

wireframe plot for FLQuant wireframe plot for FLQuant
wireframe-method wireframe plot for FLQuant
wt-method Model parameters class
wt-method S4 class 'a4aFitSA'
wt-method Stock parameters class

-- misc --

* * methods
*-method * methods
+-method + methods