A B C D F G H I L M N P Q R S T V W misc
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 |
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 |
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 |
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 |
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 |
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 |
hakeGSA7 | hakeGSA7 |
hakeGSA7.idx | hakeGSA7.idx |
harvest-method | S4 class 'a4aFit' |
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 |
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 | 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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
* | * methods |
*-method | * methods |
+-method | + methods |